Alignments for a candidate for gatB in Desulfallas geothermicus DSM 3669

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfallas geothermicus DSM 3669

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_092481824.1 BM299_RS02210 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_900115975.1:WP_092481824.1
          Length = 480

 Score =  572 bits (1473), Expect = e-167
 Identities = 282/475 (59%), Positives = 366/475 (77%), Gaps = 4/475 (0%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E VIGLEVHVELKT +KIF +S T FGA+ N     + LG PGVLPV+NK+ VE+A+KA
Sbjct: 4   YEAVIGLEVHVELKTNTKIFCNSSTEFGADPNHHVCPVCLGLPGVLPVINKKVVEYAIKA 63

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122
            +ALNC+IA  +KFDRKNY+YPD PK YQISQ+D PI E+G +EI + G+TKRIGITR+H
Sbjct: 64  GLALNCKIAPFSKFDRKNYYYPDLPKNYQISQYDLPIAEHGQLEINLDGETKRIGITRVH 123

Query: 123 LEEDAGKLTHTGD----GYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYT 178
           +EEDAGKL H G      YSLVD+NR G PL+EIVSEPD+R+PEEA AYLEKLK+IIQYT
Sbjct: 124 MEEDAGKLVHQGTISTTPYSLVDYNRTGVPLIEIVSEPDMRSPEEAVAYLEKLKAIIQYT 183

Query: 179 GVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLS 238
            VSDCKM+EGSLRCDANIS+RP+GQ EFGTKTELKN+NSF  + K + +E +RQ  VL  
Sbjct: 184 EVSDCKMQEGSLRCDANISVRPVGQVEFGTKTELKNMNSFKALHKAITYEIERQIDVLDE 243

Query: 239 GFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPD 298
           G  + QETR +DE    T+ +R KE + DYRYFP+PDLV L I + W + ++AS+PELPD
Sbjct: 244 GGQVVQETRTWDEDKGVTLPLRSKEEAHDYRYFPDPDLVPLVISEAWVDEIRASLPELPD 303

Query: 299 ERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQK 358
           ER+ R++ E G   YDA+VLT T+E+AD+FE+ V+     K  SNW+MG+++  +NA  +
Sbjct: 304 ERKARFVNEYGLPEYDALVLTSTRELADYFEQCVELFNNPKTVSNWVMGDLARMMNATGR 363

Query: 359 ELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGV 418
           E+  V + P  LA M+KL++KGTIS KIAK VF+E+   G D   IV+EKGLVQISDEG 
Sbjct: 364 EIGAVRIKPAQLAEMLKLLDKGTISGKIAKTVFEEMFNTGKDPGVIVEEKGLVQISDEGK 423

Query: 419 LLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEI 473
           + K+V++ +  NP+S+ED++ GK +AIGFLVGQ+MKA+KG+ANP +VNK+L E++
Sbjct: 424 IEKIVSDVIAANPKSVEDYRGGKKQAIGFLVGQVMKATKGKANPGLVNKLLKEKL 478


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: 724
Number of extensions: 29
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: 480
Length adjustment: 34
Effective length of query: 442
Effective length of database: 446
Effective search space:   197132
Effective search space used:   197132
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_092481824.1 BM299_RS02210 (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.31074.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-201  654.5   0.0   4.7e-201  654.4   0.0    1.0  1  lcl|NCBI__GCF_900115975.1:WP_092481824.1  BM299_RS02210 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092481824.1  BM299_RS02210 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 !  654.4   0.0  4.7e-201  4.7e-201       1     480 [.       1     478 [.       1     479 [. 0.99

  Alignments for each domain:
  == domain 1  score: 654.4 bits;  conditional E-value: 4.7e-201
                                 TIGR00133   1 kieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalaln 69 
                                               + +ye+viGlEvHv l t++K+Fc++s+e+    pN++vcpvclglPG+lPv+Nk++v+ A+k +laln
  lcl|NCBI__GCF_900115975.1:WP_092481824.1   1 MAQYEAVIGLEVHVELKTNTKIFCNSSTEFGA-DPNHHVCPVCLGLPGVLPVINKKVVEYAIKAGLALN 68 
                                               679***************************99.9*********************************** PP

                                 TIGR00133  70 skivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykes 138
                                               +k ++++s+FdRK+Y+YpDlPk+yqi+q+dlPiae+G+lei+l+++ k+igi+r+h+EeD+gk++++++
  lcl|NCBI__GCF_900115975.1:WP_092481824.1  69 CK-IAPFSKFDRKNYYYPDLPKNYQISQYDLPIAEHGQLEINLDGETKRIGITRVHMEEDAGKLVHQGT 136
                                               **.668**************************************************************9 PP

                                 TIGR00133 139 dk.dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirl 206
                                                  + +slvD+NR+gvPL+EiV++Pd++s++ea+a+l+kl++i++y+e+sd++++eGs+R+D+N+s+r+
  lcl|NCBI__GCF_900115975.1:WP_092481824.1 137 IStTPYSLVDYNRTGVPLIEIVSEPDMRSPEEAVAYLEKLKAIIQYTEVSDCKMQEGSLRCDANISVRP 205
                                               87588**************************************************************** PP

                                 TIGR00133 207 kGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYR 275
                                               +Gq ++gt+ E+KN+ns+k+++kai yEieRq+++l +g +v+qetr++de k +t+ lR+Kee++DYR
  lcl|NCBI__GCF_900115975.1:WP_092481824.1 206 VGQVEFGTKTELKNMNSFKALHKAITYEIERQIDVLDEGGQVVQETRTWDEDKGVTLPLRSKEEAHDYR 274
                                               ********************************************************************* PP

                                 TIGR00133 276 YfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklike 344
                                               Yfp+Pdl+p++i+e +v+e +++ lpelP+++++r+++eygl e+da vl+s +el+d+fe+ v+l ++
  lcl|NCBI__GCF_900115975.1:WP_092481824.1 275 YFPDPDLVPLVISEAWVDE-IRASLPELPDERKARFVNEYGLPEYDALVLTSTRELADYFEQCVELFNN 342
                                               *******************.************************************************* PP

                                 TIGR00133 345 pklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklie 413
                                               pk++ nW++ +l++ +n++  ++ ++ +kp +lae++kl+++g+is+k+ak+++ee+++++kdp  ++e
  lcl|NCBI__GCF_900115975.1:WP_092481824.1 343 PKTVSNWVMGDLARMMNATGREIGAVRIKPAQLAEMLKLLDKGTISGKIAKTVFEEMFNTGKDPGVIVE 411
                                               ********************************************************************* PP

                                 TIGR00133 414 klgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               ++gl+qisde ++ kiv +vi+ npk+ve+y+ gk++a++flvGqvmk tkg+a+p  v+kllke+l
  lcl|NCBI__GCF_900115975.1:WP_092481824.1 412 EKGLVQISDEGKIEKIVSDVIAANPKSVEDYRGGKKQAIGFLVGQVMKATKGKANPGLVNKLLKEKL 478
                                               *****************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (480 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: 7.88
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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