Alignments for a candidate for gatB in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Pseudomonas stutzeri RCH2

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate GFF3267 Psest_3330 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__psRCH2:GFF3267
          Length = 481

 Score =  477 bits (1227), Expect = e-139
 Identities = 238/480 (49%), Positives = 337/480 (70%), Gaps = 7/480 (1%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +ETVIGLE+H +L T SK+FS S   FGAEPN+  +++DL  PG LPV+N  AV  A 
Sbjct: 1   MQWETVIGLEIHAQLATQSKIFSGSATTFGAEPNTQASLVDLGMPGTLPVLNAEAVRMAC 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
           +  +A+  EIA ++ F RKNYFYPD PK YQ SQ D PI   GY+DI + DG ++RIGIT
Sbjct: 61  KFGLAIEAEIAPKNVFARKNYFYPDLPKGYQTSQMDHPIVGKGYLDITLEDGSSRRIGIT 120

Query: 120 RLHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYT 177
           R H+EEDAGKS H+  + +  +DLNR GTPL+EIVSEPDIRS KEA AY++ + ++++Y 
Sbjct: 121 RAHLEEDAGKSLHEDFHGMSGIDLNRAGTPLLEIVSEPDIRSAKEAVAYVKAIHALVRYL 180

Query: 178 GVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLS 237
           G+ D  M EGSLRCD N+S+RP GQ +FGT+AE+KN+NSF ++ K + +E +RQ E +  
Sbjct: 181 GICDGNMAEGSLRCDCNVSVRPKGQAEFGTRAEIKNVNSFRFIEKAINHEVQRQIELIED 240

Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297
           GG++ QETR +D +  +T  MR KE ++DYRYFP PD++P+ I+ ++ + VR ++PELP 
Sbjct: 241 GGKVVQETRLYDPNKDETRSMRSKEEANDYRYFPCPDLLPVVIEQSFLDEVRASLPELPV 300

Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQV 357
           +++ ++ +E GL AYDA VL  ++E++D+FE       D KL +NW+MG ++  LNK+ +
Sbjct: 301 QKRERFESEFGLSAYDATVLAASRELADYFEQVNATCGDAKLAANWVMGELSSLLNKDGL 360

Query: 358 ELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEAT 417
           ++  + +T E L GMI  I+D T+S KIAK VF  +AA  G+A +I+E  GL Q++D   
Sbjct: 361 DIEQSPVTAEQLGGMILRIKDDTISGKIAKMVFEAMAAGEGSADEIIEKKGLKQVTDSGA 420

Query: 418 LLKFVNEALDNNEQSVEDYK----NGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473
           + K ++E L  N + VE Y+      +GK  GF VGQ MKASKG+ANP  VNQLLK++L+
Sbjct: 421 IEKMLDEVLAANAEQVEQYRASDETKRGKMFGFFVGQAMKASKGKANPGQVNQLLKKKLE 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: 623
Number of extensions: 22
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 GFF3267 Psest_3330 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit)
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.4969.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.6e-175  567.9   0.0   8.5e-175  567.8   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3267  Psest_3330 aspartyl/glutamyl-tRN


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3267  Psest_3330 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  567.8   0.0  8.5e-175  8.5e-175       3     480 ..       2     479 ..       1     480 [. 0.98

  Alignments for each domain:
  == domain 1  score: 567.8 bits;  conditional E-value: 8.5e-175
                           TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsevs 77 
                                         ++e viGlE+H ql t+sK+F+ + + +   +pNt+ + v+lg+PG+lPvlN eav++A k +la++++ ++++ 
  lcl|FitnessBrowser__psRCH2:GFF3267   2 QWETVIGLEIHAQLATQSKIFSGSATTFGA-EPNTQASLVDLGMPGTLPVLNAEAVRMACKFGLAIEAE-IAPKN 74 
                                         7899************************99.**************************************.668** PP

                           TIGR00133  78 vFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvDfNRs 151
                                         vF+RK+YfYpDlPkgyq +q d Pi+ +G+l+i le+++ ++igi+r hlEeD+gks ++    + +s +D+NR+
  lcl|FitnessBrowser__psRCH2:GFF3267  75 VFARKNYFYPDLPKGYQTSQMDHPIVGKGYLDITLEDGSsRRIGITRAHLEEDAGKSLHEDF--HGMSGIDLNRA 147
                                         **********************************9987669******************944..689******** PP

                           TIGR00133 152 gvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNlnslks 226
                                         g+PLlEiV++Pd++sakea+a++k +++++ryl+i dg++ eGs+R+D+Nvs+r+kGq ++gtr+EiKN+ns++ 
  lcl|FitnessBrowser__psRCH2:GFF3267 148 GTPLLEIVSEPDIRSAKEAVAYVKAIHALVRYLGICDGNMAEGSLRCDCNVSVRPKGQAEFGTRAEIKNVNSFRF 222
                                         *************************************************************************** PP

                           TIGR00133 227 iekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekveeklp 301
                                         iekai++E++Rq++l+++g +v+qetr +d +k  t s+R+Kee++DYRYfp Pdl p++i++++++e v++ lp
  lcl|FitnessBrowser__psRCH2:GFF3267 223 IEKAINHEVQRQIELIEDGGKVVQETRLYDPNKDETRSMRSKEEANDYRYFPCPDLLPVVIEQSFLDE-VRASLP 296
                                         *****************************************************************999.****** PP

                           TIGR00133 302 elPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaeallkpee 376
                                         elP +kr+r+++e+gls++da vl + +el+d+fe+v+ + +++kla+nW++ el + Lnk  ++++++ +++e+
  lcl|FitnessBrowser__psRCH2:GFF3267 297 ELPVQKRERFESEFGLSAYDATVLAASRELADYFEQVNATCGDAKLAANWVMGELSSLLNKDGLDIEQSPVTAEQ 371
                                         *************************************************************************** PP

                           TIGR00133 377 laeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenpkevekyk....sg 447
                                         l  +i  ik+++is+k+ak+++e +   +++++++iek+gl q++d  ++ k+++ev++ n+++ve+y+     +
  lcl|FitnessBrowser__psRCH2:GFF3267 372 LGGMILRIKDDTISGKIAKMVFEAMAAGEGSADEIIEKKGLKQVTDSGAIEKMLDEVLAANAEQVEQYRasdeTK 446
                                         ********************************************************************9887778 PP

                           TIGR00133 448 kekalkflvGqvmkktkgradpkevekllkell 480
                                         + k+++f+vGq+mk +kg+a+p +v++llk++l
  lcl|FitnessBrowser__psRCH2:GFF3267 447 RGKMFGFFVGQAMKASKGKANPGQVNQLLKKKL 479
                                         889****************************98 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.50
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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