Alignments for a candidate for gatB in Hydrogenovibrio halophilus DSM 15072

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Hydrogenovibrio halophilus DSM 15072

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_019894379.1 A377_RS0101710 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000384235.1:WP_019894379.1
          Length = 478

 Score =  439 bits (1129), Expect = e-127
 Identities = 223/473 (47%), Positives = 322/473 (68%), Gaps = 4/473 (0%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E VIGLE+H +L T +K+FS SP  +GAEPNS  N++DL  PG LPV+NK  +  A+R 
Sbjct: 4   WEVVIGLEIHAQLTTHTKIFSGSPIAYGAEPNSQANLLDLGMPGQLPVLNKAVIPKAIRF 63

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENG-YIDIEVDGETKRIGITRL 121
            +A+   I   S FDRKNYFYPD PK YQ SQF  PI E+G  +DIEVDG+T+RIGITR 
Sbjct: 64  GLAVGANIGRRSVFDRKNYFYPDLPKGYQTSQFTYPIVEDGGSLDIEVDGQTRRIGITRA 123

Query: 122 HMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           H+EEDAGKS H     +  VDLNR GTPL+EIVSEPD+RS +EA AY  K+  ++Q+  +
Sbjct: 124 HLEEDAGKSIHDAFPGMTGVDLNRAGTPLLEIVSEPDMRSAQEAVAYARKMHELVQFLDI 183

Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGG 239
            D  M+EGS R D+N+S+   G   FGT+AELKN+NSF ++ + +E+E +RQ E + SGG
Sbjct: 184 CDGNMQEGSFRVDSNVSIHKPGTP-FGTRAELKNINSFRFIEQAIEFEIERQIEIVESGG 242

Query: 240 EIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDER 299
           E+ QETR +D    +T  MR KE ++DYRYFP PD++P+ I+    ++  + +PELPD +
Sbjct: 243 EVIQETRLYDPERNETRSMREKEEANDYRYFPCPDLLPVVIEQTDIDQEARAMPELPDAK 302

Query: 300 KAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVEL 359
           + +Y    GL   DA +LT ++ M+D+FE+ ++   + K  +NW+MG +++ LN++ + +
Sbjct: 303 RVRYQENWGLSQEDAQMLTASRAMADYFETLVDLTGEAKKAANWVMGDLSKALNQDGLTI 362

Query: 360 LDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLL 419
             + ++ + LAG++  ++DGT+S K+AK+VF  + A  G+A  ++E  GL QI+DE  + 
Sbjct: 363 DRSPVSAKMLAGLMARVDDGTISGKMAKQVFAAMWAGEGHADDVIEAKGLKQITDEGAIG 422

Query: 420 KFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
           + V+  L  +   V  Y+ G+ K +GF VGQ+MKASKGQANP  VN +LK  L
Sbjct: 423 EMVDRVLAEHPDQVAAYQAGQEKMLGFFVGQVMKASKGQANPAQVNAVLKARL 475


Lambda     K      H
   0.313    0.133    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: 605
Number of extensions: 18
Number of successful extensions: 4
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: 475
Length of database: 478
Length adjustment: 33
Effective length of query: 442
Effective length of database: 445
Effective search space:   196690
Effective search space used:   196690
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_019894379.1 A377_RS0101710 (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.22792.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-171  556.5   0.0   2.5e-171  556.3   0.0    1.0  1  lcl|NCBI__GCF_000384235.1:WP_019894379.1  A377_RS0101710 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384235.1:WP_019894379.1  A377_RS0101710 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 !  556.3   0.0  2.5e-171  2.5e-171       1     480 [.       1     475 [.       1     476 [. 0.98

  Alignments for each domain:
  == domain 1  score: 556.3 bits;  conditional E-value: 2.5e-171
                                 TIGR00133   1 kieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalaln 69 
                                               ++++e+viGlE+H ql t++K+F+ ++  +   +pN++ + ++lg+PG lPvlNk ++ kA+  +la++
  lcl|NCBI__GCF_000384235.1:WP_019894379.1   1 MQDWEVVIGLEIHAQLTTHTKIFSGSPIAYGA-EPNSQANLLDLGMPGQLPVLNKAVIPKAIRFGLAVG 68 
                                               5789**************************99.************************************ PP

                                 TIGR00133  70 skivsevsvFdRKhYfYpDlPkgyqitqqdlPiaed.GkleieleekekeigierlhlEeDtgksqyke 137
                                               ++i    svFdRK+YfYpDlPkgyq +q+ +Pi+ed G+l+ie++++ ++igi+r hlEeD+gks +  
  lcl|NCBI__GCF_000384235.1:WP_019894379.1  69 ANIG-RRSVFDRKNYFYPDLPKGYQTSQFTYPIVEDgGSLDIEVDGQTRRIGITRAHLEEDAGKSIHDA 136
                                               **66.69***************************97369****************************95 PP

                                 TIGR00133 138 sdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirl 206
                                                  + ++ vD+NR+g+PLlEiV++Pd++sa+ea+a+ +k+++++++l+i dg+++eGs+RvD Nvsi+ 
  lcl|NCBI__GCF_000384235.1:WP_019894379.1 137 F--PGMTGVDLNRAGTPLLEIVSEPDMRSAQEAVAYARKMHELVQFLDICDGNMQEGSFRVDSNVSIH- 202
                                               5..79***************************************************************. PP

                                 TIGR00133 207 kGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYR 275
                                               k  + +gtr+E+KN+ns++ ie+aie+EieRq++++++g ev qetr +d +++ t s+R+Kee++DYR
  lcl|NCBI__GCF_000384235.1:WP_019894379.1 203 KPGTPFGTRAELKNINSFRFIEQAIEFEIERQIEIVESGGEVIQETRLYDPERNETRSMREKEEANDYR 271
                                               66789**************************************************************** PP

                                 TIGR00133 276 YfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklike 344
                                               Yfp Pdl p++i+++ +++  +  +pelP+akr r++++ gls+eda++l++ + ++d+fe++v l++e
  lcl|NCBI__GCF_000384235.1:WP_019894379.1 272 YFPCPDLLPVVIEQTDIDQ-EARAMPELPDAKRVRYQENWGLSQEDAQMLTASRAMADYFETLVDLTGE 339
                                               ******************9.999********************************************** PP

                                 TIGR00133 345 pklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklie 413
                                               +k+a+nW++ +l + Ln+  +++  + +++++la l++ +++g+is+k+ak+++  +   +++++ +ie
  lcl|NCBI__GCF_000384235.1:WP_019894379.1 340 AKKAANWVMGDLSKALNQDGLTIDRSPVSAKMLAGLMARVDDGTISGKMAKQVFAAMWAGEGHADDVIE 408
                                               ********************************************************************* PP

                                 TIGR00133 414 klgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               ++gl qi+de ++ ++v+ v++e+p++v  y++g+ek+l+f+vGqvmk +kg+a+p++v+++lk +l
  lcl|NCBI__GCF_000384235.1:WP_019894379.1 409 AKGLKQITDEGAIGEMVDRVLAEHPDQVAAYQAGQEKMLGFFVGQVMKASKGQANPAQVNAVLKARL 475
                                               ***************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (478 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: 00:00:00.03
# Mc/sec: 7.66
//
[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