Alignments for a candidate for gatA in Desulfovibrio bastinii DSM 16055

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Desulfovibrio bastinii DSM 16055

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_027180517.1 G496_RS0118105 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000429985.1:WP_027180517.1
          Length = 487

 Score =  526 bits (1354), Expect = e-154
 Identities = 259/476 (54%), Positives = 350/476 (73%), Gaps = 6/476 (1%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           L++  +TE+ +LI   EI ++D V    +RI + +  ++A LA + + A   A E+D   
Sbjct: 4   LYEKSLTEISELIASGEITVTDAVKSCLERIDSTEPAIEALLAQNRDEALKQAAEMD--A 61

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
            G  +   L+G+P+ +KD + TK ++TTC SKILE+F P YDAT + +L++A A+ + K 
Sbjct: 62  QGPDKSKPLWGVPVIIKDVLATKNIKTTCGSKILEDFTPFYDATAITKLKEAGAIILAKA 121

Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182
           NMDEFAMGS+TENSAYK T+NPWN D VPGGSSGGS A VAAG+   +LG+DTGGSIR P
Sbjct: 122 NMDEFAMGSTTENSAYKTTRNPWNTDRVPGGSSGGSGATVAAGQAFAALGTDTGGSIRLP 181

Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242
           ASFCG+VG+KPTYGRVSRYG++A+ SSLDQIGP+TRTVED+A +L  ISG DK DSTS  
Sbjct: 182 ASFCGIVGVKPTYGRVSRYGMIAYGSSLDQIGPMTRTVEDSARILNVISGHDKRDSTSVE 241

Query: 243 VDVPDFLSSL--TGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLP 300
            DVPDF++ L    D+ GL + +P+EY GEG+ +E  E+  AA+K  E LGA    V L 
Sbjct: 242 CDVPDFVAELKKRTDLSGLTLGLPEEYWGEGLSEEVSEACKAAIKKAEELGAKTVPVKLS 301

Query: 301 HSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIM 360
            ++YA+ATYY+++ +EAS+NL+RFDGIRYGYR   AD LIDLY ++R E FG+EV+RRI+
Sbjct: 302 MTEYAIATYYIIAMAEASSNLSRFDGIRYGYRNKEADELIDLYTKSRTEAFGDEVQRRII 361

Query: 361 LGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLT 420
           +GT+ LS+GYYDAYYKKA ++R ++++DFE  FE  D+I+GP  PT AF +G+ T DPL 
Sbjct: 362 IGTYVLSAGYYDAYYKKAAQIRRILRQDFEKAFESCDLILGPACPTTAFPVGDFTSDPLQ 421

Query: 421 MYANDILTIPVNLAGVPGISVPCGLA--DGLPLGLQIIGKHFDESTVYRVAHAFEQ 474
           MY  DI TI +NLAG+PG+S+P GL    G+P+GLQI+   FDEST+ + A+  E+
Sbjct: 422 MYLMDIFTISLNLAGLPGMSLPVGLGKESGMPVGLQIMAPAFDESTMLQAANILEK 477


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: 617
Number of extensions: 30
Number of successful extensions: 3
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: 487
Length adjustment: 34
Effective length of query: 451
Effective length of database: 453
Effective search space:   204303
Effective search space used:   204303
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_027180517.1 G496_RS0118105 (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.7279.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.4e-190  618.0   0.0   6.2e-190  617.8   0.0    1.0  1  lcl|NCBI__GCF_000429985.1:WP_027180517.1  G496_RS0118105 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429985.1:WP_027180517.1  G496_RS0118105 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 !  617.8   0.0  6.2e-190  6.2e-190       3     463 ..      14     478 ..      12     481 .. 0.98

  Alignments for each domain:
  == domain 1  score: 617.8 bits;  conditional E-value: 6.2e-190
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkvake.kklagipiavKdnia 70 
                                               el+ + e++++++++++leri++++  i+a+l+ ++++alk+a+++d++  ++ k+l g+p+ +Kd++a
  lcl|NCBI__GCF_000429985.1:WP_027180517.1  14 ELIASGEITVTDAVKSCLERIDSTEPAIEALLAQNRDEALKQAAEMDAQGPDKsKPLWGVPVIIKDVLA 82 
                                               6788999*****************************************9885548************** PP

                                 TIGR00132  71 vkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpG 139
                                               +k+i+ttc+SkiLe++++ ydat +++lkeaga+i+ k+N+DEFamGs+te+Sa++ t+nP+n++rvpG
  lcl|NCBI__GCF_000429985.1:WP_027180517.1  83 TKNIKTTCGSKILEDFTPFYDATAITKLKEAGAIILAKANMDEFAMGSTTENSAYKTTRNPWNTDRVPG 151
                                               ********************************************************************* PP

                                 TIGR00132 140 GSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkve 208
                                               GSsgGs+a+vaa+++  alg+DTGgSiR PAsfcg+vG+KPtYG+vSRyG++ay sSldqiG+++++ve
  lcl|NCBI__GCF_000429985.1:WP_027180517.1 152 GSSGGSGATVAAGQAFAALGTDTGGSIRLPASFCGIVGVKPTYGRVSRYGMIAYGSSLDQIGPMTRTVE 220
                                               ********************************************************************* PP

                                 TIGR00132 209 dialvldvisgkDkkDstslevkveelleelkk..dlkglkvgvvkelseesldkevkekfekllekle 275
                                               d a +l+visg+Dk+Dsts+e +v++++ elkk  dl gl +g+ +e+ +e+l++ev+e+ +++++k e
  lcl|NCBI__GCF_000429985.1:WP_027180517.1 221 DSARILNVISGHDKRDSTSVECDVPDFVAELKKrtDLSGLTLGLPEEYWGEGLSEEVSEACKAAIKKAE 289
                                               ******************************9998899******************************** PP

                                 TIGR00132 276 elgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkr 344
                                               elga+ v+v+l   ++a+a+Yyii+++Eassnl+r+dgiryG+r +e+++l +ly+k+R e fg+ev+r
  lcl|NCBI__GCF_000429985.1:WP_027180517.1 290 ELGAKTVPVKLSMTEYAIATYYIIAMAEASSNLSRFDGIRYGYRNKEADELIDLYTKSRTEAFGDEVQR 358
                                               ********************************************************************* PP

                                 TIGR00132 345 RimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDv 413
                                               Ri++G+y+ls++yyd+yykkA ++r++++++fek+fe++D+i++p+ pt+af +g+ ++dpl+myl D+
  lcl|NCBI__GCF_000429985.1:WP_027180517.1 359 RIIIGTYVLSAGYYDAYYKKAAQIRRILRQDFEKAFESCDLILGPACPTTAFPVGDFTSDPLQMYLMDI 427
                                               ********************************************************************* PP

                                 TIGR00132 414 ltvpanlaGlpaisvPlgkke.kglpiGlqiigkafddkkllsvakaleqa 463
                                               +t+ +nlaGlp++s+P+g  + +g+p+Glqi++ afd++++l++a+ le++
  lcl|NCBI__GCF_000429985.1:WP_027180517.1 428 FTISLNLAGLPGMSLPVGLGKeSGMPVGLQIMAPAFDESTMLQAANILEKN 478
                                               *****************985538**********************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (487 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.08
//
[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