Alignments for a candidate for gatB in Arcobacter nitrofigilis DSM 7299

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Arcobacter nitrofigilis DSM 7299

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_013133930.1 ARNIT_RS00590 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000092245.1:WP_013133930.1
          Length = 472

 Score =  425 bits (1093), Expect = e-123
 Identities = 229/474 (48%), Positives = 299/474 (63%), Gaps = 8/474 (1%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           FE +IGLEVHV+L T+SK+F      FG +PN+N     L  PG LPV+NK AV  A+  
Sbjct: 2   FEVIIGLEVHVQLNTNSKLFCSCATSFGEDPNTNVCPTCLGLPGALPVLNKEAVHKAIML 61

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121
             AL  +I  +S F+RKNYFYPD P  YQISQF+ P+   G + I+  DG  K IG+TR 
Sbjct: 62  GTALKSKINQKSIFNRKNYFYPDLPSGYQISQFEVPVVGLGELVIDFPDGSQKTIGVTRA 121

Query: 122 HMEEDAGKSTHKGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGVSD 181
           H+E DAGK+ H G  S VDLNR GTPL+EIVSEPD+R+ +EA  YL+KL SI++Y G+SD
Sbjct: 122 HLENDAGKNIHAGAVSHVDLNRAGTPLLEIVSEPDMRTAEEAILYLKKLHSIVRYLGISD 181

Query: 182 VKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSG--- 238
             M+EGS RCD N+S+RP G     T+ E+KN+NSF ++ K + YE  R  E    G   
Sbjct: 182 ANMQEGSFRCDVNVSIRPKGDTNLYTRCEIKNMNSFKFIEKAIAYEVNRHIEAWEDGIHS 241

Query: 239 GEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDE 298
            EI QETR FD   G+T  MR KE + DYRYFP+PD+ P+ I D   E+  Q IPELPDE
Sbjct: 242 TEIVQETRLFDPEKGETRSMRGKEDAADYRYFPDPDLRPVIITDEMLEKYSQ-IPELPDE 300

Query: 299 RKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVE 358
           +KA++V + G+  YDA V+T   EM++FFE  +  G   K    WL   +   L  +   
Sbjct: 301 KKARFVKDYGIKDYDASVITSQLEMANFFEEMLAEGISGKNAVTWLTVELQGRLTDS--- 357

Query: 359 LLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATL 418
           L  + +  + LA ++K IED T+S K AK+V   L     +   ++E  GL Q+SD+  L
Sbjct: 358 LATSPVDAKKLATIVKKIEDNTISGKAAKEVLDYLMENDASVDSVIEKLGLKQVSDDGAL 417

Query: 419 LKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
           L  ++E L NN+  VE+YK GK K   F VGQ MKASKG ANPQ V++LLKQ L
Sbjct: 418 LTMIDEILANNQDKVEEYKAGKEKMFAFFVGQTMKASKGTANPQKVSELLKQRL 471


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: 623
Number of extensions: 26
Number of successful extensions: 5
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: 472
Length adjustment: 33
Effective length of query: 442
Effective length of database: 439
Effective search space:   194038
Effective search space used:   194038
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_013133930.1 ARNIT_RS00590 (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.6596.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-187  609.7   0.1   1.8e-187  609.6   0.1    1.0  1  lcl|NCBI__GCF_000092245.1:WP_013133930.1  ARNIT_RS00590 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092245.1:WP_013133930.1  ARNIT_RS00590 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 !  609.6   0.1  1.8e-187  1.8e-187       4     480 ..       2     471 ..       1     472 [] 0.98

  Alignments for each domain:
  == domain 1  score: 609.6 bits;  conditional E-value: 1.8e-187
                                 TIGR00133   4 yelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnski 72 
                                               +e++iGlEvHvqlnt+sKlFc+c +++ e  pNtnvcp clglPGalPvlNkeav+kA++l++al+ski
  lcl|NCBI__GCF_000092245.1:WP_013133930.1   2 FEVIIGLEVHVQLNTNSKLFCSCATSFGE-DPNTNVCPTCLGLPGALPVLNKEAVHKAIMLGTALKSKI 69 
                                               89***************************.9*************************************6 PP

                                 TIGR00133  73 vsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdk 140
                                               + ++s+F+RK+YfYpDlP+gyqi+q+++P++  G+l i++ +++ k+ig++r hlE+D+gk+ +++   
  lcl|NCBI__GCF_000092245.1:WP_013133930.1  70 N-QKSIFNRKNYFYPDLPSGYQISQFEVPVVGLGELVIDFPDGSqKTIGVTRAHLENDAGKNIHAGA-- 135
                                               6.6************************************9876549*******************65.. PP

                                 TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209
                                                  s vD+NR+g+PLlEiV++Pd+++a+ea  +lkkl++i+ryl+isd++++eGs+R+DvNvsir+kG+
  lcl|NCBI__GCF_000092245.1:WP_013133930.1 136 --VSHVDLNRAGTPLLEIVSEPDMRTAEEAILYLKKLHSIVRYLGISDANMQEGSFRCDVNVSIRPKGD 202
                                               ..79***************************************************************** PP

                                 TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkg...eevkqetrafdekksitvslRkKeeseDYR 275
                                               ++ +tr EiKN+ns+k iekai yE++R ++++++g   +e++qetr fd +k  t s+R Ke+++DYR
  lcl|NCBI__GCF_000092245.1:WP_013133930.1 203 TNLYTRCEIKNMNSFKFIEKAIAYEVNRHIEAWEDGihsTEIVQETRLFDPEKGETRSMRGKEDAADYR 271
                                               *************************************999***************************** PP

                                 TIGR00133 276 YfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklike 344
                                               Yfp+Pdl p+ i++e++++    ++pelP++k++r++k+yg++++da v++s+le+++ fee+     +
  lcl|NCBI__GCF_000092245.1:WP_013133930.1 272 YFPDPDLRPVIITDEMLEK--YSQIPELPDEKKARFVKDYGIKDYDASVITSQLEMANFFEEMLAEGIS 338
                                               ***************9988..99********************************************** PP

                                 TIGR00133 345 pklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklie 413
                                                k+av+W++ el+g+L ++   la + +++++la+++k i++++is+k+ake+l+ l+en  +++++ie
  lcl|NCBI__GCF_000092245.1:WP_013133930.1 339 GKNAVTWLTVELQGRLTDS---LATSPVDAKKLATIVKKIEDNTISGKAAKEVLDYLMENDASVDSVIE 404
                                               ****************987...*********************************************** PP

                                 TIGR00133 414 klgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               klgl q+sd+ +l  +++e++++n+++ve+yk+gkek++ f+vGq mk +kg a+p++v +llk++l
  lcl|NCBI__GCF_000092245.1:WP_013133930.1 405 KLGLKQVSDDGALLTMIDEILANNQDKVEEYKAGKEKMFAFFVGQTMKASKGTANPQKVSELLKQRL 471
                                               ****************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (472 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.03
//
[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