Alignments for a candidate for gatB in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfovibrio vulgaris Hildenborough

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate 207351 DVU1885 glutamyl-tRNA(Gln) amidotransferase, B subunit

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



>MicrobesOnline__882:207351
          Length = 476

 Score =  460 bits (1183), Expect = e-134
 Identities = 228/473 (48%), Positives = 321/473 (67%), Gaps = 1/473 (0%)

Query: 2   NFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMK 61
           ++E VIGLEVH +L+T+SK+F S  T FGA+ N     +  G PGVLPVLN++AVEFA +
Sbjct: 3   SYEAVIGLEVHAQLRTRSKLFCSCSTAFGADPNAHVCEVCAGMPGVLPVLNEKAVEFAAR 62

Query: 62  AAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRL 121
             +A+ C +   + F RKNYFYPD PK YQISQ+++PI E+G ++I VG   KRIGITR+
Sbjct: 63  MGIAVGCTVNRTSVFARKNYFYPDLPKGYQISQYEQPICEHGHLDISVGDAVKRIGITRI 122

Query: 122 HLEEDAGKLTHT-GDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGV 180
           HLE+DAGK  H+ G+  S VD NR G PL+EIVSEPD+R+ EEA AYL+ L++I+ + G+
Sbjct: 123 HLEDDAGKNIHSAGENVSYVDLNRTGVPLIEIVSEPDLRSAEEAVAYLKALRAIVVHLGI 182

Query: 181 SDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGF 240
            D  MEEGS RCDAN+SLRP G  EFGT+ ELKNLNSF  VQ+ +E+E  RQ  +L  G 
Sbjct: 183 CDGNMEEGSFRCDANVSLRPRGAAEFGTRAELKNLNSFRHVQRAIEYEISRQADLLDDGD 242

Query: 241 FIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDER 300
            + QETR YD     T+ MR KE + DYRYFP+PDL+ ++ID+      +A++PELP  R
Sbjct: 243 KVVQETRLYDSVKNITVSMRGKEEAHDYRYFPDPDLIPIHIDEARLAEWQATLPELPQAR 302

Query: 301 RKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKEL 360
            +R++   G +A DA VLT  ++ A+FFE  V+   + ++ +N ++G +   LN     L
Sbjct: 303 LERFMSSFGLSAQDAEVLTAERDHAEFFEAAVKLYDQPRKIANMMLGPLQRELNQRGTSL 362

Query: 361 ADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVLL 420
           A  A+ PE LA ++++I+ G IS+KI   VF EL E G   E  V+E+GLVQISD   + 
Sbjct: 363 AVSAMRPEALAELVRIIDAGLISAKIGNDVFGELFENGAMPEAFVRERGLVQISDTSAIE 422

Query: 421 KLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEI 473
           + V E +  NP  +E ++ GK + + F VGQ+M+ ++G+ANP +VN++L  ++
Sbjct: 423 QAVDEVIAENPAEVEAYRGGKTKLVSFFVGQVMRKTRGKANPALVNELLASKL 475


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: 559
Number of extensions: 19
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: 476
Length of database: 476
Length adjustment: 33
Effective length of query: 443
Effective length of database: 443
Effective search space:   196249
Effective search space used:   196249
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 207351 DVU1885 (glutamyl-tRNA(Gln) amidotransferase, B subunit)
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.6899.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.4e-185  603.3   0.0   1.6e-185  603.1   0.0    1.0  1  lcl|MicrobesOnline__882:207351  DVU1885 glutamyl-tRNA(Gln) amido


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207351  DVU1885 glutamyl-tRNA(Gln) amidotransferase, B subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  603.1   0.0  1.6e-185  1.6e-185       1     480 [.       1     475 [.       1     476 [] 0.99

  Alignments for each domain:
  == domain 1  score: 603.1 bits;  conditional E-value: 1.6e-185
                       TIGR00133   1 kieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsevsvF 79 
                                     + +ye+viGlEvH ql t+sKlFc+cs+ +    pN +vc vc g+PG+lPvlN++av++A  ++ a+++ ++  +svF
  lcl|MicrobesOnline__882:207351   1 MASYEAVIGLEVHAQLRTRSKLFCSCSTAFGA-DPNAHVCEVCAGMPGVLPVLNEKAVEFAARMGIAVGCTVN-RTSVF 77 
                                     5689**************************99.9*************************************66.5**** PP

                       TIGR00133  80 dRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdkqslvDfNRsgvPLlEi 158
                                     +RK+YfYpDlPkgyqi+q+++Pi+e+G+l+i++ +  k+igi+r+hlE+D+gk+ +     ++ s+vD+NR+gvPL+Ei
  lcl|MicrobesOnline__882:207351  78 ARKNYFYPDLPKGYQISQYEQPICEHGHLDISVGDAVKRIGITRIHLEDDAGKNIHSAG--ENVSYVDLNRTGVPLIEI 154
                                     ********************************************************966..58**************** PP

                       TIGR00133 159 VtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNlnslksiekaieyEieR 237
                                     V++Pdl+sa+ea+a+lk lr+i+ +l+i dg++eeGs+R+D+Nvs+r++G  ++gtr+E+KNlns++ +++aieyEi R
  lcl|MicrobesOnline__882:207351 155 VSEPDLRSAEEAVAYLKALRAIVVHLGICDGNMEEGSFRCDANVSLRPRGAAEFGTRAELKNLNSFRHVQRAIEYEISR 233
                                     ******************************************************************************* PP

                       TIGR00133 238 qkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyg 316
                                     q +ll +g++v+qetr +d  k+itvs+R Kee++DYRYfp+Pdl pi+ide  + e ++++lpelP+a+ +r+++ +g
  lcl|MicrobesOnline__882:207351 234 QADLLDDGDKVVQETRLYDSVKNITVSMRGKEEAHDYRYFPDPDLIPIHIDEARLAE-WQATLPELPQARLERFMSSFG 311
                                     ******************************************************999.********************* PP

                       TIGR00133 317 lseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksak 395
                                     ls++da+vl+++++ ++ fe +vkl ++p++ +n +l  l++eLn++ +sla ++++pe+lael+++i++g is+k++ 
  lcl|MicrobesOnline__882:207351 312 LSAQDAEVLTAERDHAEFFEAAVKLYDQPRKIANMMLGPLQRELNQRGTSLAVSAMRPEALAELVRIIDAGLISAKIGN 390
                                     ******************************************************************************* PP

                       TIGR00133 396 elleellenkkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevek 474
                                     +++ el+en+ +p++ ++++gl+qisd++++ ++v+evi+enp eve y+ gk k++ f+vGqvm+kt+g+a+p+ v++
  lcl|MicrobesOnline__882:207351 391 DVFGELFENGAMPEAFVRERGLVQISDTSAIEQAVDEVIAENPAEVEAYRGGKTKLVSFFVGQVMRKTRGKANPALVNE 469
                                     ******************************************************************************* PP

                       TIGR00133 475 llkell 480
                                     ll  +l
  lcl|MicrobesOnline__882:207351 470 LLASKL 475
                                     *98876 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: 8.74
//
[ok]

This GapMind analysis is from Apr 09 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