Alignments for a candidate for gatB in Methylosarcina fibrata AML-C10

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Methylosarcina fibrata AML-C10

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_020562002.1 A3OW_RS0103285 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000372865.1:WP_020562002.1
          Length = 484

 Score =  479 bits (1234), Expect = e-140
 Identities = 239/473 (50%), Positives = 334/473 (70%), Gaps = 2/473 (0%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E VIGLE+H +L T+SKIFS +PT +GAE NTQ   +DLG PGVLPVLN+EAV  A+K 
Sbjct: 10  WEAVIGLEIHTQLATRSKIFSGAPTAYGAEPNTQACAVDLGLPGVLPVLNEEAVTMAVKF 69

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122
            +A+  EIA  + F RKNYFYPD PK YQISQF+ PI   G ++I+V G+ KRIGITR H
Sbjct: 70  GLAIEAEIAPYSVFARKNYFYPDLPKGYQISQFELPIVGRGHLDIDVDGERKRIGITRAH 129

Query: 123 LEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGVS 181
           LEEDAGK  H    G S +D NR GTPL+EIVSEPD+R+ +EA AY++ L  +++Y G+ 
Sbjct: 130 LEEDAGKSLHEDFHGLSGIDLNRAGTPLLEIVSEPDLRSAKEAVAYMKTLHELVRYLGIC 189

Query: 182 DCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGFF 241
           D  M+EGS RCDAN+S+RP G++ FGT+TELKN+NSF FV+K + +E +RQ  ++ SG  
Sbjct: 190 DGNMQEGSFRCDANVSVRPKGRQAFGTRTELKNINSFKFVEKAINYEIERQIDLIESGGK 249

Query: 242 IQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDERR 301
           + QETR YD A   T  MR KE ++DYRYFP+PDL+ ++I +E+K +V+A +PELP  +R
Sbjct: 250 VVQETRLYDSAKDLTRSMRSKEEANDYRYFPDPDLLPVFISEEFKAQVRADLPELPWVKR 309

Query: 302 KRYIEELGFAAYDAMVLTLTKEMADFFEETVQ-KGAEAKQASNWLMGEVSAYLNAEQKEL 360
           +R++E          +LT ++EMAD+FE  +Q  G E +  +NW+ GE+SA LN    E+
Sbjct: 310 RRFLEHYRLDEESIHLLTSSREMADYFEALIQASGCEPRLCANWVAGELSAALNKSGLEI 369

Query: 361 ADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVLL 420
           A   +    LAG++  I   TIS KIAK+VF ++ + G  A++I+  KGL QISD GV+ 
Sbjct: 370 AGSPVDYRRLAGLLARIADNTISGKIAKQVFDDMWQTGAGADEIIAAKGLQQISDSGVIA 429

Query: 421 KLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEI 473
            ++ + + +NP  +E +++GKD+  GF VGQ+MKA +G+ANP  VNK+L +++
Sbjct: 430 SIIDKIIADNPAQVEQYRSGKDKVFGFFVGQVMKAMQGKANPEEVNKMLKDKL 482


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: 623
Number of extensions: 21
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_020562002.1 A3OW_RS0103285 (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.23392.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-183  595.8   0.0     3e-183  595.6   0.0    1.0  1  lcl|NCBI__GCF_000372865.1:WP_020562002.1  A3OW_RS0103285 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000372865.1:WP_020562002.1  A3OW_RS0103285 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 !  595.6   0.0    3e-183    3e-183       3     480 ..       9     482 ..       7     483 .. 0.98

  Alignments for each domain:
  == domain 1  score: 595.6 bits;  conditional E-value: 3e-183
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               ++e+viGlE+H+ql t+sK+F+ +++ +   +pNt+ c+v+lglPG+lPvlN+eav++A+k +la++++
  lcl|NCBI__GCF_000372865.1:WP_020562002.1   9 KWEAVIGLEIHTQLATRSKIFSGAPTAYGA-EPNTQACAVDLGLPGVLPVLNEEAVTMAVKFGLAIEAE 76 
                                               689*************************99.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140
                                                ++++svF+RK+YfYpDlPkgyqi+q++lPi+  G+l+i+++++ k+igi+r hlEeD+gks ++    
  lcl|NCBI__GCF_000372865.1:WP_020562002.1  77 -IAPYSVFARKNYFYPDLPKGYQISQFELPIVGRGHLDIDVDGERKRIGITRAHLEEDAGKSLHEDF-- 142
                                               .668************************************************************944.. PP

                                 TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209
                                               +  s +D+NR+g+PLlEiV++Pdl+sakea+a++k l++++ryl+i dg+++eGs+R+D+Nvs+r+kG+
  lcl|NCBI__GCF_000372865.1:WP_020562002.1 143 HGLSGIDLNRAGTPLLEIVSEPDLRSAKEAVAYMKTLHELVRYLGICDGNMQEGSFRCDANVSVRPKGR 211
                                               5899***************************************************************** PP

                                 TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278
                                               +++gtr E+KN+ns+k +ekai+yEieRq++l+++g +v+qetr +d +k  t s+R+Kee++DYRYfp
  lcl|NCBI__GCF_000372865.1:WP_020562002.1 212 QAFGTRTELKNINSFKFVEKAINYEIERQIDLIESGGKVVQETRLYDSAKDLTRSMRSKEEANDYRYFP 280
                                               ********************************************************************* PP

                                 TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklik.epk 346
                                               +Pdl p+ i+ee+   +v++ lpelP  kr r+ ++y l+ee  ++l+s +e++d+fe + ++++ ep+
  lcl|NCBI__GCF_000372865.1:WP_020562002.1 281 DPDLLPVFISEEFK-AQVRADLPELPWVKRRRFLEHYRLDEESIHLLTSSREMADYFEALIQASGcEPR 348
                                               ************85.55*****************************************9887665277* PP

                                 TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415
                                               l +nW+  el + Lnk+ +++a + ++   la l++ i +++is+k+ak++++ + +++  ++++i ++
  lcl|NCBI__GCF_000372865.1:WP_020562002.1 349 LCANWVAGELSAALNKSGLEIAGSPVDYRRLAGLLARIADNTISGKIAKQVFDDMWQTGAGADEIIAAK 417
                                               ********************************************************************* PP

                                 TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               gl+qisd   + +i++++i++np +ve+y+sgk+k+++f+vGqvmk  +g+a+p+ev+k+lk++l
  lcl|NCBI__GCF_000372865.1:WP_020562002.1 418 GLQQISDSGVIASIIDKIIADNPAQVEQYRSGKDKVFGFFVGQVMKAMQGKANPEEVNKMLKDKL 482
                                               **************************************************************998 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.16
//
[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