Alignments for a candidate for gatB in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfovibrio vulgaris Miyazaki F

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate 8499813 DvMF_0578 aspartyl/glutamyl-tRNA amidotransferase subunit B (RefSeq)

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



>FitnessBrowser__Miya:8499813
          Length = 476

 Score =  456 bits (1172), Expect = e-132
 Identities = 232/472 (49%), Positives = 314/472 (66%), Gaps = 1/472 (0%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E VIGLEVH +L+T+SK+F S  T FG+  NT    +  G PGVLPV N  AVE+A + 
Sbjct: 4   YEAVIGLEVHAQLRTRSKLFCSCSTAFGSAPNTNVCEVCSGMPGVLPVPNARAVEYAARM 63

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122
            MA+NC +   + F RKNYFYPD PK YQISQF+ PI E+G + I V G+T+RIGITR+H
Sbjct: 64  GMAVNCTVNPVSVFARKNYFYPDLPKGYQISQFETPICEHGHLNISVNGQTRRIGITRIH 123

Query: 123 LEEDAGKLTHT-GDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGVS 181
           +E+DAGK  H+ GD  S VD NR G PL+EIVSEPD+R+ EEA AYL+ L +I+ Y G+ 
Sbjct: 124 MEDDAGKNIHSAGDNASYVDLNRSGVPLIEIVSEPDMRSAEEAVAYLKALHAIVVYLGIC 183

Query: 182 DCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGFF 241
           D  MEEGS RCDAN+S+RP GQ+EFGT+ ELKNLNSF  VQ+ +E+E  RQ+ VL  G  
Sbjct: 184 DGNMEEGSFRCDANVSIRPKGQQEFGTRAELKNLNSFRNVQRAIEYEIARQQDVLEDGDA 243

Query: 242 IQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDERR 301
           + QETR YD     T+ MR KE + DYRYFP+PDL+ + I ++   R +A +PELP  R 
Sbjct: 244 VVQETRLYDAVKNVTVSMRGKEEAHDYRYFPDPDLMPVRIAEDDLVRWRADLPELPQARV 303

Query: 302 KRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKELA 361
            R++     +  DA VLT  + +ADFFE       + K+ +N + G +   LN     + 
Sbjct: 304 ARFMSAYDLSEQDADVLTADRALADFFEAATAACGQPKKVANLMQGALLRELNQRAVTVD 363

Query: 362 DVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVLLK 421
            +A+ PE L  ++++IE G IS+KIA  +F EL+E G   E  VKE+GLVQISD   +  
Sbjct: 364 AIAMRPEALGELVRIIEAGLISAKIANDIFGELVETGAMPEAFVKERGLVQISDTSAIET 423

Query: 422 LVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEI 473
            V EA+  NP  +E +K GK + I F +GQIM+ +KG+ANP +V ++L +++
Sbjct: 424 AVDEAIAENPAEVEAYKGGKTKLISFFMGQIMRKTKGKANPALVTELLQKKL 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: 580
Number of extensions: 17
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 8499813 DvMF_0578 (aspartyl/glutamyl-tRNA amidotransferase subunit B (RefSeq))
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.26743.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.2e-191  621.5   0.0   4.7e-191  621.4   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499813  DvMF_0578 aspartyl/glutamyl-tRNA


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499813  DvMF_0578 aspartyl/glutamyl-tRNA amidotransferase subunit B (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  621.4   0.0  4.7e-191  4.7e-191       3     480 ..       3     475 ..       1     476 [] 0.99

  Alignments for each domain:
  == domain 1  score: 621.4 bits;  conditional E-value: 4.7e-191
                         TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsevsvF 79 
                                        ye+viGlEvH ql t+sKlFc+cs+ + +  pNtnvc vc g+PG+lPv+N +av+ A  +++a+n+  v++vsvF
  lcl|FitnessBrowser__Miya:8499813   3 LYEAVIGLEVHAQLRTRSKLFCSCSTAFGS-APNTNVCEVCSGMPGVLPVPNARAVEYAARMGMAVNCT-VNPVSVF 77 
                                       69****************************.9*************************************.568**** PP

                         TIGR00133  80 dRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdkqslvDfNRsgvPLl 156
                                       +RK+YfYpDlPkgyqi+q+++Pi+e+G+l+i+++++ ++igi+r+h+E+D+gk+ +   d  + s+vD+NRsgvPL+
  lcl|FitnessBrowser__Miya:8499813  78 ARKNYFYPDLPKGYQISQFETPICEHGHLNISVNGQTRRIGITRIHMEDDAGKNIHSAGD--NASYVDLNRSGVPLI 152
                                       ********************************************************9775..8************** PP

                         TIGR00133 157 EiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNlnslksiekaiey 233
                                       EiV++Pd++sa+ea+a+lk l++i+ yl+i dg++eeGs+R+D+Nvsir+kGq+++gtr+E+KNlns++++++aiey
  lcl|FitnessBrowser__Miya:8499813 153 EIVSEPDMRSAEEAVAYLKALHAIVVYLGICDGNMEEGSFRCDANVSIRPKGQQEFGTRAELKNLNSFRNVQRAIEY 229
                                       ***************************************************************************** PP

                         TIGR00133 234 EieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekveeklpelPeakrir 310
                                       Ei+Rq+++l++g+ v+qetr +d  k++tvs+R Kee++DYRYfp+Pdl+p+ i+e+ + + +++ lpelP+a+ +r
  lcl|FitnessBrowser__Miya:8499813 230 EIARQQDVLEDGDAVVQETRLYDAVKNVTVSMRGKEEAHDYRYFPDPDLMPVRIAEDDLVR-WRADLPELPQARVAR 305
                                       *********************************************************9888.*************** PP

                         TIGR00133 311 lkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaeallkpeelaeliklikeg 387
                                       +++ y+lse+da vl++d+ l+d fe ++ + ++pk+++n +   ll+eLn++ +++ + +++pe+l el+++i++g
  lcl|FitnessBrowser__Miya:8499813 306 FMSAYDLSEQDADVLTADRALADFFEAATAACGQPKKVANLMQGALLRELNQRAVTVDAIAMRPEALGELVRIIEAG 382
                                       ***************************************************************************** PP

                         TIGR00133 388 kisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktk 464
                                        is+k+a +++ el+e++ +p++ ++++gl+qisd++++  +v+e+i+enp eve yk gk k++ f++Gq+m+ktk
  lcl|FitnessBrowser__Miya:8499813 383 LISAKIANDIFGELVETGAMPEAFVKERGLVQISDTSAIETAVDEAIAENPAEVEAYKGGKTKLISFFMGQIMRKTK 459
                                       ***************************************************************************** PP

                         TIGR00133 465 gradpkevekllkell 480
                                       g+a+p+ v++ll+++l
  lcl|FitnessBrowser__Miya:8499813 460 GKANPALVTELLQKKL 475
                                       *************998 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.07
//
[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