Question: Using hhblits against ncbi nr database
gravatar for chanda.pritam
3.5 years ago by
chanda.pritam0 wrote:

I am using the software hhsuite from Dr. Soeding ( for my research projects. I have a very specific question regarding the output it generates, inputs from anybody who has used the software will help greatly. 

For a query to search the nr20 database using hhblits, the output .hhr file outputs the hits against clusters of proteins hits in the database. How can I get the profile-profile similarity score for each protein within each cluster to get an ordering of the proteins that are closer homologs to the query ?

For example (please refer to hhblits output below):   For cluster NR20|XULHUQABA, the database a3m file (nr20_xxx_a3m_db has 17 proteins. The output .hhr file contains only a single profile alignment against the consensus sequence of NR20|XULHUQABA (profile-profile similarity score is 1233.89). The other hits are for other clusters.

How can we get all the pairwise profile-profile scores of our query sequence against all 17 proteins in cluster NR20|XULHUQABA ?




Example output from running hhblits server (


Query Acetylcholine_receptor_protein_delta_chain_Torpedo_californica (seq=MGNIHFVYLL...DYSSDHPRCA Len=522 Neff=1.0 Nseqs=1)

Parameters  search:local realign with MAC:yes MAC threshold=0.35 


   No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM

  1 NR20|XULHUQABA|16|534 Neuronal 100.0  3E-166  4E-171 1233.9   0.0  496   16-520    35-532 (534)

  2 NR20|GODXONABE|128|541 Acetylc 100.0  8E-164  1E-168 1219.9   0.0  493   10-521    30-524 (541)

  3 NR20|XOZLIBEBA|11|444 Chain C, 100.0  8E-138  8E-143 1014.5   0.0  388   18-521    54-443 (444)

  4 NR20|SANVERABE|40|532 Acetylch 100.0  4E-116  5E-121  876.3   0.0  463   18-516    46-529 (532)

  5 NR20|GUTVEBEBA|2|417 PREDICTED 100.0  5E-111  4E-116  812.4   0.0  401  110-521     1-416 (417)

  6 NR20|YIXVUYEBA|4|248 Chain B,  100.0  2E-106  2E-111  750.6   0.0  247  246-504     1-247 (248)



Followed by profile alignments, one per cluster:

>NR20|XULHUQABA|16|534 Neuronal acetylcholine receptor subunit alpha-3; Acetylcholine receptor subunit

  epsilon; Neuronal acetylcholine receptor subunit eat-2; Neuronal acetylcholine receptor subunit alpha-2;

  Flags: Precursor; Neuronal acetylcholine receptor subunit beta-2. [Xenopus laevis]|148227704 [Equus caballus

  |194217616 [Ciona intestinalis]|198429844|320089451|198429842|320089453 [Meleagris gallopavo]|326926016

  [Taeniopygia guttata]|224060672 [Torpedinoidei]|113101|64394|39653647|39653655|39653653 [Canis lupus

  familiaris]|73994148 [Danio rerio]|122890898 [Takifugu rubripes]|31559081.

    Probab=100.00  E-value=3.4e-166  Score=1233.89  Aligned_cols=496  Identities=54%  Similarity=0.949  Sum_probs=465.1



  Q Consensus        16 ysgcsgvneeerlindllivnkynkhvrpvkhnnevvnialsltlsnlislketdetltsnvwmdhawydhrltwnasey   95 (522)

                        -+|-.+.|||+|||++|+  +.|||.+||++|-++.|..-+.|||+|||||+|.+||+|+||||+++|-|.||.||.|+|

  T Consensus        35 l~~~~~~n~E~rLi~~Lf--~~Yn~~vRP~~~~d~kv~V~v~lTLtnLISLnEkeE~ltTnVwie~~W~DyRl~Wn~s~y  112 (534)


  Confidence            344444699999999987  569999999999999999999999999999999999999999999999999999999999


hhsearch homology hhblits protein • 1.8k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 3.5 years ago by chanda.pritam0
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