Alignments for a candidate for gatB in Methylococcus capsulatus str. Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Methylococcus capsulatus str. Bath

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_010959467.1 MCA_RS00485 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000008325.1:WP_010959467.1
          Length = 476

 Score =  478 bits (1231), Expect = e-139
 Identities = 238/476 (50%), Positives = 332/476 (69%), Gaps = 2/476 (0%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M +ETVIGLE+H +L T+SKIFS +PT +GAE NTQ   IDLG PGVLPVLN+EAV  A+
Sbjct: 1   MEWETVIGLEIHAQLATRSKIFSGAPTAYGAEPNTQACAIDLGLPGVLPVLNREAVRMAV 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120
           K  +A+  EIA  + F RKNYFYPD PK YQISQ+D P+   G + I V GK   IGITR
Sbjct: 61  KFGLAIGAEIAPVSVFARKNYFYPDLPKGYQISQYDLPVVARGKLSINVDGKALTIGITR 120

Query: 121 LHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179
            HLEEDAGK  H    GY+ +D NR GTPL+EIVSEPD+R+ +EA AY++KL ++++Y  
Sbjct: 121 AHLEEDAGKSLHEDFHGYTGIDLNRAGTPLLEIVSEPDLRSAKEAVAYMKKLHALVRYLE 180

Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSG 239
           + D  M+EGS RCDAN+S+RP GQ +FGT+ E+KNLNSF FV+K + HE  RQ ++L  G
Sbjct: 181 ICDGNMQEGSFRCDANVSVRPKGQTKFGTRAEIKNLNSFRFVEKAINHEIARQIEILEGG 240

Query: 240 FFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDE 299
             + QETR YD    +T  MR KE ++DYRYFP+PDL+ L I   + E VKA++PELPD 
Sbjct: 241 GEVIQETRLYDSVKDETRSMRSKEEANDYRYFPDPDLLPLEISSGFIEEVKATLPELPDA 300

Query: 300 RRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGA-EAKQASNWLMGEVSAYLNAEQK 358
           +R R+  + G + YDA VLT ++EMADF+E  V++ A + K  +NW+M E+S  LN +  
Sbjct: 301 KRDRFKAQYGLSDYDAEVLTASREMADFYETVVREAAGDPKLCANWVMVELSGLLNKDGL 360

Query: 359 ELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGV 418
           E+    +   GLA +++ I   TIS KIAK+V + +  +GG A+ I++ +GL QI+D G 
Sbjct: 361 EITASKIDAAGLASLVRRIADATISGKIAKQVLETMWNEGGSADDIIERQGLKQITDTGA 420

Query: 419 LLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIK 474
           +  ++ + +  NP+ +  ++ GKD+  GF VGQ MKA++G+ANP  +N++L ++++
Sbjct: 421 IESIIDQIIAANPEQLAQYRAGKDKLFGFFVGQAMKATQGKANPAQLNELLKKKLQ 476


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: 604
Number of extensions: 19
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: 476
Length adjustment: 33
Effective length of query: 443
Effective length of database: 443
Effective search space:   196249
Effective search space used:   196249
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_010959467.1 MCA_RS00485 (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.2627475.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-186  607.1   0.0   1.1e-186  607.0   0.0    1.0  1  NCBI__GCF_000008325.1:WP_010959467.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008325.1:WP_010959467.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.0   0.0  1.1e-186  1.1e-186       2     480 ..       1     475 [.       1     476 [] 0.98

  Alignments for each domain:
  == domain 1  score: 607.0 bits;  conditional E-value: 1.1e-186
                             TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivs 74 
                                           +e+e viGlE+H ql t+sK+F+ +++ +   +pNt+ c+++lglPG+lPvlN+eav++A+k +la++++ ++
  NCBI__GCF_000008325.1:WP_010959467.1   1 MEWETVIGLEIHAQLATRSKIFSGAPTAYGA-EPNTQACAIDLGLPGVLPVLNREAVRMAVKFGLAIGAE-IA 71 
                                           57899************************99.**************************************.66 PP

                             TIGR00133  75 evsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdkqslvD 147
                                           +vsvF+RK+YfYpDlPkgyqi+q+dlP++  Gkl+i++++k+ +igi+r hlEeD+gks ++    + ++ +D
  NCBI__GCF_000008325.1:WP_010959467.1  72 PVSVFARKNYFYPDLPKGYQISQYDLPVVARGKLSINVDGKALTIGITRAHLEEDAGKSLHEDF--HGYTGID 142
                                           8************************************************************944..68***** PP

                             TIGR00133 148 fNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKN 220
                                           +NR+g+PLlEiV++Pdl+sakea+a++kkl++++rylei dg+++eGs+R+D+Nvs+r+kGq+k+gtr+EiKN
  NCBI__GCF_000008325.1:WP_010959467.1 143 LNRAGTPLLEIVSEPDLRSAKEAVAYMKKLHALVRYLEICDGNMQEGSFRCDANVSVRPKGQTKFGTRAEIKN 215
                                           ************************************************************************* PP

                             TIGR00133 221 lnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvk 293
                                           lns++ +ekai++Ei+Rq+++l+ g ev qetr +d  k  t s+R+Kee++DYRYfp+Pdl p+ei+  +++
  NCBI__GCF_000008325.1:WP_010959467.1 216 LNSFRFVEKAINHEIARQIEILEGGGEVIQETRLYDSVKDETRSMRSKEEANDYRYFPDPDLLPLEISSGFIE 288
                                           ************************************************************************* PP

                             TIGR00133 294 ekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvk.likepklavnWileellgeLnkkki 365
                                           e v+++lpelP+akr r+k +ygls++da+vl++ +e++d +e+vv+ ++++pkl +nW++ el g Lnk  +
  NCBI__GCF_000008325.1:WP_010959467.1 289 E-VKATLPELPDAKRDRFKAQYGLSDYDAEVLTASREMADFYETVVReAAGDPKLCANWVMVELSGLLNKDGL 360
                                           *.******************************************986256789******************** PP

                             TIGR00133 366 slaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenp 438
                                           +++++ +++  la+l++ i +++is+k+ak++le++ +++++++ +ie++gl qi+d+ ++ +i++++i+ np
  NCBI__GCF_000008325.1:WP_010959467.1 361 EITASKIDAAGLASLVRRIADATISGKIAKQVLETMWNEGGSADDIIERQGLKQITDTGAIESIIDQIIAANP 433
                                           ************************************************************************* PP

                             TIGR00133 439 kevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           +++ +y++gk+k+++f+vGq+mk t+g+a+p++ ++llk++l
  NCBI__GCF_000008325.1:WP_010959467.1 434 EQLAQYRAGKDKLFGFFVGQAMKATQGKANPAQLNELLKKKL 475
                                           ****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (476 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: 00:00:00.00
# Mc/sec: 29.00
//
[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