Alignments for a candidate for gatB in Hydrogenovibrio marinus DSM 11271

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Hydrogenovibrio marinus DSM 11271

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_029912908.1 P166_RS0111585 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000711315.1:WP_029912908.1
          Length = 475

 Score =  462 bits (1188), Expect = e-134
 Identities = 230/475 (48%), Positives = 330/475 (69%), Gaps = 4/475 (0%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +E VIGLE+H +L T++K+FS S   +GAEPN+  N++DL  PG LPV+NK  +  A+
Sbjct: 1   MTWEVVIGLEIHAQLNTNTKIFSGSSIAYGAEPNTQANLLDLGMPGQLPVLNKAVLPKAI 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPI-GENGYIDIEVDGETKRIGIT 119
           R  +A+   I   S FDRKNYFYPD PK YQ SQF  PI  + G ++IEVDGETK+IGIT
Sbjct: 61  RFGLAVGATIGRRSVFDRKNYFYPDLPKGYQTSQFSYPIVDKGGVLEIEVDGETKKIGIT 120

Query: 120 RLHMEEDAGKSTHKG--EYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYT 177
           R H+EEDAGKS H      + +DLNR GTPL+EIVSEPD+RS +EA AY  K+  ++QY 
Sbjct: 121 RAHLEEDAGKSVHDAFPGQTGIDLNRAGTPLLEIVSEPDMRSAQEAVAYARKMHELVQYL 180

Query: 178 GVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLS 237
           G+ D  M+EGS R D+N+S+   G   FGT+AELKN+NSF ++ + +EYE  RQ E L S
Sbjct: 181 GICDGNMQEGSFRVDSNVSIHKPGTP-FGTRAELKNINSFKFIEQAIEYEIARQIEILES 239

Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297
           GG++ QETR +D    +T  MR KE ++DYRYFP PD++P+ + D   E +R  +PELP 
Sbjct: 240 GGKVVQETRLYDSEKNETRSMRAKEEANDYRYFPCPDLLPVVVTDEDIEAIRAEMPELPG 299

Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQV 357
            ++A+YV+E GL  YDA  LT ++ M+++FE+ + H  D K+++NW+MG +++ LN+  +
Sbjct: 300 AKRARYVSEFGLSDYDASFLTGSRAMAEYFEAVVSHSKDAKMSANWVMGELSKSLNQQGI 359

Query: 358 ELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEAT 417
           ++ ++ ++ E LAG++  I+D T+S KIAK+VF  +  + G+A +I+   GL QI+D + 
Sbjct: 360 DINESPVSAEALAGLLARIQDNTISGKIAKQVFDAMWNQEGSADEIITAKGLKQITDSSA 419

Query: 418 LLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
           +   V+E L  N   VE Y+NG+ K  G+ VGQ+MK S+GQANP  VN++LK++L
Sbjct: 420 IEALVDEVLAANTAQVEAYRNGQDKMFGYFVGQVMKVSQGQANPGQVNEILKRKL 474


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: 636
Number of extensions: 27
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: 475
Length adjustment: 33
Effective length of query: 442
Effective length of database: 442
Effective search space:   195364
Effective search space used:   195364
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_029912908.1 P166_RS0111585 (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.8884.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-175  569.1   0.0   3.9e-175  568.9   0.0    1.0  1  lcl|NCBI__GCF_000711315.1:WP_029912908.1  P166_RS0111585 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000711315.1:WP_029912908.1  P166_RS0111585 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 !  568.9   0.0  3.9e-175  3.9e-175       3     480 ..       2     474 ..       1     475 [] 0.98

  Alignments for each domain:
  == domain 1  score: 568.9 bits;  conditional E-value: 3.9e-175
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                                +e+viGlE+H qlnt++K+F+ +s  +   +pNt+ + ++lg+PG lPvlNk ++ kA+  +la+++ 
  lcl|NCBI__GCF_000711315.1:WP_029912908.1   2 TWEVVIGLEIHAQLNTNTKIFSGSSIAYGA-EPNTQANLLDLGMPGQLPVLNKAVLPKAIRFGLAVGAT 69 
                                               689*************************99.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPia.edGkleieleekekeigierlhlEeDtgksqykesd 139
                                               i    svFdRK+YfYpDlPkgyq +q+ +Pi+ ++G+leie++++ k+igi+r hlEeD+gks++    
  lcl|NCBI__GCF_000711315.1:WP_029912908.1  70 IG-RRSVFDRKNYFYPDLPKGYQTSQFSYPIVdKGGVLEIEVDGETKKIGITRAHLEEDAGKSVHDAF- 136
                                               65.69**************************9346789***************************955. PP

                                 TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208
                                                + q+ +D+NR+g+PLlEiV++Pd++sa+ea+a+ +k++++++yl+i dg+++eGs+RvD Nvsi+ k 
  lcl|NCBI__GCF_000711315.1:WP_029912908.1 137 -PGQTGIDLNRAGTPLLEIVSEPDMRSAQEAVAYARKMHELVQYLGICDGNMQEGSFRVDSNVSIH-KP 203
                                               .79***************************************************************.66 PP

                                 TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277
                                                + +gtr+E+KN+ns+k ie+aieyEi+Rq+++l++g +v+qetr +d +k+ t s+R Kee++DYRYf
  lcl|NCBI__GCF_000711315.1:WP_029912908.1 204 GTPFGTRAELKNINSFKFIEQAIEYEIARQIEILESGGKVVQETRLYDSEKNETRSMRAKEEANDYRYF 272
                                               789****************************************************************** PP

                                 TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346
                                               p Pdl p+++++e ++  +++++pelP akr+r+++e+gls++da  l+  + ++++fe vv+ +k++k
  lcl|NCBI__GCF_000711315.1:WP_029912908.1 273 PCPDLLPVVVTDEDIEA-IRAEMPELPGAKRARYVSEFGLSDYDASFLTGSRAMAEYFEAVVSHSKDAK 340
                                               ***************99.*************************************************** PP

                                 TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415
                                                ++nW++ el ++Ln++ i+++e+ +++e+la l++ i++++is+k+ak++++ + +++++++++i+++
  lcl|NCBI__GCF_000711315.1:WP_029912908.1 341 MSANWVMGELSKSLNQQGIDINESPVSAEALAGLLARIQDNTISGKIAKQVFDAMWNQEGSADEIITAK 409
                                               ********************************************************************* PP

                                 TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               gl qi+d +++ ++v+ev++ n+ +ve y++g++k+++++vGqvmk ++g+a+p +v+++lk +l
  lcl|NCBI__GCF_000711315.1:WP_029912908.1 410 GLKQITDSSAIEALVDEVLAANTAQVEAYRNGQDKMFGYFVGQVMKVSQGQANPGQVNEILKRKL 474
                                               **************************************************************998 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.05
//
[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