Answers.Body: <p>This is what is known as a feature, not a bug. Note that your identical proteins all have accessions starting with <code>WP_</code>. These are special &quot;non-redundant proteins&quot;. Many sequences—particularly bacterial sequences—are identical between various different species so having a separate RefSeq entry for each of them would be inefficient. Therefore, RefSeq combines multiple such proteins into a single <code>WP_</code> record. This is documented <a href="https://www.ncbi.nlm.nih.gov/refseq/about/nonredundantproteins/" rel="nofollow noreferrer">here</a> (emphasis mine):</p>
  <blockquote>
  <p>A new type of RefSeq protein record which represents non-redundant protein sequences was introduced in mid-2013. This record type was introduced to address a growing issue with redundancy in the Prokaryotic RefSeq protein dataset that coincided with a significant increase in bacterial genome submissions from individual isolates and closely related bacterial strains. For example, a large number of high-quality bacterial genomes may be submitted during a disease outbreak. The submitted sequences may reflect pathogen evolution during the course of the outbreak but the majority of the encoded proteins from these genomes may be identical to each other. As RefSeq includes these genomes, per community requests, this resulted in increased redundancy. <strong>By representing identical proteins using a single non-redundant protein accession number (with the prefix 'WP_'), redundancy in the database is significantly reduced.</strong></p>
  <p>[ . . . ]</p>
  <p>Because a non-redundant protein sequence may be found in RefSeq genomes from multiple species, <strong>the organism information provided on the protein record reflects the lowest-common taxonomic node ranging from the genus species level to super-kingdom</strong>. A non-redundant protein record that provides organism information at the level of a genus, family, or even super-kingdom does not mean that the protein is found in all RefSeq genomes below that taxonomic classification. It only indicates that the protein is found in more than one genome of different species for which the genus, family, or super-kingdom classification is the lowest common taxonomic node.</p>
  </blockquote>
  <p>So, your query was <a href="https://www.ncbi.nlm.nih.gov/protein/NP_418578" rel="nofollow noreferrer">NP_418578.1</a>, anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit from <em>E. coli</em> strain K-12, substrain MG1655. The first thing to notice is how specific that is. This is the protein found from one specific substrain of one specific strain of one specific bacterial species. It is reasonable to expect that there will be identical sequences from many, many closely related species. Both from, most probably, all other strains and substrains of <em>E. coli</em> and from other, related bacteria.</p>
  <p>Now, the specific sequences you mention are actually <em>slightly</em> different and not 100% identical. Below is a multiple alignment of NP_418578.1 and the 4 WP_ sequences you mentioned. Note that each of the 5 entries is slightly different. Each has one residue that differs from the rest. Look for the <code>:</code> in the identity line, there are 4 <code>:</code> and all others are <code>*</code> (I am only showing the relevant alignment blocks here and have removed those where all 4 sequences were identical):</p>
  <pre><code>WP_001401474.1      MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
  WP_062863447.1      MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
  WP_064226696.1      MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
  NP_418578.1         MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
  WP_078165098.1      MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAIAQDH
                      *******************************************************:****
  
  [ . . . ]
  
  WP_001401474.1      KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
  WP_062863447.1      KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
  WP_064226696.1      KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHIRGLVAMNMMEGT
  NP_418578.1         KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
  WP_078165098.1      KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
                      ***********************************************:************
  
  [ . . . ]
  
  WP_001401474.1      GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
  WP_062863447.1      GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKISQAFWHEWR
  WP_064226696.1      GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
  NP_418578.1         GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
  WP_078165098.1      GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
                      **************************************************:*********
  
  WP_001401474.1      KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGIDPVKEPIPVRPTAHYTMG
  WP_062863447.1      KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
  WP_064226696.1      KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
  NP_418578.1         KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
  WP_078165098.1      KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
                      *****************************************:******************
  
  [ . . . ]
  </code></pre>
  <p>Your sequence (NP_418578.1) is only identical to one <code>WP_*</code> multi-species sequence, WP_001192973:</p>
  <pre><code>WP_001192973.1      MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
  NP_418578.1         MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
                      ************************************************************
  
  WP_001192973.1      DSFEYHFHDTVAGGDWLCEQDVVDYFVHHCPTEMTQLELWGCPWSRRPDGSVNVRRFGGM
  NP_418578.1         DSFEYHFHDTVAGGDWLCEQDVVDYFVHHCPTEMTQLELWGCPWSRRPDGSVNVRRFGGM
                      ************************************************************
  
  WP_001192973.1      KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
  NP_418578.1         KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
                      ************************************************************
  
  WP_001192973.1      LVQIRANAVVMATGGAGRVYRYNTNGGIVTGDGMGMALSHGVPLRDMEFVQYHPTGLPGS
  NP_418578.1         LVQIRANAVVMATGGAGRVYRYNTNGGIVTGDGMGMALSHGVPLRDMEFVQYHPTGLPGS
                      ************************************************************
  
  WP_001192973.1      GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
  NP_418578.1         GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
                      ************************************************************
  
  WP_001192973.1      KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
  NP_418578.1         KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
                      ************************************************************
  
  WP_001192973.1      GIETDQNCETRIKGLFAVGECSSVGLHGANRLGSNSLAELVVFGRLAGEQATERAATAGN
  NP_418578.1         GIETDQNCETRIKGLFAVGECSSVGLHGANRLGSNSLAELVVFGRLAGEQATERAATAGN
                      ************************************************************
  
  WP_001192973.1      GNEAAIEAQAAGVEQRLKDLVNQDGGENWAKIRDEMGLAMEEGCGIYRTPELMQKTIDKL
  NP_418578.1         GNEAAIEAQAAGVEQRLKDLVNQDGGENWAKIRDEMGLAMEEGCGIYRTPELMQKTIDKL
                      ************************************************************
  
  WP_001192973.1      AELQERFKRVRITDTSSVFNTDLLYTIELGHGLNVAECMAHSAMARKESRGAHQRLDEGC
  NP_418578.1         AELQERFKRVRITDTSSVFNTDLLYTIELGHGLNVAECMAHSAMARKESRGAHQRLDEGC
                      ************************************************************
  
  WP_001192973.1      TERDDVNFLKHTLAFRDADGTTRLEYSDVKITTLPPAKRVYGGEADAADKAEAANKKEKA
  NP_418578.1         TERDDVNFLKHTLAFRDADGTTRLEYSDVKITTLPPAKRVYGGEADAADKAEAANKKEKA
                      ************************************************************
  
  WP_001192973.1      NG
  NP_418578.1         NG
                      **
  </code></pre>
  <p>So, in summary, RefSeq will combine multiple identical sequences into a single <code>WP_*</code> multi-species accession. You should therefore expect to find one 100% identical <code>WP_*</code> sequence for your query and multiple, <em>almost</em> identical <code>WP_*</code> entries. And that's precisely what you see here.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-20T14:28:32.463Z
Answers.Text: Dear terdon, thank you very much for your nice answer. It seems that it's  better for me to do BLAST for this multi-species WP_* accession instead of the specific NP_* accession, isn't it?
Answers.UserDisplayName: Sara
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-20T14:33:55.777Z
Answers.Text: @Sara if this is still about finding homologs, then just include whatever you find. The more (relevant) sequences you include, the better your results will be. Now, if the NP and the WP sequences are 100% identical, it makes no difference at all which one of the two you use as a query since they are the same sequence. By the way, feel free to ping me (`@terdon`)  in the [Bioinformatics chat room](http://frt.saphetor.hcuge.ch:12032/sample/127/coverage/127000001) if you need more clarifications.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-20T12:11:46.953Z
Answers.LastActivityDate: 2017-06-20T12:11:46.953Z
Answers.LastEditDate: 2020-06-18T08:30:41.743Z
Answers.UserDisplayName: terdon
Body: <p>I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. After BLASTing my sequence, at first iteration I got 1000 hits and among them there were a lot of redundant sequences! </p>
  
  <p>My sequence had 241 amino acids and I found a lot of sequences with 100% identity, 100% cover and 0 E-value exactly the same as my sequence but with different IDs. All of these IDs were from RefSeq! In other iterations and after adjusting format options, I got this redundancy with other sequences from other species. My sequence is related to a chain of a multichain protein (E.coli fumarate reductase)</p>
  
  <p>For example, when using NP_418578 as a query, I found WP_078165098.1, WP_064226696.1, WP_062863447.1, WP_001401474.1 and other that were identical.</p>
  
  <p>I want to know what is wrong with Refseq. Is it really a Reference sequence database? If it is, where does this redundancy come from and why?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-19T17:53:37.023Z
Comments.Text: I assume you were using the protein version of the database, right? And were all the hits from the same species? Please [edit] your question and show us a specific example. Show us your query sequence and a few of the redundant results.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-19T18:08:49.230Z
Comments.Text: Yes, I am using the protein version of the database and my Refseq ID is: NP_418578.1  other Refseq IDs the same as this one are: WP_078165098.1, WP_064226696.1, WP_062863447.1, WP_001401474.1 and others
Comments.UserDisplayName: Sara
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-20T08:51:55.793Z
Comments.Text: @Sara Maybe you could post a screenshot of your results (and queries). But having a short sequence of 241aa in several sequence might indicate good conservation (maybe it is a domain?)
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-20T10:25:03.593Z
Comments.Text: @Sara Please [edit] your question to add extra information. Comments are easy to miss, hard to read and can be deleted without warning.
Comments.UserDisplayName: terdon
Tags: <blast><sequence-homology><refseq>
Title: Duplicate long hits from PSI-BLAST
ThreadText: # Duplicate long hits from PSI-BLAST
  
  (Asked by: username_0 on 2017-06-19)
  
  I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. After BLASTing my sequence, at first iteration I got 1000 hits and among them there were a lot of redundant sequences!
  
  My sequence had 241 amino acids and I found a lot of sequences with 100% identity, 100% cover and 0 E-value exactly the same as my sequence but with different IDs. All of these IDs were from RefSeq! In other iterations and after adjusting format options, I got this redundancy with other sequences from other species. My sequence is related to a chain of a multichain protein (E.coli fumarate reductase)
  
  For example, when using NP\_418578 as a query, I found WP\_078165098.1, WP\_064226696.1, WP\_062863447.1, WP\_001401474.1 and other that were identical.
  
  I want to know what is wrong with Refseq. Is it really a Reference sequence database? If it is, where does this redundancy come from and why?
  
  **Tags:** blast, sequence-homology, refseq
  
  > **Comments:**
  > **username_1**: I assume you were using the protein version of the database, right? And were all the hits from the same species? Please [edit] your question and show us a specific example. Show us your query sequence and a few of the redundant results.  
  > **username_0**: Yes, I am using the protein version of the database and my Refseq ID is: NP_418578.1  other Refseq IDs the same as this one are: WP_078165098.1, WP_064226696.1, WP_062863447.1, WP_001401474.1 and others  
  > **username_2**: @username_0 Maybe you could post a screenshot of your results (and queries). But having a short sequence of 241aa in several sequence might indicate good conservation (maybe it is a domain?)  
  > **username_1**: @username_0 Please [edit] your question to add extra information. Comments are easy to miss, hard to read and can be deleted without warning.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-06-20. Score: 2 | Accepted answer
  
  This is what is known as a feature, not a bug. Note that your identical proteins all have accessions starting with `WP_`. These are special "non-redundant proteins". Many sequences—particularly bacterial sequences—are identical between various different species so having a separate RefSeq entry for each of them would be inefficient. Therefore, RefSeq combines multiple such proteins into a single `WP_` record. This is documented [here](https://www.ncbi.nlm.nih.gov/refseq/about/nonredundantproteins/) (emphasis mine):
  
  > A new type of RefSeq protein record which represents non-redundant protein sequences was introduced in mid-2013. This record type was introduced to address a growing issue with redundancy in the Prokaryotic RefSeq protein dataset that coincided with a significant increase in bacterial genome submissions from individual isolates and closely related bacterial strains. For example, a large number of high-quality bacterial genomes may be submitted during a disease outbreak. The submitted sequences may reflect pathogen evolution during the course of the outbreak but the majority of the encoded proteins from these genomes may be identical to each other. As RefSeq includes these genomes, per community requests, this resulted in increased redundancy. **By representing identical proteins using a single non-redundant protein accession number (with the prefix 'WP\_'), redundancy in the database is significantly reduced.**
  >
  > [ . . . ]
  >
  > Because a non-redundant protein sequence may be found in RefSeq genomes from multiple species, **the organism information provided on the protein record reflects the lowest-common taxonomic node ranging from the genus species level to super-kingdom**. A non-redundant protein record that provides organism information at the level of a genus, family, or even super-kingdom does not mean that the protein is found in all RefSeq genomes below that taxonomic classification. It only indicates that the protein is found in more than one genome of different species for which the genus, family, or super-kingdom classification is the lowest common taxonomic node.
  
  So, your query was [NP\_418578.1](https://www.ncbi.nlm.nih.gov/protein/NP_418578), anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit from *E. coli* strain K-12, substrain MG1655. The first thing to notice is how specific that is. This is the protein found from one specific substrain of one specific strain of one specific bacterial species. It is reasonable to expect that there will be identical sequences from many, many closely related species. Both from, most probably, all other strains and substrains of *E. coli* and from other, related bacteria.
  
  Now, the specific sequences you mention are actually *slightly* different and not 100% identical. Below is a multiple alignment of NP\_418578.1 and the 4 WP\_ sequences you mentioned. Note that each of the 5 entries is slightly different. Each has one residue that differs from the rest. Look for the `:` in the identity line, there are 4 `:` and all others are `*` (I am only showing the relevant alignment blocks here and have removed those where all 4 sequences were identical):
  
  ```
  WP_001401474.1      MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
  WP_062863447.1      MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
  WP_064226696.1      MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
  NP_418578.1         MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
  WP_078165098.1      MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAIAQDH
                      *******************************************************:****
  
  [ . . . ]
  
  WP_001401474.1      KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
  WP_062863447.1      KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
  WP_064226696.1      KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHIRGLVAMNMMEGT
  NP_418578.1         KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
  WP_078165098.1      KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
                      ***********************************************:************
  
  [ . . . ]
  
  WP_001401474.1      GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
  WP_062863447.1      GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKISQAFWHEWR
  WP_064226696.1      GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
  NP_418578.1         GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
  WP_078165098.1      GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
                      **************************************************:*********
  
  WP_001401474.1      KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGIDPVKEPIPVRPTAHYTMG
  WP_062863447.1      KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
  WP_064226696.1      KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
  NP_418578.1         KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
  WP_078165098.1      KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
                      *****************************************:******************
  
  [ . . . ]
  
  ```
  
  Your sequence (NP\_418578.1) is only identical to one `WP_*` multi-species sequence, WP\_001192973:
  
  ```
  WP_001192973.1      MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
  NP_418578.1         MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH
                      ************************************************************
  
  WP_001192973.1      DSFEYHFHDTVAGGDWLCEQDVVDYFVHHCPTEMTQLELWGCPWSRRPDGSVNVRRFGGM
  NP_418578.1         DSFEYHFHDTVAGGDWLCEQDVVDYFVHHCPTEMTQLELWGCPWSRRPDGSVNVRRFGGM
                      ************************************************************
  
  WP_001192973.1      KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
  NP_418578.1         KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT
                      ************************************************************
  
  WP_001192973.1      LVQIRANAVVMATGGAGRVYRYNTNGGIVTGDGMGMALSHGVPLRDMEFVQYHPTGLPGS
  NP_418578.1         LVQIRANAVVMATGGAGRVYRYNTNGGIVTGDGMGMALSHGVPLRDMEFVQYHPTGLPGS
                      ************************************************************
  
  WP_001192973.1      GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
  NP_418578.1         GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
                      ************************************************************
  
  WP_001192973.1      KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
  NP_418578.1         KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG
                      ************************************************************
  
  WP_001192973.1      GIETDQNCETRIKGLFAVGECSSVGLHGANRLGSNSLAELVVFGRLAGEQATERAATAGN
  NP_418578.1         GIETDQNCETRIKGLFAVGECSSVGLHGANRLGSNSLAELVVFGRLAGEQATERAATAGN
                      ************************************************************
  
  WP_001192973.1      GNEAAIEAQAAGVEQRLKDLVNQDGGENWAKIRDEMGLAMEEGCGIYRTPELMQKTIDKL
  NP_418578.1         GNEAAIEAQAAGVEQRLKDLVNQDGGENWAKIRDEMGLAMEEGCGIYRTPELMQKTIDKL
                      ************************************************************
  
  WP_001192973.1      AELQERFKRVRITDTSSVFNTDLLYTIELGHGLNVAECMAHSAMARKESRGAHQRLDEGC
  NP_418578.1         AELQERFKRVRITDTSSVFNTDLLYTIELGHGLNVAECMAHSAMARKESRGAHQRLDEGC
                      ************************************************************
  
  WP_001192973.1      TERDDVNFLKHTLAFRDADGTTRLEYSDVKITTLPPAKRVYGGEADAADKAEAANKKEKA
  NP_418578.1         TERDDVNFLKHTLAFRDADGTTRLEYSDVKITTLPPAKRVYGGEADAADKAEAANKKEKA
                      ************************************************************
  
  WP_001192973.1      NG
  NP_418578.1         NG
                      **
  
  ```
  
  So, in summary, RefSeq will combine multiple identical sequences into a single `WP_*` multi-species accession. You should therefore expect to find one 100% identical `WP_*` sequence for your query and multiple, *almost* identical `WP_*` entries. And that's precisely what you see here.
  
  > **Comments:**
  > **username_0**: Dear username_1, thank you very much for your nice answer. It seems that it's  better for me to do BLAST for this multi-species WP_* accession instead of the specific NP_* accession, isn't it?  
  > **username_1**: @username_0 if this is still about finding homologs, then just include whatever you find. The more (relevant) sequences you include, the better your results will be. Now, if the NP and the WP sequences are 100% identical, it makes no difference at all which one of the two you use as a query since they are the same sequence. By the way, feel free to ping me (`@username_1`)  in the [Bioinformatics chat room](http://frt.saphetor.hcuge.ch:12032/sample/127/coverage/127000001) if you need more clarifications.  
  
  ---
  
  