Alignments for a candidate for gatB in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfitobacterium hafniense DCB-2

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_005812379.1 DHAF_RS07585 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000021925.1:WP_005812379.1
          Length = 484

 Score =  525 bits (1351), Expect = e-153
 Identities = 266/478 (55%), Positives = 345/478 (72%), Gaps = 6/478 (1%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E V G+EVHVEL TK+KIF +  T FG E NT    + LG PGVLPVLN+E V  A+KA
Sbjct: 7   YEMVCGVEVHVELATKTKIFCNCSTEFGGEQNTHVCPVCLGLPGVLPVLNREVVNLAIKA 66

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122
            +ALNC+IA  +KFDRKNYFYPD PK +Q SQ+D PI +NGW+E  V G+ KR+GITR H
Sbjct: 67  GLALNCDIADFSKFDRKNYFYPDAPKNFQTSQYDLPICKNGWLEFAVDGEKKRVGITRAH 126

Query: 123 LEEDAGKLTHTG-----DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQY 177
           +E+DAGKL H+G        S VD+NR G PL+EIVSEPD+R+  E  ++LE++   IQY
Sbjct: 127 MEDDAGKLVHSGATISTSEESFVDYNRTGVPLLEIVSEPDMRSIAEVVSFLEEMVRTIQY 186

Query: 178 TGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLL 237
           T VSDC+ME+GS+R D N+SLRP GQ+EFGT+TE KNLNSF+ V++ LE+E +RQ ++L 
Sbjct: 187 TEVSDCRMEQGSVRFDINVSLRPHGQKEFGTRTETKNLNSFSSVRRCLEYEIERQARLLD 246

Query: 238 SGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELP 297
            G  + QETR +DE    T+ +R KE + DYRYFPEPDLV L I  EW E ++ ++PE+P
Sbjct: 247 DGEKVIQETRTWDEGKGVTLSLRSKEEAHDYRYFPEPDLVPLVIAREWVEEIRQTLPEMP 306

Query: 298 DERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQ 357
             RR+RY + LG   YDA VLT  K ++DFF+E +Q  ++AK  +NW+MGE +  LNA+Q
Sbjct: 307 GARRERY-QSLGLTEYDAGVLTAAKALSDFFDEALQSYSDAKALANWVMGEFTRLLNAKQ 365

Query: 358 KELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEG 417
             + +  + P  LA ++ LIEKG IS KI K V + + E G D E I+KEKGL QISD  
Sbjct: 366 ISVEESPVRPSQLAELLTLIEKGAISGKIGKTVIEAMFESGKDPEVIIKEKGLAQISDTA 425

Query: 418 VLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIKK 475
            LLKLV E +  +PQS+ED+K GKDRAIGFLVGQIMKA+KGQANP +VN +L E++ K
Sbjct: 426 ALLKLVDEVIAAHPQSVEDYKAGKDRAIGFLVGQIMKATKGQANPGVVNDLLKEQLAK 483


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: 676
Number of extensions: 31
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: 484
Length adjustment: 34
Effective length of query: 442
Effective length of database: 450
Effective search space:   198900
Effective search space used:   198900
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_005812379.1 DHAF_RS07585 (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.21841.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.4e-186  604.7   0.0   6.2e-186  604.5   0.0    1.0  1  lcl|NCBI__GCF_000021925.1:WP_005812379.1  DHAF_RS07585 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_005812379.1  DHAF_RS07585 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 !  604.5   0.0  6.2e-186  6.2e-186       3     480 ..       6     481 ..       4     482 .. 0.98

  Alignments for each domain:
  == domain 1  score: 604.5 bits;  conditional E-value: 6.2e-186
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                                ye+v+G+EvHv l tk+K+Fc+cs+e+   ++Nt+vcpvclglPG+lPvlN+e+v+ A+k +laln+ 
  lcl|NCBI__GCF_000021925.1:WP_005812379.1   6 RYEMVCGVEVHVELATKTKIFCNCSTEFGG-EQNTHVCPVCLGLPGVLPVLNREVVNLAIKAGLALNCD 73 
                                               69****************************.9************************************* PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140
                                                ++++s+FdRK+YfYpD Pk++q +q+dlPi+++G le  +++++k++gi+r h+E+D+gk+++ + + 
  lcl|NCBI__GCF_000021925.1:WP_005812379.1  74 -IADFSKFDRKNYFYPDAPKNFQTSQYDLPICKNGWLEFAVDGEKKRVGITRAHMEDDAGKLVHSGATI 141
                                               .668************************************************************98754 PP

                                 TIGR00133 141 ..dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk 207
                                                 ++ s+vD+NR+gvPLlEiV++Pd++s+ e++ fl+++ + ++y+e+sd+ +e+Gs+R D+Nvs+r++
  lcl|NCBI__GCF_000021925.1:WP_005812379.1 142 stSEESFVDYNRTGVPLLEIVSEPDMRSIAEVVSFLEEMVRTIQYTEVSDCRMEQGSVRFDINVSLRPH 210
                                               45899**************************************************************** PP

                                 TIGR00133 208 GqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRY 276
                                               Gq+++gtr E KNlns++s+ + +eyEieRq +ll +ge+v qetr++de k +t+slR+Kee++DYRY
  lcl|NCBI__GCF_000021925.1:WP_005812379.1 211 GQKEFGTRTETKNLNSFSSVRRCLEYEIERQARLLDDGEKVIQETRTWDEGKGVTLSLRSKEEAHDYRY 279
                                               ********************************************************************* PP

                                 TIGR00133 277 fpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep 345
                                               fpePdl+p++i+ e+v+e ++++lpe+P a+r+r+ + +gl e+da vl++ + l d f+e+ ++ +++
  lcl|NCBI__GCF_000021925.1:WP_005812379.1 280 FPEPDLVPLVIAREWVEE-IRQTLPEMPGARRERY-QSLGLTEYDAGVLTAAKALSDFFDEALQSYSDA 346
                                               ******************.**************98.579****************************** PP

                                 TIGR00133 346 klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliek 414
                                               k+ +nW++ e+++ Ln+k+is++e+ ++p++lael+ li++g is+k++k+++e ++e +kdp+ +i++
  lcl|NCBI__GCF_000021925.1:WP_005812379.1 347 KALANWVMGEFTRLLNAKQISVEESPVRPSQLAELLTLIEKGAISGKIGKTVIEAMFESGKDPEVIIKE 415
                                               ********************************************************************* PP

                                 TIGR00133 415 lgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               +gl qisd+ +l k+v+evi+ +p++ve+yk+gk++a++flvGq+mk tkg+a+p  v+ llke+l
  lcl|NCBI__GCF_000021925.1:WP_005812379.1 416 KGLAQISDTAALLKLVDEVIAAHPQSVEDYKAGKDRAIGFLVGQIMKATKGQANPGVVNDLLKEQL 481
                                               ****************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (484 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: 12.32
//
[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