Alignments for a candidate for gatA in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Kyrpidia tusciae DSM 2912

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_013076726.1 BTUS_RS14020 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000092905.1:WP_013076726.1
          Length = 494

 Score =  640 bits (1652), Expect = 0.0
 Identities = 314/475 (66%), Positives = 389/475 (81%), Gaps = 1/475 (0%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           MS++   + E+   + ++E+K S+L +    RI+  DD+V+AFL +DE+R    A+E+DE
Sbjct: 1   MSMWRWSVREMADKVRRREVKPSELAEAVLGRIRETDDRVRAFLHIDEDRVLEKAREMDE 60

Query: 61  AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIG 120
           A       GLLFG+P  VKDN+ T+G+RTTC+SKIL N+ P Y AT V++L+DA AV +G
Sbjct: 61  AAAAGRGEGLLFGVPGAVKDNLCTEGVRTTCASKILANYVPPYTATAVRKLEDARAVIVG 120

Query: 121 KLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIR 180
           K NMDEFAMGSSTENSA++ T NPW+L  VPGGSSGGSAAAVAAG+VPF+LGSDTGGSIR
Sbjct: 121 KTNMDEFAMGSSTENSAFQQTANPWDLGRVPGGSSGGSAAAVAAGQVPFALGSDTGGSIR 180

Query: 181 QPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTS 240
           QPA+FCGVVGLKPTYGRVSRYGLVAFASSLDQIGPIT TVED A +LQAI+G D +DSTS
Sbjct: 181 QPAAFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITLTVEDAAAVLQAIAGHDPLDSTS 240

Query: 241 ANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLP 300
           A V+VPDF  +LTGD+KG+++AVP+EY+GEG       +V  A+  L GLGA  EEVSLP
Sbjct: 241 APVEVPDFSGALTGDVKGMRLAVPREYIGEGTDPGVAAAVKRAVDALAGLGAEVEEVSLP 300

Query: 301 HSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIM 360
           H+KYA+ATYYL++ +EAS+NLAR+DG+RYG R +  DNLID+Y++TR+EGFG EVKRRIM
Sbjct: 301 HTKYAVATYYLIAPAEASSNLARYDGVRYGVRVE-GDNLIDMYRRTRSEGFGPEVKRRIM 359

Query: 361 LGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLT 420
           LGT+ALSSGYYDAYY +AQKVRTLI++DF+ VFE++D +V PTTPT AF+ GE   DPLT
Sbjct: 360 LGTYALSSGYYDAYYLRAQKVRTLIRRDFDAVFERFDAVVAPTTPTVAFRFGEKVSDPLT 419

Query: 421 MYANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
           MY NDILTIPVNLAG+P +SVPCGL DG+P+GLQ+IGK FDE+ V RVAHA+EQA
Sbjct: 420 MYLNDILTIPVNLAGLPAVSVPCGLVDGMPVGLQVIGKAFDEAAVLRVAHAYEQA 474


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: 704
Number of extensions: 25
Number of successful extensions: 2
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: 494
Length adjustment: 34
Effective length of query: 451
Effective length of database: 460
Effective search space:   207460
Effective search space used:   207460
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_013076726.1 BTUS_RS14020 (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.3449.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.5e-202  657.3   0.0   7.7e-202  657.0   0.0    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013076726.1  BTUS_RS14020 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013076726.1  BTUS_RS14020 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  657.0   0.0  7.7e-202  7.7e-202       3     463 ..      13     474 ..      11     477 .. 0.98

  Alignments for each domain:
  == domain 1  score: 657.0 bits;  conditional E-value: 7.7e-202
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva...kekklagipiavKdn 68 
                                               +++ ++ev+ +e++e++l ri +++d+++afl+++++++l+ka+++d+++a    e +l+g+p avKdn
  lcl|NCBI__GCF_000092905.1:WP_013076726.1  13 DKVRRREVKPSELAEAVLGRIRETDDRVRAFLHIDEDRVLEKAREMDEAAAagrGEGLLFGVPGAVKDN 81 
                                               678899******************************************999864446************ PP

                                 TIGR00132  69 iavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneerv 137
                                               +++++++ttcaSkiL nyv+py at v++l++a a+i+GktN+DEFamGsste+Saf+ t+nP++  rv
  lcl|NCBI__GCF_000092905.1:WP_013076726.1  82 LCTEGVRTTCASKILANYVPPYTATAVRKLEDARAVIVGKTNMDEFAMGSSTENSAFQQTANPWDLGRV 150
                                               ********************************************************************* PP

                                 TIGR00132 138 pGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakk 206
                                               pGGSsgGsaaavaa++vp+algsDTGgSiRqPA+fcgvvGlKPtYG+vSRyGlva+asSldqiG+++ +
  lcl|NCBI__GCF_000092905.1:WP_013076726.1 151 PGGSSGGSAAAVAAGQVPFALGSDTGGSIRQPAAFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITLT 219
                                               ********************************************************************* PP

                                 TIGR00132 207 vedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekle 275
                                               ved+a vl++i+g+D  Dsts+ v+v+++  +l+ d+kg++++v +e+++e++d +v++++++++++l 
  lcl|NCBI__GCF_000092905.1:WP_013076726.1 220 VEDAAAVLQAIAGHDPLDSTSAPVEVPDFSGALTGDVKGMRLAVPREYIGEGTDPGVAAAVKRAVDALA 288
                                               ********************************************************************* PP

                                 TIGR00132 276 elgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkr 344
                                                lgae++evslp+ k+a+a+Yy+i+p+Eassnlarydg+ryG rve ++ l ++y +tRsegfg evkr
  lcl|NCBI__GCF_000092905.1:WP_013076726.1 289 GLGAEVEEVSLPHTKYAVATYYLIAPAEASSNLARYDGVRYGVRVEGDN-LIDMYRRTRSEGFGPEVKR 356
                                               *********************************************9999.******************* PP

                                 TIGR00132 345 RimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDv 413
                                               RimlG+yals++yyd+yy++Aqkvrtli+++f+ +fe  D +v+pt+pt+af++gek +dpl+myl+D+
  lcl|NCBI__GCF_000092905.1:WP_013076726.1 357 RIMLGTYALSSGYYDAYYLRAQKVRTLIRRDFDAVFERFDAVVAPTTPTVAFRFGEKVSDPLTMYLNDI 425
                                               ********************************************************************* PP

                                 TIGR00132 414 ltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               lt+p+nlaGlpa+svP+g   +g+p+Glq+igkafd+  +l+va+a+eqa
  lcl|NCBI__GCF_000092905.1:WP_013076726.1 426 LTIPVNLAGLPAVSVPCGLV-DGMPVGLQVIGKAFDEAAVLRVAHAYEQA 474
                                               ********************.7**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (494 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: 00:00:00.01
# Mc/sec: 11.83
//
[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