Alignments for a candidate for gatA in Thioalkalivibrio denitrificans ALJD

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Thioalkalivibrio denitrificans ALJD

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_077279618.1 B1C78_RS13080 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_002000365.1:WP_077279618.1
          Length = 484

 Score =  486 bits (1250), Expect = e-142
 Identities = 248/481 (51%), Positives = 333/481 (69%), Gaps = 1/481 (0%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           + D  I EL   + + E    +L +    RI+++D  + +F+ +  E+A A A+E D A 
Sbjct: 1   MHDKTIAELSAALARGEFSSVELTEHFLGRIESLDGGLNSFVTITGEQALAAAREAD-AR 59

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
             R E G L G+P+  KD   T G+RTTC SK+L+NF   YDA VV+R + A    +GK 
Sbjct: 60  RARGEAGPLTGVPMAHKDIFCTDGVRTTCGSKMLDNFIAPYDAGVVERFRAAGCPMLGKT 119

Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182
           NMDEFAMGSS E S +   KNPW+   VPGGSSGGSAAAVAA   P + G+DTGGSIRQP
Sbjct: 120 NMDEFAMGSSNETSFHGPVKNPWDTGRVPGGSSGGSAAAVAARLTPSATGTDTGGSIRQP 179

Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242
           AS CGV G+KPTYGRVSR+G++AFASSLDQ GP+  + ED A L   + G D  DSTS  
Sbjct: 180 ASLCGVTGMKPTYGRVSRWGMIAFASSLDQGGPMAASAEDCALLANVMCGFDGRDSTSIE 239

Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHS 302
               DF + L   +KGL+I +P+E+ G+G+      +V  A+     LGA  ++V+LP+S
Sbjct: 240 CADEDFTARLDEPLKGLRIGLPREFFGDGMAPGVAAAVDEAIGEYRKLGAEVKDVTLPNS 299

Query: 303 KYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLG 362
             ++  YY+++ +E S+NLARFDG+RYGYR +N  +L+DLY ++R EGFG EVKRRIM+G
Sbjct: 300 GLSVPAYYVVAPAECSSNLARFDGVRYGYRCENPKDLMDLYTRSRGEGFGAEVKRRIMVG 359

Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMY 422
           T+ALS+GY+DAYY KAQKVR LI +DF   FE  DVI+GPT+PT AF++GE T DP++MY
Sbjct: 360 TYALSAGYFDAYYLKAQKVRRLIAEDFRKAFEDVDVIMGPTSPTTAFRLGEKTDDPVSMY 419

Query: 423 ANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAK 482
            +DI TI VNLAG+PG+S+P G +DGLP+GLQ+IG +F+E+ +  VAH ++  TD H+  
Sbjct: 420 LSDIYTIAVNLAGLPGMSIPAGFSDGLPVGLQLIGNYFEEARLLGVAHQYQLVTDWHQRI 479

Query: 483 P 483
           P
Sbjct: 480 P 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: 622
Number of extensions: 28
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: 484
Length adjustment: 34
Effective length of query: 451
Effective length of database: 450
Effective search space:   202950
Effective search space used:   202950
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_077279618.1 B1C78_RS13080 (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.2311839.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.6e-187  608.0   0.0   6.3e-187  607.9   0.0    1.0  1  NCBI__GCF_002000365.1:WP_077279618.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002000365.1:WP_077279618.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.9   0.0  6.3e-187  6.3e-187       3     461 ..      11     470 ..       9     475 .. 0.98

  Alignments for each domain:
  == domain 1  score: 607.9 bits;  conditional E-value: 6.3e-187
                             TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkd 73 
                                           ++l + e+s++e++e++l rie+ +  +n+f+++t e+al++a++ d++ a  e  +l+g+p+a Kd +++ +
  NCBI__GCF_002000365.1:WP_077279618.1  11 AALARGEFSSVELTEHFLGRIESLDGGLNSFVTITGEQALAAAREADARRArGEaGPLTGVPMAHKDIFCTDG 83 
                                           567788999***************************************99975646***************** PP

                             TIGR00132  74 iettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsa 146
                                           ++ttc+Sk+L+n+++pyda Vver ++ag  ++GktN+DEFamGss etS++g++knP+++ rvpGGSsgGsa
  NCBI__GCF_002000365.1:WP_077279618.1  84 VRTTCGSKMLDNFIAPYDAGVVERFRAAGCPMLGKTNMDEFAMGSSNETSFHGPVKNPWDTGRVPGGSSGGSA 156
                                           ************************************************************************* PP

                             TIGR00132 147 aavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisg 219
                                           aavaa l p a g+DTGgSiRqPAs+cgv G+KPtYG+vSR+G++a+asSldq G++a++ ed al+ +v++g
  NCBI__GCF_002000365.1:WP_077279618.1 157 AAVAARLTPSATGTDTGGSIRQPASLCGVTGMKPTYGRVSRWGMIAFASSLDQGGPMAASAEDCALLANVMCG 229
                                           ************************************************************************* PP

                             TIGR00132 220 kDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvkla 292
                                            D +Dsts+e ++e+++ +l + lkgl++g+ +e++++++  +v++++++++ + ++lgae+++v lp++ l+
  NCBI__GCF_002000365.1:WP_077279618.1 230 FDGRDSTSIECADEDFTARLDEPLKGLRIGLPREFFGDGMAPGVAAAVDEAIGEYRKLGAEVKDVTLPNSGLS 302
                                           ************************************************************************* PP

                             TIGR00132 293 laiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkA 365
                                           +++Yy+++p+E ssnlar+dg+ryG+r e++k+l++ly+++R egfg+evkrRim+G+yals++y+d+yy+kA
  NCBI__GCF_002000365.1:WP_077279618.1 303 VPAYYVVAPAECSSNLARFDGVRYGYRCENPKDLMDLYTRSRGEGFGAEVKRRIMVGTYALSAGYFDAYYLKA 375
                                           ************************************************************************* PP

                             TIGR00132 366 qkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglp 438
                                           qkvr+li+++f+k+fe+vDvi++pt+pt+af+lgek++dp++mylsD++t+ +nlaGlp++s+P+g + +glp
  NCBI__GCF_002000365.1:WP_077279618.1 376 QKVRRLIAEDFRKAFEDVDVIMGPTSPTTAFRLGEKTDDPVSMYLSDIYTIAVNLAGLPGMSIPAGFS-DGLP 447
                                           ********************************************************************.8*** PP

                             TIGR00132 439 iGlqiigkafddkkllsvakale 461
                                           +Glq+ig++f++ +ll va++++
  NCBI__GCF_002000365.1:WP_077279618.1 448 VGLQLIGNYFEEARLLGVAHQYQ 470
                                           *******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (484 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 21.92
//
[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