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.13263.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  lcl|NCBI__GCF_000375485.1:WP_018123948.1  B149_RS0104370 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000375485.1:WP_018123948.1  B149_RS0104370 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 !  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 kieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalaln 69 
                                               ++ ye viGlEvH qlnt+sKlFc cs+++ + +pN nvcpvc g+PG+lPvlN +av+ A kl+la++
  lcl|NCBI__GCF_000375485.1:WP_018123948.1   1 MPAYESVIGLEVHAQLNTESKLFCACSTKFGN-EPNDNVCPVCSGMPGVLPVLNAKAVEYAAKLGLATG 68 
                                               5689****************************.************************************ PP

                                 TIGR00133  70 skivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykes 138
                                               +  v+++svF+RK+YfYpDlPkgyqi+q ++ i++ G+l+ie+++k+++++i+r+++EeD+gk+ +   
  lcl|NCBI__GCF_000375485.1:WP_018123948.1  69 CT-VQNKSVFERKNYFYPDLPKGYQISQLQQSICTAGNLSIEVDGKKRNVRINRIQIEEDAGKNIHSAA 136
                                               **.668************************************************************976 PP

                                 TIGR00133 139 dkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk 207
                                                 ++ s+vD+NR++vPLlEiV++Pdl++a+ea+a+lk lr+il yl+isdg++eeGs+R+D+Nvsir k
  lcl|NCBI__GCF_000375485.1:WP_018123948.1 137 --ENASFVDLNRTSVPLLEIVSEPDLRTAEEAVAYLKALRSILLYLGISDGNMEEGSFRCDANVSIREK 203
                                               ..58***************************************************************** PP

                                 TIGR00133 208 GqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRY 276
                                               G+e+ gtr E+KNlns++ ++kaieyEi Rq++l+++geev qetr ++ +k+ t ++R Kee++DYRY
  lcl|NCBI__GCF_000375485.1:WP_018123948.1 204 GSEEYGTRCELKNLNSFRFVQKAIEYEIDRQIDLIEDGEEVDQETRLYNPEKNATFTMRGKEEAHDYRY 272
                                               ********************************************************************* PP

                                 TIGR00133 277 fpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep 345
                                               fp+Pdl+p+ i++e++   ++ +lpelP++k +r+ ++++l +++a++l  +l +++ fe  v++ k  
  lcl|NCBI__GCF_000375485.1:WP_018123948.1 273 FPDPDLVPVLIEDETIAA-WQSELPELPSEKLERFLEDFKLPADEAELLSGELAVAEFFEASVEAYKGD 340
                                               ****************99.*****************************************999876543 PP

                                 TIGR00133 346 ..klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkli 412
                                                 ++++nWi+ +ll +Ln++ +sl+++ l+pe+la l++l+++g isqk++++++ el e++ dp+kl+
  lcl|NCBI__GCF_000375485.1:WP_018123948.1 341 tpRKVANWIIGDLLPHLNDNGMSLSDCKLTPESLAGLVELLDKGDISQKIGRKIFPELCETGADPEKLV 409
                                               34******************************************************************* PP

                                 TIGR00133 413 eklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               + +gl+q+sd+ +l  +v+evi+enp+e e y+ gk+k++ f++Gq+m+ktkg+a+p  v++ll+++l
  lcl|NCBI__GCF_000375485.1:WP_018123948.1 410 KDKGLVQVSDTGALEGVVDEVIQENPDEAEAYRGGKKKLMSFFMGQIMRKTKGQANPGVVTELLQKKL 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.61
//
[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