Alignments for a candidate for gatA in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Mycolicibacterium vanbaalenii PYR-1

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_011779344.1 MVAN_RS10605 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000015305.1:WP_011779344.1
          Length = 498

 Score =  437 bits (1125), Expect = e-127
 Identities = 240/475 (50%), Positives = 311/475 (65%), Gaps = 14/475 (2%)

Query: 15  IHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGL---- 70
           I  +E+  +++      +I A D +  AFL +  ++A A A  +D+A+   +  G     
Sbjct: 16  IAAREVSATEVTQACLDQIAATDAEYHAFLHVAGDQALAAAATVDKAIHEATAAGERLPS 75

Query: 71  -LFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAM 129
            L G+P+ +KD   T  + TTC SKILE +   YDATV  +L+ A    +GK NMDEFAM
Sbjct: 76  PLAGVPLALKDVFTTTDMPTTCGSKILEGWTSPYDATVTAKLRAAGIPILGKTNMDEFAM 135

Query: 130 GSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVV 189
           GSSTENSAY  T+NPWN+D VPGGS GGSAAA+AA + P ++GSDTGGSIRQPA+    V
Sbjct: 136 GSSTENSAYGPTRNPWNVDCVPGGSGGGSAAALAAFQAPLAIGSDTGGSIRQPAALTATV 195

Query: 190 GLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFL 249
           G+KPTYG VSRYGL+A ASSLDQ GP  RTV D A L Q I+G D  DSTS N  VPD +
Sbjct: 196 GVKPTYGTVSRYGLIACASSLDQGGPCARTVLDTALLHQVIAGHDPRDSTSVNAAVPDVV 255

Query: 250 ----SSLTGDIKGLKIAVPKEY-LGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKY 304
               +   GD+KG++I V K+   GEG       S  AA++ L  LGA   EV  PH  +
Sbjct: 256 GAARAGARGDLKGVRIGVVKQLRSGEGYQPGVLASFTAAVEQLTALGAEVSEVDCPHFDH 315

Query: 305 ALATYYLLSSSEASANLARFDGIRYGYRT--DNADNLIDLYKQTRAEGFGNEVKRRIMLG 362
           +LA YYL+  SE S+NLA+FDG+RYG R   D   +  ++   TRA GFG EVKRRIM+G
Sbjct: 316 SLAAYYLILPSEVSSNLAKFDGMRYGLRVGDDGTTSAEEVMAMTRAAGFGAEVKRRIMIG 375

Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMY 422
           T+ALS+GYYDAYY +AQKVRTLI +D ++ +   DV+V P TP+ AF++GE   DPL MY
Sbjct: 376 TYALSAGYYDAYYNQAQKVRTLIARDLDEAYRSVDVLVSPATPSTAFRLGEKVDDPLAMY 435

Query: 423 ANDILTIPVNLAGVPGISVPCGLA--DGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
             D+ T+P+NLAG  G+SVP GL+  D LP+GLQI+     +  +YRV  A+E A
Sbjct: 436 LFDLCTLPLNLAGHCGMSVPSGLSADDNLPVGLQIMAPALADDRLYRVGAAYEAA 490


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: 609
Number of extensions: 18
Number of successful extensions: 6
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: 498
Length adjustment: 34
Effective length of query: 451
Effective length of database: 464
Effective search space:   209264
Effective search space used:   209264
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 WP_011779344.1 MVAN_RS10605 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A)
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.5886.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-190  619.0   0.0   3.2e-190  618.7   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011779344.1  MVAN_RS10605 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011779344.1  MVAN_RS10605 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.7   0.0  3.2e-190  3.2e-190       3     463 ..      14     490 ..      12     492 .. 0.96

  Alignments for each domain:
  == domain 1  score: 618.7 bits;  conditional E-value: 3.2e-190
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva......ke..kklagipi 63 
                                               +++ ++evs++ev++++l++i a++ +++afl+v+ ++al++a+ +dk+++      ++  ++lag+p+
  lcl|NCBI__GCF_000015305.1:WP_011779344.1  14 AKIAAREVSATEVTQACLDQIAATDAEYHAFLHVAGDQALAAAATVDKAIHeataagERlpSPLAGVPL 82 
                                               68999******************************************9987777786334459****** PP

                                 TIGR00132  64 avKdniavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPe 132
                                               a+Kd++++ d++ttc+SkiLe+++spydatV+ +l++ag+ i+GktN+DEFamGsste+Sa+g+t+nP+
  lcl|NCBI__GCF_000015305.1:WP_011779344.1  83 ALKDVFTTTDMPTTCGSKILEGWTSPYDATVTAKLRAAGIPILGKTNMDEFAMGSSTENSAYGPTRNPW 151
                                               ********************************************************************* PP

                                 TIGR00132 133 neervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiG 201
                                               n + vpGGS+gGsaaa+aa+++pla+gsDTGgSiRqPA+++++vG+KPtYG+vSRyGl+a+asSldq G
  lcl|NCBI__GCF_000015305.1:WP_011779344.1 152 NVDCVPGGSGGGSAAALAAFQAPLAIGSDTGGSIRQPAALTATVGVKPTYGTVSRYGLIACASSLDQGG 220
                                               ********************************************************************* PP

                                 TIGR00132 202 ilakkvedialvldvisgkDkkDstslevkveelleelkk....dlkglkvgvvkels.eesldkevke 265
                                               ++a++v d+al+++vi+g+D +Dsts++++v++++ ++++    dlkg+++gvvk+l+ +e+++ +v +
  lcl|NCBI__GCF_000015305.1:WP_011779344.1 221 PCARTVLDTALLHQVIAGHDPRDSTSVNAAVPDVVGAARAgargDLKGVRIGVVKQLRsGEGYQPGVLA 289
                                               **********************************99988777889***********962789******* PP

                                 TIGR00132 266 kfekllekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelks..lkelyak 332
                                               +f +++e+l++lgae++ev++p+++ +la+Yy+i psE+ssnla++dg+ryG rv ++    ++e++a 
  lcl|NCBI__GCF_000015305.1:WP_011779344.1 290 SFTAAVEQLTALGAEVSEVDCPHFDHSLAAYYLILPSEVSSNLAKFDGMRYGLRVGDDGTtsAEEVMAM 358
                                               *******************************************************9987655999**** PP

                                 TIGR00132 333 tRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgek 401
                                               tR++gfg+evkrRim+G+yals++yyd+yy++Aqkvrtli++++++++++vDv+vsp++p +af+lgek
  lcl|NCBI__GCF_000015305.1:WP_011779344.1 359 TRAAGFGAEVKRRIMIGTYALSAGYYDAYYNQAQKVRTLIARDLDEAYRSVDVLVSPATPSTAFRLGEK 427
                                               ********************************************************************* PP

                                 TIGR00132 402 aedplemylsDvltvpanlaGlpaisvPlgkke.kglpiGlqiigkafddkkllsvakaleqa 463
                                                +dpl+myl D++t+p+nlaG++++svP g +  ++lp+Glqi++ a++d++l++v++a+e+a
  lcl|NCBI__GCF_000015305.1:WP_011779344.1 428 VDDPLAMYLFDLCTLPLNLAGHCGMSVPSGLSAdDNLPVGLQIMAPALADDRLYRVGAAYEAA 490
                                               *****************************9886489***********************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (498 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: 7.75
//
[ok]

This GapMind analysis is from Apr 10 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