Alignments for a candidate for gatA in Phaeacidiphilus oryzae TH49

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Phaeacidiphilus oryzae TH49

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_037572612.1 BS73_RS14775 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000744815.1:WP_037572612.1
          Length = 499

 Score =  456 bits (1172), Expect = e-132
 Identities = 247/471 (52%), Positives = 314/471 (66%), Gaps = 5/471 (1%)

Query: 10  ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHG 69
           E  + +   ++   ++      RI AVD KV AFL +D + A A A+ +D   +   + G
Sbjct: 13  ETAEAVAAGKVTAVEVTQAHLDRIAAVDGKVHAFLHVDADGALAQARAVDAKREAGEKLG 72

Query: 70  LLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAM 129
            L G+P+ +KD   T+G+ TT  SKILE + P YDAT+ +RL+DA+ V +GK NMDEFAM
Sbjct: 73  PLAGVPLALKDVFTTEGIPTTAGSKILEGWIPPYDATLTKRLKDADVVILGKTNMDEFAM 132

Query: 130 GSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVV 189
           GSSTENSAY  T NPW+L  +PGGS GGSAAA+AA E P ++G+DTGGSIRQP +  G V
Sbjct: 133 GSSTENSAYGPTGNPWDLARIPGGSGGGSAAALAAYEAPLAIGTDTGGSIRQPGAVTGTV 192

Query: 190 GLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFL 249
           G+KPTYG VSRYGL+AF+SSLDQ GP  RTV D A L +AI+G D +DSTS +  VP  +
Sbjct: 193 GVKPTYGAVSRYGLIAFSSSLDQGGPCARTVLDAALLHEAIAGHDPLDSTSIDAPVPPVV 252

Query: 250 -SSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALAT 308
            ++  G + G++I V KE+ GEG      +    ++++L  LGA   EVS P   YAL  
Sbjct: 253 EAARNGSVDGMRIGVVKEFGGEGYQPGVMQRFNESVELLRELGAEVVEVSCPSFTYALPA 312

Query: 309 YYLLSSSEASANLARFDGIRYGYRT--DNADNLIDLYKQTRAEGFGNEVKRRIMLGTFAL 366
           YYL++ SE S+NLARFD +RYG R   D   +  D+   TR  GFG EVKRRIMLGT+AL
Sbjct: 313 YYLIAPSECSSNLARFDAMRYGLRVGDDGTRSAEDVTALTREAGFGPEVKRRIMLGTYAL 372

Query: 367 SSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDI 426
           SSGYYDAYY  AQKVRTLI +DF+  F   DV++ PTTPT AF IGE   DP+ MY  D+
Sbjct: 373 SSGYYDAYYGSAQKVRTLITRDFDRAFADVDVLISPTTPTTAFPIGERADDPMAMYLADL 432

Query: 427 LTIPVNLAGVPGISVPCGLA--DGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
            TIP NLAG   +SVPCGLA  D LP+GLQII     +  +YRV  A E+A
Sbjct: 433 CTIPSNLAGNAAMSVPCGLAPEDNLPVGLQIIAPAMADDRLYRVGAAVERA 483


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: 629
Number of extensions: 31
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: 485
Length of database: 499
Length adjustment: 34
Effective length of query: 451
Effective length of database: 465
Effective search space:   209715
Effective search space used:   209715
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_037572612.1 BS73_RS14775 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
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.2314173.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-189  615.9   0.0   2.6e-189  615.7   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037572612.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037572612.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  615.7   0.0  2.6e-189  2.6e-189       3     465 ..      16     485 ..      14     486 .. 0.97

  Alignments for each domain:
  == domain 1  score: 615.7 bits;  conditional E-value: 2.6e-189
                             TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKdniavk 72 
                                           e++ + +v+++ev+++ l+ri av+ k++afl+v+++ al++a+++d+k +  ++  +lag+p+a+Kd+++++
  NCBI__GCF_000744815.1:WP_037572612.1  16 EAVAAGKVTAVEVTQAHLDRIAAVDGKVHAFLHVDADGALAQARAVDAKREagEKlGPLAGVPLALKDVFTTE 88 
                                           56778899***************************************9988864446**************** PP

                             TIGR00132  73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGs 145
                                           +i+tt++SkiLe++++pydat ++rlk+a+++i+GktN+DEFamGsste+Sa+g+t nP++ +r+pGGS+gGs
  NCBI__GCF_000744815.1:WP_037572612.1  89 GIPTTAGSKILEGWIPPYDATLTKRLKDADVVILGKTNMDEFAMGSSTENSAYGPTGNPWDLARIPGGSGGGS 161
                                           ************************************************************************* PP

                             TIGR00132 146 aaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvis 218
                                           aaa+aa ++pla+g+DTGgSiRqP +++g+vG+KPtYG+vSRyGl+a++sSldq G++a++v d+al++++i+
  NCBI__GCF_000744815.1:WP_037572612.1 162 AAALAAYEAPLAIGTDTGGSIRQPGAVTGTVGVKPTYGAVSRYGLIAFSSSLDQGGPCARTVLDAALLHEAIA 234
                                           ************************************************************************* PP

                             TIGR00132 219 gkDkkDstslevkveelleelkk.dlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvk 290
                                           g+D  Dsts++++v+ ++e++++  + g+++gvvke+ +e+++ +v+++f++ +e l+elgae+vevs+ps+ 
  NCBI__GCF_000744815.1:WP_037572612.1 235 GHDPLDSTSIDAPVPPVVEAARNgSVDGMRIGVVKEFGGEGYQPGVMQRFNESVELLRELGAEVVEVSCPSFT 307
                                           ***************99999998899*********************************************** PP

                             TIGR00132 291 lalaiYyiispsEassnlarydgiryGkrveelks..lkelyaktRsegfgeevkrRimlGayalskeyydky 361
                                           +al++Yy+i+psE ssnlar+d++ryG rv ++    ++++ a tR++gfg evkrRimlG+yals++yyd+y
  NCBI__GCF_000744815.1:WP_037572612.1 308 YALPAYYLIAPSECSSNLARFDAMRYGLRVGDDGTrsAEDVTALTREAGFGPEVKRRIMLGTYALSSGYYDAY 380
                                           ******************************9987655999********************************* PP

                             TIGR00132 362 ykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkke 434
                                           y  Aqkvrtli+++f+ +f +vDv++spt+pt+af +ge+a+dp++myl+D++t+p nlaG+ a+svP+g + 
  NCBI__GCF_000744815.1:WP_037572612.1 381 YGSAQKVRTLITRDFDRAFADVDVLISPTTPTTAFPIGERADDPMAMYLADLCTIPSNLAGNAAMSVPCGLAP 453
                                           **********************************************************************987 PP

                             TIGR00132 435 .kglpiGlqiigkafddkkllsvakaleqald 465
                                            ++lp+Glqii+ a++d++l++v++a+e+a++
  NCBI__GCF_000744815.1:WP_037572612.1 454 eDNLPVGLQIIAPAMADDRLYRVGAAVERAFT 485
                                           589*************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (499 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: 29.81
//
[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