Alignments for a candidate for gatB in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Pseudomonas simiae WCS417

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate GFF834 PS417_04235 glutamyl-tRNA amidotransferase

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__WCS417:GFF834
          Length = 481

 Score =  457 bits (1175), Expect = e-133
 Identities = 225/481 (46%), Positives = 331/481 (68%), Gaps = 9/481 (1%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +E VIGLE+H +L T SK+FS S   FG+EPN+  +++DL  PGVLPV+N+ AV  A+
Sbjct: 1   MQWEVVIGLEIHTQLATQSKIFSGSATTFGSEPNTQASLVDLGMPGVLPVLNQEAVRMAV 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
              +A++ EI   + F RKNYFYPD PK YQISQ + PI   G++DI + DG  KR+G+T
Sbjct: 61  MFGLAIDAEIGQHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIPLEDGTIKRVGVT 120

Query: 120 RLHMEEDAGKSTHKGEY---SLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQY 176
           R H+EEDAGKS H+ E+   + +DLNR GTPL+EIVSEPD+RS KEA AY++ + ++++Y
Sbjct: 121 RAHLEEDAGKSLHE-EFPGATGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKTIHALVRY 179

Query: 177 TGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELL 236
            G+ D  M EGSLRCD N+S+RP GQ +FGT+ E+KN+NSF ++ K +  E +RQ E + 
Sbjct: 180 LGICDGNMAEGSLRCDCNVSIRPKGQVEFGTRCEIKNVNSFRFIEKAINSEVRRQIELIE 239

Query: 237 SGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELP 296
            GG++ Q+TR +D +  +T  MR KE ++DYRYFP+PD++P+ ++D++   +R T+PELP
Sbjct: 240 DGGKVIQQTRLYDPNKDETRAMRSKEEANDYRYFPDPDLLPVVLEDSFLNDIRATLPELP 299

Query: 297 DERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQ 356
            +++ ++  + GL  YDA VL  ++E +++FE  +    D KL +NW+M  +   LNK  
Sbjct: 300 QQKRERFQAQFGLSVYDASVLASSREQANYFEKVVSIAGDAKLAANWVMVELGSLLNKQG 359

Query: 357 VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEA 416
           +E+ +  ++ E L GM+  I+D T+S KIAK VF  +A+  G+A +I+E  GL Q++D  
Sbjct: 360 LEIDEAPVSAEQLGGMLLRIKDNTISGKIAKTVFEAMASGEGSADEIIEKRGLKQVTDSG 419

Query: 417 TLLKFVNEALDNNEQSVEDYKNG----KGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
            +   ++E L  N + VE Y+      +GK  GF VGQ MKASKG+ANPQ VN+LLK +L
Sbjct: 420 AISAVLDEMLAANAEQVEQYRAADEAKRGKMFGFFVGQAMKASKGKANPQQVNELLKSKL 479

Query: 473 D 473
           +
Sbjct: 480 E 480


Lambda     K      H
   0.313    0.133    0.373 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 636
Number of extensions: 24
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 475
Length of database: 481
Length adjustment: 34
Effective length of query: 441
Effective length of database: 447
Effective search space:   197127
Effective search space used:   197127
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate GFF834 PS417_04235 (glutamyl-tRNA amidotransferase)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00133.hmm
# target sequence database:        /tmp/gapView.1435549.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                      -----------
   1.8e-173  563.4   0.0     2e-173  563.3   0.0    1.0  1  FitnessBrowser__WCS417:GFF834  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__WCS417:GFF834  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  563.3   0.0    2e-173    2e-173       2     480 ..       1     479 [.       1     480 [. 0.98

  Alignments for each domain:
  == domain 1  score: 563.3 bits;  conditional E-value: 2e-173
                      TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsevsvFdR 81 
                                    +++e+viGlE+H+ql t+sK+F+ + + + + +pNt+ + v+lg+PG+lPvlN+eav++A++ +la++++i  +  vF+R
  FitnessBrowser__WCS417:GFF834   1 MQWEVVIGLEIHTQLATQSKIFSGSATTFGS-EPNTQASLVDLGMPGVLPVLNQEAVRMAVMFGLAIDAEIG-QHNVFAR 78 
                                    5789***************************.**************************************55.79***** PP

                      TIGR00133  82 KhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvDfNRsgvPLlEiVt 160
                                    K+YfYpDlPkgyqi+q +lPi+ +G+l+i le++  k++g++r hlEeD+gks ++e   +  + +D+NR+g+PLlEiV+
  FitnessBrowser__WCS417:GFF834  79 KNYFYPDLPKGYQISQMELPIVGKGHLDIPLEDGTiKRVGVTRAHLEEDAGKSLHEEF--PGATGIDLNRAGTPLLEIVS 156
                                    ******************************999888*******************965..789***************** PP

                      TIGR00133 161 kPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkk 240
                                    +Pd++sakea+a++k +++++ryl+i dg++ eGs+R+D+Nvsir+kGq ++gtr EiKN+ns++ iekai+ E+ Rq++
  FitnessBrowser__WCS417:GFF834 157 EPDMRSAKEAVAYVKTIHALVRYLGICDGNMAEGSLRCDCNVSIRPKGQVEFGTRCEIKNVNSFRFIEKAINSEVRRQIE 236
                                    ******************************************************************************** PP

                      TIGR00133 241 llkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglsee 320
                                    l+++g +v q+tr +d +k  t ++R+Kee++DYRYfp+Pdl p++++++++++ ++++lpelP++kr+r++ ++gls +
  FitnessBrowser__WCS417:GFF834 237 LIEDGGKVIQQTRLYDPNKDETRAMRSKEEANDYRYFPDPDLLPVVLEDSFLND-IRATLPELPQQKRERFQAQFGLSVY 315
                                    **************************************************9999.************************* PP

                      TIGR00133 321 dakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakellee 400
                                    da vl s +e +++fe+vv+ ++++kla+nW++ el + Lnk+ +++ ea +++e+l  ++  ik+++is+k+ak+++e 
  FitnessBrowser__WCS417:GFF834 316 DASVLASSREQANYFEKVVSIAGDAKLAANWVMVELGSLLNKQGLEIDEAPVSAEQLGGMLLRIKDNTISGKIAKTVFEA 395
                                    ******************************************************************************** PP

                      TIGR00133 401 llenkkdpkklieklgliqisdekelvkiveevikenpkevekyk....sgkekalkflvGqvmkktkgradpkevekll 476
                                    + + +++++++iek+gl q++d  ++ ++++e+++ n+++ve+y+    +++ k+++f+vGq+mk +kg+a+p++v++ll
  FitnessBrowser__WCS417:GFF834 396 MASGEGSADEIIEKRGLKQVTDSGAISAVLDEMLAANAEQVEQYRaadeAKRGKMFGFFVGQAMKASKGKANPQQVNELL 475
                                    ********************************************9888778899************************** PP

                      TIGR00133 477 kell 480
                                    k +l
  FitnessBrowser__WCS417:GFF834 476 KSKL 479
                                    *988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (481 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.22
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis