Alignments for a candidate for gatA in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Pseudomonas stutzeri RCH2

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate GFF3266 Psest_3329 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__psRCH2:GFF3266
          Length = 483

 Score =  506 bits (1303), Expect = e-148
 Identities = 249/476 (52%), Positives = 349/476 (73%), Gaps = 1/476 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           + E+ + + +K     +L      RI+ +D ++ +F+++ +E A A AK  D A     E
Sbjct: 6   LAEIARNLAEKRFSAEELTRTLLARIEQLDPQLNSFISVTDELAIAQAKAAD-ARRAAGE 64

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L G PIG KD   T+G+RT+C SKIL+NF   Y+ATVV+RL  A  VT+GKLNMDEF
Sbjct: 65  SGALLGAPIGHKDLFCTQGIRTSCGSKILDNFKAPYNATVVERLAAAGTVTLGKLNMDEF 124

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGS+ E+S Y   KNPW+   VPGGSSGGSAAA+AA  +P + G+DTGGSIRQPA+   
Sbjct: 125 AMGSANESSYYGPVKNPWDPSRVPGGSSGGSAAAIAARLLPAATGTDTGGSIRQPAALTN 184

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           + GLKPTYGRVSR+G+VA+ASSLDQ GP+ RT ED A LL A++G D  DSTS +  + D
Sbjct: 185 LTGLKPTYGRVSRWGMVAYASSLDQGGPMARTAEDCALLLSAMAGFDAKDSTSVDQPLDD 244

Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307
           +L++L+  + GL+I +PKEY G G+  +  ++V+A+++ L+ LGAT +++SLP+ ++A+ 
Sbjct: 245 YLAALSQPLAGLRIGLPKEYFGAGLDPKIADAVMASVEELKKLGATVKDISLPNMQHAIP 304

Query: 308 TYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALS 367
           +YY+++ +EAS+NL+RFDG+R+GYR +N  +L DLYK++RAEGFG+EVKRRIM+GT+ALS
Sbjct: 305 SYYVIAPAEASSNLSRFDGVRFGYRCENPVDLTDLYKRSRAEGFGDEVKRRIMVGTYALS 364

Query: 368 SGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDIL 427
           +GYYDAYY KAQK+R LIK+DF   FE+ D+I+GPTTP  A+K+GE   DP++ Y  DI 
Sbjct: 365 AGYYDAYYLKAQKIRRLIKQDFVTAFEQVDLILGPTTPNLAWKLGEKNADPVSAYLEDIY 424

Query: 428 TIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483
           TI  NLAG+PG+S+P G  DGLP+G+Q++  +F E+ +  VAH ++Q TD H   P
Sbjct: 425 TITANLAGIPGLSMPAGFIDGLPVGVQLLAPYFQEARLLNVAHQYQQVTDWHARAP 480


Lambda     K      H
   0.315    0.134    0.381 

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: 590
Number of extensions: 21
Number of successful extensions: 1
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: 485
Length of database: 483
Length adjustment: 34
Effective length of query: 451
Effective length of database: 449
Effective search space:   202499
Effective search space used:   202499
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate GFF3266 Psest_3329 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A 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/TIGR00132.hmm
# target sequence database:        /tmp/gapView.6947.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00132  [M=466]
Accession:   TIGR00132
Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.2e-184  598.3   0.0   5.9e-184  598.1   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3266  Psest_3329 aspartyl/glutamyl-tRN


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3266  Psest_3329 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.1   0.0  5.9e-184  5.9e-184       4     465 ..      12     474 ..       9     475 .. 0.98

  Alignments for each domain:
  == domain 1  score: 598.1 bits;  conditional E-value: 5.9e-184
                           TIGR00132   4 llkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdiet 76 
                                          l +k++s++e+++++l+rie+ + ++n+f++vt+e a+++ak+ d++ a  e   l g pi+ Kd +++++i+t
  lcl|FitnessBrowser__psRCH2:GFF3266  12 NLAEKRFSAEELTRTLLARIEQLDPQLNSFISVTDELAIAQAKAADARRAaGEsGALLGAPIGHKDLFCTQGIRT 86 
                                         6788999***************************************998876636******************** PP

                           TIGR00132  77 tcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaavaa 151
                                         +c+SkiL+n+++py+atVverl +ag++++Gk N+DEFamGs+ e+S++g++knP++ +rvpGGSsgGsaaa+aa
  lcl|FitnessBrowser__psRCH2:GFF3266  87 SCGSKILDNFKAPYNATVVERLAAAGTVTLGKLNMDEFAMGSANESSYYGPVKNPWDPSRVPGGSSGGSAAAIAA 161
                                         *************************************************************************** PP

                           TIGR00132 152 dlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDst 226
                                          l p a g+DTGgSiRqPA++++  GlKPtYG+vSR+G+vayasSldq G++a++ ed al+l++++g D+kDst
  lcl|FitnessBrowser__psRCH2:GFF3266 162 RLLPAATGTDTGGSIRQPAALTNLTGLKPTYGRVSRWGMVAYASSLDQGGPMARTAEDCALLLSAMAGFDAKDST 236
                                         *************************************************************************** PP

                           TIGR00132 227 slevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiisp 301
                                         s++ + +++l +l + l gl++g+ ke+++ +ld ++++++ + +e+l++lga+++++slp+++ a++ Yy+i+p
  lcl|FitnessBrowser__psRCH2:GFF3266 237 SVDQPLDDYLAALSQPLAGLRIGLPKEYFGAGLDPKIADAVMASVEELKKLGATVKDISLPNMQHAIPSYYVIAP 311
                                         *************************************************************************** PP

                           TIGR00132 302 sEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidef 376
                                         +Eassnl+r+dg+r+G+r e++ +l++ly+++R+egfg+evkrRim+G+yals++yyd+yy+kAqk+r+li+++f
  lcl|FitnessBrowser__psRCH2:GFF3266 312 AEASSNLSRFDGVRFGYRCENPVDLTDLYKRSRAEGFGDEVKRRIMVGTYALSAGYYDAYYLKAQKIRRLIKQDF 386
                                         *************************************************************************** PP

                           TIGR00132 377 eklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddk 451
                                           +fe+vD+i++pt+p la klgek++dp++ yl+D++t++anlaG+p++s+P+g   +glp+G+q+ + +f++ 
  lcl|FitnessBrowser__psRCH2:GFF3266 387 VTAFEQVDLILGPTTPNLAWKLGEKNADPVSAYLEDIYTITANLAGIPGLSMPAGFI-DGLPVGVQLLAPYFQEA 460
                                         *********************************************************.7**************** PP

                           TIGR00132 452 kllsvakaleqald 465
                                         +ll+va++++q +d
  lcl|FitnessBrowser__psRCH2:GFF3266 461 RLLNVAHQYQQVTD 474
                                         *********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (483 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.79
//
[ok]

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