Alignments for a candidate for gatB in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfovibrio oxyclinae DSM 11498

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_018123948.1 B149_RS0104370 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000375485.1:WP_018123948.1
          Length = 478

 Score =  455 bits (1171), Expect = e-132
 Identities = 230/474 (48%), Positives = 320/474 (67%), Gaps = 3/474 (0%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E+VIGLEVH +L T+SK+F +  T FG E N     +  G PGVLPVLN +AVE+A K 
Sbjct: 4   YESVIGLEVHAQLNTESKLFCACSTKFGNEPNDNVCPVCSGMPGVLPVLNAKAVEYAAKL 63

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122
            +A  C +   + F+RKNYFYPD PK YQISQ  + I   G + IEV GK + + I R+ 
Sbjct: 64  GLATGCTVQNKSVFERKNYFYPDLPKGYQISQLQQSICTAGNLSIEVDGKKRNVRINRIQ 123

Query: 123 LEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGVS 181
           +EEDAGK  H+  +  S VD NR   PL+EIVSEPD+RT EEA AYL+ L+SI+ Y G+S
Sbjct: 124 IEEDAGKNIHSAAENASFVDLNRTSVPLLEIVSEPDLRTAEEAVAYLKALRSILLYLGIS 183

Query: 182 DCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGFF 241
           D  MEEGS RCDAN+S+R  G EE+GT+ ELKNLNSF FVQK +E+E  RQ  ++  G  
Sbjct: 184 DGNMEEGSFRCDANVSIREKGSEEYGTRCELKNLNSFRFVQKAIEYEIDRQIDLIEDGEE 243

Query: 242 IQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDERR 301
           + QETR Y+     T  MR KE + DYRYFP+PDLV + I+DE     ++ +PELP E+ 
Sbjct: 244 VDQETRLYNPEKNATFTMRGKEEAHDYRYFPDPDLVPVLIEDETIAAWQSELPELPSEKL 303

Query: 302 KRYIEELGFAAYDAMVLTLTKEMADFFEETVQ--KGAEAKQASNWLMGEVSAYLNAEQKE 359
           +R++E+    A +A +L+    +A+FFE +V+  KG   ++ +NW++G++  +LN     
Sbjct: 304 ERFLEDFKLPADEAELLSGELAVAEFFEASVEAYKGDTPRKVANWIIGDLLPHLNDNGMS 363

Query: 360 LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVL 419
           L+D  LTPE LAG+++L++KG IS KI +K+F EL E G D EK+VK+KGLVQ+SD G L
Sbjct: 364 LSDCKLTPESLAGLVELLDKGDISQKIGRKIFPELCETGADPEKLVKDKGLVQVSDTGAL 423

Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEI 473
             +V E +  NP   E ++ GK + + F +GQIM+ +KGQANP +V ++L +++
Sbjct: 424 EGVVDEVIQENPDEAEAYRGGKKKLMSFFMGQIMRKTKGQANPGVVTELLQKKL 477


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: 678
Number of extensions: 36
Number of successful extensions: 3
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: 478
Length adjustment: 33
Effective length of query: 443
Effective length of database: 445
Effective search space:   197135
Effective search space used:   197135
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_018123948.1 B149_RS0104370 (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.3484599.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-184  598.4   0.0   4.8e-184  598.3   0.0    1.0  1  NCBI__GCF_000375485.1:WP_018123948.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000375485.1:WP_018123948.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.3   0.0  4.8e-184  4.8e-184       1     480 [.       1     477 [.       1     478 [] 0.98

  Alignments for each domain:
  == domain 1  score: 598.3 bits;  conditional E-value: 4.8e-184
                             TIGR00133   1 kieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskiv 73 
                                           ++ ye viGlEvH qlnt+sKlFc cs+++ + +pN nvcpvc g+PG+lPvlN +av+ A kl+la+++  v
  NCBI__GCF_000375485.1:WP_018123948.1   1 MPAYESVIGLEVHAQLNTESKLFCACSTKFGN-EPNDNVCPVCSGMPGVLPVLNAKAVEYAAKLGLATGCT-V 71 
                                           5689****************************.**************************************.6 PP

                             TIGR00133  74 sevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdkqslv 146
                                           +++svF+RK+YfYpDlPkgyqi+q ++ i++ G+l+ie+++k+++++i+r+++EeD+gk+ +     ++ s+v
  NCBI__GCF_000375485.1:WP_018123948.1  72 QNKSVFERKNYFYPDLPKGYQISQLQQSICTAGNLSIEVDGKKRNVRINRIQIEEDAGKNIHSAA--ENASFV 142
                                           68************************************************************976..58**** PP

                             TIGR00133 147 DfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiK 219
                                           D+NR++vPLlEiV++Pdl++a+ea+a+lk lr+il yl+isdg++eeGs+R+D+Nvsir kG+e+ gtr E+K
  NCBI__GCF_000375485.1:WP_018123948.1 143 DLNRTSVPLLEIVSEPDLRTAEEAVAYLKALRSILLYLGISDGNMEEGSFRCDANVSIREKGSEEYGTRCELK 215
                                           ************************************************************************* PP

                             TIGR00133 220 NlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevv 292
                                           Nlns++ ++kaieyEi Rq++l+++geev qetr ++ +k+ t ++R Kee++DYRYfp+Pdl+p+ i++e++
  NCBI__GCF_000375485.1:WP_018123948.1 216 NLNSFRFVQKAIEYEIDRQIDLIEDGEEVDQETRLYNPEKNATFTMRGKEEAHDYRYFPDPDLVPVLIEDETI 288
                                           ************************************************************************* PP

                             TIGR00133 293 kekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep..klavnWileellgeLnkk 363
                                              ++ +lpelP++k +r+ ++++l +++a++l  +l +++ fe  v++ k    ++++nWi+ +ll +Ln++
  NCBI__GCF_000375485.1:WP_018123948.1 289 AA-WQSELPELPSEKLERFLEDFKLPADEAELLSGELAVAEFFEASVEAYKGDtpRKVANWIIGDLLPHLNDN 360
                                           99.*****************************************99987654334****************** PP

                             TIGR00133 364 kislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevike 436
                                            +sl+++ l+pe+la l++l+++g isqk++++++ el e++ dp+kl++ +gl+q+sd+ +l  +v+evi+e
  NCBI__GCF_000375485.1:WP_018123948.1 361 GMSLSDCKLTPESLAGLVELLDKGDISQKIGRKIFPELCETGADPEKLVKDKGLVQVSDTGALEGVVDEVIQE 433
                                           ************************************************************************* PP

                             TIGR00133 437 npkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           np+e e y+ gk+k++ f++Gq+m+ktkg+a+p  v++ll+++l
  NCBI__GCF_000375485.1:WP_018123948.1 434 NPDEAEAYRGGKKKLMSFFMGQIMRKTKGQANPGVVTELLQKKL 477
                                           *****************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (478 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 18.71
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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