Alignments for a candidate for gatA in Sulfurivirga caldicuralii DSM 17737

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Sulfurivirga caldicuralii DSM 17737

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_074200974.1 BUQ81_RS03260 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_900141795.1:WP_074200974.1
          Length = 483

 Score =  501 bits (1291), Expect = e-146
 Identities = 247/478 (51%), Positives = 338/478 (70%), Gaps = 1/478 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           + EL   +H++EI   +L      RI+ +D ++ +F+ +  + A   AK  D A+     
Sbjct: 6   LRELSDKLHRREISSVELTQYFLGRIEKLDPELNSFITVTPDVALEMAKMADAAI-AEGS 64

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L G+PI  KD   T G+RT+C+S++L+NF   YDA VV++L+ A    +GK NMDEF
Sbjct: 65  AGSLTGIPIAHKDLFTTDGIRTSCASRMLDNFIAPYDAHVVEKLKQAGMPILGKTNMDEF 124

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSS+E S Y   +NPW+ D VPGGSSGGSAAAVAAG  P + GSDTGGSIRQPASFCG
Sbjct: 125 AMGSSSETSYYGPVRNPWDRDAVPGGSSGGSAAAVAAGLTPAATGSDTGGSIRQPASFCG 184

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           + G+KPTYG VSRYG++A+ASS DQ GP+ R+ ED A+LL A++G DK DSTS   ++PD
Sbjct: 185 ITGIKPTYGLVSRYGMIAYASSFDQGGPMARSAEDAAWLLNAMAGFDKRDSTSLERELPD 244

Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307
           +   L   ++GL+I +PKEY  EG+  E  + + AA+  LE LGAT  EVSLP+   A+ 
Sbjct: 245 YTVHLNDSLEGLRIGLPKEYFSEGLDDEVAQVIEAAITELEKLGATVVEVSLPNKDLAVP 304

Query: 308 TYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALS 367
            YY+L+ +EAS+NLAR+DG+RYG+R ++  +L D+Y ++RAEGFG+EVKRRIM+G +ALS
Sbjct: 305 AYYVLAPAEASSNLARYDGVRYGHRCEDPKDLKDMYTRSRAEGFGDEVKRRIMIGAYALS 364

Query: 368 SGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDIL 427
           +GYYDAYY KAQ++R +++ DF   FE+ DVI GP  PT A+ +GE + DP++MY  D+ 
Sbjct: 365 AGYYDAYYLKAQQLRRMVRDDFVRAFEQCDVIAGPVAPTVAWNLGEKSDDPVSMYLADLY 424

Query: 428 TIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPEL 485
           TIPVNLAG+PG+SVP G A G P+GL ++G +F E+ +  + H F+Q TD H   PEL
Sbjct: 425 TIPVNLAGLPGMSVPAGFAKGRPVGLHLVGPYFSEAKLLNIGHQFQQHTDWHTRTPEL 482


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: 591
Number of extensions: 16
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: 483
Length adjustment: 34
Effective length of query: 451
Effective length of database: 449
Effective search space:   202499
Effective search space used:   202499
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_074200974.1 BUQ81_RS03260 (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.178494.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.8e-195  633.9   0.0   8.9e-195  633.7   0.0    1.0  1  NCBI__GCF_900141795.1:WP_074200974.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900141795.1:WP_074200974.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  633.7   0.0  8.9e-195  8.9e-195       3     465 ..      11     474 ..       9     475 .. 0.99

  Alignments for each domain:
  == domain 1  score: 633.7 bits;  conditional E-value: 8.9e-195
                             TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkd 73 
                                           ++l+++e+s++e+++ +l rie+ + ++n+f++vt++ al++ak  d+++a  +   l+gipia Kd +++ +
  NCBI__GCF_900141795.1:WP_074200974.1  11 DKLHRREISSVELTQYFLGRIEKLDPELNSFITVTPDVALEMAKMADAAIAeGSaGSLTGIPIAHKDLFTTDG 83 
                                           68999*********************************************953335***************** PP

                             TIGR00132  74 iettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsa 146
                                           i+t+caS++L+n+++pyda+Vve+lk+ag+ i+GktN+DEFamGss+etS++g+++nP++++ vpGGSsgGsa
  NCBI__GCF_900141795.1:WP_074200974.1  84 IRTSCASRMLDNFIAPYDAHVVEKLKQAGMPILGKTNMDEFAMGSSSETSYYGPVRNPWDRDAVPGGSSGGSA 156
                                           ************************************************************************* PP

                             TIGR00132 147 aavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisg 219
                                           aavaa+l p a gsDTGgSiRqPAsfcg+ G+KPtYGlvSRyG++ayasS+dq G++a++ ed+a +l++++g
  NCBI__GCF_900141795.1:WP_074200974.1 157 AAVAAGLTPAATGSDTGGSIRQPASFCGITGIKPTYGLVSRYGMIAYASSFDQGGPMARSAEDAAWLLNAMAG 229
                                           ************************************************************************* PP

                             TIGR00132 220 kDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvkla 292
                                            Dk+Dstsle + ++++ +l++ l gl++g+ ke++ e+ld+ev++ +e+++ +le+lga++vevslp+ +la
  NCBI__GCF_900141795.1:WP_074200974.1 230 FDKRDSTSLERELPDYTVHLNDSLEGLRIGLPKEYFSEGLDDEVAQVIEAAITELEKLGATVVEVSLPNKDLA 302
                                           ************************************************************************* PP

                             TIGR00132 293 laiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkA 365
                                           +++Yy+++p+Eassnlarydg+ryG+r e++k+lk++y+++R+egfg+evkrRim+Gayals++yyd+yy+kA
  NCBI__GCF_900141795.1:WP_074200974.1 303 VPAYYVLAPAEASSNLARYDGVRYGHRCEDPKDLKDMYTRSRAEGFGDEVKRRIMIGAYALSAGYYDAYYLKA 375
                                           ************************************************************************* PP

                             TIGR00132 366 qkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglp 438
                                           q++r++++d+f  +fe++Dvi++p+apt+a +lgek +dp++myl+D++t+p+nlaGlp++svP+g + kg p
  NCBI__GCF_900141795.1:WP_074200974.1 376 QQLRRMVRDDFVRAFEQCDVIAGPVAPTVAWNLGEKSDDPVSMYLADLYTIPVNLAGLPGMSVPAGFA-KGRP 447
                                           ********************************************************************.8*** PP

                             TIGR00132 439 iGlqiigkafddkkllsvakaleqald 465
                                           +Gl ++g +f++ kll+++++++q++d
  NCBI__GCF_900141795.1:WP_074200974.1 448 VGLHLVGPYFSEAKLLNIGHQFQQHTD 474
                                           ***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (483 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: 31.92
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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