Alignments for a candidate for gatB in Sulfuricurvum kujiense DSM 16994

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Sulfuricurvum kujiense DSM 16994

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_013459685.1 SULKU_RS04185 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= metacyc::MONOMER-13956
         (476 letters)



>NCBI__GCF_000183725.1:WP_013459685.1
          Length = 475

 Score =  414 bits (1064), Expect = e-120
 Identities = 220/471 (46%), Positives = 307/471 (65%), Gaps = 7/471 (1%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           FET+IGLEVHV+L T+SK+F S PT F  E NT T    L  PG LPVLNKEA+  A   
Sbjct: 2   FETIIGLEVHVQLNTQSKLFCSCPTSFNHEQNTNTCPTCLALPGALPVLNKEALRKAGMF 61

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-GGKTKRIGITRL 121
             A+   I   + FDRK+YFYPD+P AYQI+Q   PI E+G + I+   G  K I I R 
Sbjct: 62  GTAVGATINRTSFFDRKSYFYPDSPSAYQITQLYTPIVEHGNLTIDFEDGSHKTIRINRA 121

Query: 122 HLEEDAGKLTHTGDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGVS 181
           H+E DAGK  H G   S VD NR GTPL+EIVSEPD+R+PE+A  YL+KL SI++Y  +S
Sbjct: 122 HIEADAGKNIHEGS-ISKVDLNRAGTPLLEIVSEPDMRSPEDAILYLKKLHSIVRYIDIS 180

Query: 182 DCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGFF 241
           D  M+EGS R D N+S+RP G E+  T+ E+KN+NSF F+Q+ +E E  RQ++    G +
Sbjct: 181 DANMQEGSFRVDVNVSIRPKGDEKLYTRVEIKNINSFRFIQRAIELEVARQKEAWEDGTY 240

Query: 242 ---IQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPD 298
              I QETR +D+  ++T  MR KE + DYRYFPEPDL+++ +DD   E++  +IPELPD
Sbjct: 241 ESEIVQETRLFDQVKQETRSMRGKEEAADYRYFPEPDLLKVIVDDAMYEQI-CTIPELPD 299

Query: 299 ERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQK 358
            +++R+++E G + Y A ++T   E A +FE  +++G  AK A  WL+ E+   L+    
Sbjct: 300 AKKERFVKEFGISEYHASLITADLENAHYFEAMLEQGITAKNAVTWLIVELQGRLSGGVT 359

Query: 359 ELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGV 418
             +  +++   L  ++K IE+  IS K AK+V   L+E GGD + ++++ GL Q+SD G 
Sbjct: 360 P-STSSISAVMLGTLVKRIEESVISGKAAKEVLDYLLENGGDIDDVIEKLGLKQVSDTGA 418

Query: 419 LLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKIL 469
           L  L+ E L +N   + ++K+GKD+  GF VGQ MKASKG ANP  +N+IL
Sbjct: 419 LEALIDEILSSNADKVAEYKSGKDKLFGFFVGQAMKASKGSANPNTLNEIL 469


Lambda     K      H
   0.314    0.134    0.373 

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: 21
Number of successful extensions: 6
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: 476
Length of database: 475
Length adjustment: 33
Effective length of query: 443
Effective length of database: 442
Effective search space:   195806
Effective search space used:   195806
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate WP_013459685.1 SULKU_RS04185 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.13476.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-181  590.4   0.0   1.3e-181  590.2   0.0    1.0  1  lcl|NCBI__GCF_000183725.1:WP_013459685.1  SULKU_RS04185 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183725.1:WP_013459685.1  SULKU_RS04185 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.2   0.0  1.3e-181  1.3e-181       4     480 ..       2     473 ..       1     474 [. 0.98

  Alignments for each domain:
  == domain 1  score: 590.2 bits;  conditional E-value: 1.3e-181
                                 TIGR00133   4 yelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnski 72 
                                               +e +iGlEvHvqlnt+sKlFc+c++++++ ++Ntn+cp cl+lPGalPvlNkea++kA + ++a+++ i
  lcl|NCBI__GCF_000183725.1:WP_013459685.1   2 FETIIGLEVHVQLNTQSKLFCSCPTSFNH-EQNTNTCPTCLALPGALPVLNKEALRKAGMFGTAVGATI 69 
                                               899************************99.9*************************************7 PP

                                 TIGR00133  73 vsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdk 140
                                               +  +s FdRK YfYpD P++yqitq ++Pi+e+G+l+i++e+++ k+i+i+r h+E D+gk+ +++s  
  lcl|NCBI__GCF_000183725.1:WP_013459685.1  70 N-RTSFFDRKSYFYPDSPSAYQITQLYTPIVEHGNLTIDFEDGShKTIRINRAHIEADAGKNIHEGS-- 135
                                               6.5************************************998766********************76.. PP

                                 TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209
                                                 +s vD+NR+g+PLlEiV++Pd++s+++a  +lkkl++i+ry++isd++++eGs+RvDvNvsir+kG+
  lcl|NCBI__GCF_000183725.1:WP_013459685.1 136 --ISKVDLNRAGTPLLEIVSEPDMRSPEDAILYLKKLHSIVRYIDISDANMQEGSFRVDVNVSIRPKGD 202
                                               ..79***************************************************************** PP

                                 TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkg...eevkqetrafdekksitvslRkKeeseDYR 275
                                               ek +trvEiKN+ns++ i++aie+E++Rqk+++++g   +e++qetr fd+ k+ t s+R Kee++DYR
  lcl|NCBI__GCF_000183725.1:WP_013459685.1 203 EKLYTRVEIKNINSFRFIQRAIELEVARQKEAWEDGtyeSEIVQETRLFDQVKQETRSMRGKEEAADYR 271
                                               ************************************99999**************************** PP

                                 TIGR00133 276 YfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklike 344
                                               YfpePdl ++ +d+ + ++    ++pelP+ak++r++ke+g+se+ a ++++dle +++fe + +   +
  lcl|NCBI__GCF_000183725.1:WP_013459685.1 272 YFPEPDLLKVIVDDAMYEQ--ICTIPELPDAKKERFVKEFGISEYHASLITADLENAHYFEAMLEQGIT 338
                                               **************99888..899********************************************* PP

                                 TIGR00133 345 pklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklie 413
                                               +k+av+W++ el+g+L    ++ + + +++ +l +l+k i+e +is+k+ake+l+ llen++d++ +ie
  lcl|NCBI__GCF_000183725.1:WP_013459685.1 339 AKNAVTWLIVELQGRLSGG-VTPSTSSISAVMLGTLVKRIEESVISGKAAKEVLDYLLENGGDIDDVIE 406
                                               ****************987.7778889999*************************************** PP

                                 TIGR00133 414 klgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               klgl q+sd+ +l ++++e+++ n+++v +yksgk+k+++f+vGq+mk +kg a+p++ +++l+ +l
  lcl|NCBI__GCF_000183725.1:WP_013459685.1 407 KLGLKQVSDTGALEALIDEILSSNADKVAEYKSGKDKLFGFFVGQAMKASKGSANPNTLNEILQAKL 473
                                               ***************************************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (475 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: 7.77
//
[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