Alignments for a candidate for gatB in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfatibacillum aliphaticivorans DSM 15576

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_028314291.1 G491_RS0108460 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000429905.1:WP_028314291.1
          Length = 476

 Score =  494 bits (1273), Expect = e-144
 Identities = 249/476 (52%), Positives = 332/476 (69%), Gaps = 2/476 (0%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M FE VIGLEVH +LKT+SK+F      FGA PN++T  + L  PG LPV+NKR VD+AM
Sbjct: 1   MEFEAVIGLEVHAQLKTESKIFCGCSTAFGASPNTHTCPVCLGMPGSLPVLNKRVVDYAM 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITR 120
           R A+A    I+  S+F RKNYFYPD PK YQISQ++ PI E+G++ ++ D   K+IGITR
Sbjct: 61  RMALATQCSISPYSRFARKNYFYPDLPKGYQISQYELPIAEHGHLMVDTDQGRKKIGITR 120

Query: 121 LHMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTG 178
           +HMEEDAGK TH      S VDLNR GTPLIEIVSEPD+RSP EA AYL++L +I++Y  
Sbjct: 121 IHMEEDAGKLTHDSHRPVSRVDLNRTGTPLIEIVSEPDMRSPWEASAYLKQLHAILRYLD 180

Query: 179 VSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSG 238
           + D  MEEGS RCDAN+S+RP GQE+FGT+AE+KN+NSF  V + + YE  RQ   +  G
Sbjct: 181 ICDGNMEEGSFRCDANVSVRPRGQEEFGTRAEIKNMNSFRNVERAIAYEIDRQSTLVEEG 240

Query: 239 GEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDE 298
           GE+ QETR +D    +T  MR KE + DYRYFP+PD+VPL ID+AW E+VR  +PELP+E
Sbjct: 241 GEVIQETRLWDAEKNRTFSMRGKEEAHDYRYFPDPDLVPLVIDEAWIEQVRGLLPELPEE 300

Query: 299 RKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVE 358
           RKA+++ + GL   DA  LT  +EM+D++E+ +E   D K   NW+ G +   LN   + 
Sbjct: 301 RKARFLEQYGLAQDDAVFLTSAREMADYYEACVEIFNDPKQVCNWVTGALAALLNAKGIS 360

Query: 359 LLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATL 418
           + ++ ++ + LA ++KLI+DG +S KIAK VF  +     + + I+++ GLVQ+SD   +
Sbjct: 361 VTESPISAQRLAALLKLIKDGVISGKIAKTVFECMETDERDPEAIVKEKGLVQVSDSGEI 420

Query: 419 LKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQELDK 474
              V E LD   +  E Y+ GK K MGF VGQIMK +KG+ANPQ VNQLLK++LDK
Sbjct: 421 ESMVQEVLDACPEEAEAYRGGKKKLMGFFVGQIMKKTKGKANPQTVNQLLKEKLDK 476


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: 631
Number of extensions: 23
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: 475
Length of database: 476
Length adjustment: 33
Effective length of query: 442
Effective length of database: 443
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_028314291.1 G491_RS0108460 (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.16870.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-194  630.7   0.0   7.7e-194  630.6   0.0    1.0  1  lcl|NCBI__GCF_000429905.1:WP_028314291.1  G491_RS0108460 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429905.1:WP_028314291.1  G491_RS0108460 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 !  630.6   0.0  7.7e-194  7.7e-194       2     480 ..       1     474 [.       1     475 [. 0.99

  Alignments for each domain:
  == domain 1  score: 630.6 bits;  conditional E-value: 7.7e-194
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +e+e+viGlEvH ql t+sK+Fc cs+ +   +pNt++cpvclg+PG+lPvlNk++v  A+ +ala+++
  lcl|NCBI__GCF_000429905.1:WP_028314291.1   1 MEFEAVIGLEVHAQLKTESKIFCGCSTAFGA-SPNTHTCPVCLGMPGSLPVLNKRVVDYAMRMALATQC 68 
                                               689**************************99.9************************************ PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesd 139
                                                 +s++s F+RK+YfYpDlPkgyqi+q++lPiae+G+l ++++++ k+igi+r+h+EeD+gk+++ ++ 
  lcl|NCBI__GCF_000429905.1:WP_028314291.1  69 S-ISPYSRFARKNYFYPDLPKGYQISQYELPIAEHGHLMVDTDQGRKKIGITRIHMEEDAGKLTHDSHR 136
                                               *.779************************************************************9664 PP

                                 TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208
                                                   s vD+NR+g+PL+EiV++Pd++s+ ea a+lk+l++ilryl+i dg++eeGs+R+D+Nvs+r++G
  lcl|NCBI__GCF_000429905.1:WP_028314291.1 137 --PVSRVDLNRTGTPLIEIVSEPDMRSPWEASAYLKQLHAILRYLDICDGNMEEGSFRCDANVSVRPRG 203
                                               ..79***************************************************************** PP

                                 TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277
                                               qe++gtr+EiKN+ns++++e+ai yEi Rq+ l+++g ev qetr +d +k++t s+R Kee++DYRYf
  lcl|NCBI__GCF_000429905.1:WP_028314291.1 204 QEEFGTRAEIKNMNSFRNVERAIAYEIDRQSTLVEEGGEVIQETRLWDAEKNRTFSMRGKEEAHDYRYF 272
                                               ********************************************************************* PP

                                 TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346
                                               p+Pdl+p++ide ++++ v++ lpelPe++++r+ ++ygl ++da  l+s +e++d++e  v+  ++pk
  lcl|NCBI__GCF_000429905.1:WP_028314291.1 273 PDPDLVPLVIDEAWIEQ-VRGLLPELPEERKARFLEQYGLAQDDAVFLTSAREMADYYEACVEIFNDPK 340
                                               *****************.*************************************************** PP

                                 TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415
                                               ++ nW++  l++ Ln+k is++e+ ++++ la+l+klik+g+is+k+ak+++e + ++++dp+++++++
  lcl|NCBI__GCF_000429905.1:WP_028314291.1 341 QVCNWVTGALAALLNAKGISVTESPISAQRLAALLKLIKDGVISGKIAKTVFECMETDERDPEAIVKEK 409
                                               ********************************************************************* PP

                                 TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               gl+q+sd  e+ ++v+ev++  p+e e y+ gk+k+++f+vGq+mkktkg+a+p++v++llke+l
  lcl|NCBI__GCF_000429905.1:WP_028314291.1 410 GLVQVSDSGEIESMVQEVLDACPEEAEAYRGGKKKLMGFFVGQIMKKTKGKANPQTVNQLLKEKL 474
                                               ***************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (476 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: 7.75
//
[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