Alignments for a candidate for gatB in Methylomonas methanica MC09

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Methylomonas methanica MC09

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_013817764.1 METME_RS05375 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000214665.1:WP_013817764.1
          Length = 479

 Score =  469 bits (1208), Expect = e-137
 Identities = 236/474 (49%), Positives = 332/474 (70%), Gaps = 2/474 (0%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E VIGLE+H +L TKSKIFS + T +GAE NTQ   +DLG PGVLPVLNK+AV  A+  
Sbjct: 5   WEAVIGLEIHTQLSTKSKIFSGASTAYGAEPNTQACAVDLGLPGVLPVLNKDAVRKAVTF 64

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122
            +A++ +IA  + F RKNYFYPD PK YQISQF+ PI  NG ++IEV G TKRIGITR H
Sbjct: 65  GLAIDAQIAPHSVFARKNYFYPDLPKGYQISQFELPIVGNGHLDIEVDGVTKRIGITRAH 124

Query: 123 LEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGVS 181
           LEEDAGK  H    G + +D NR GTPL+EIVSEPD+R+ +EA AY+ KL  +++Y  + 
Sbjct: 125 LEEDAGKSLHEDFHGLTGIDLNRAGTPLLEIVSEPDMRSAKEAVAYMRKLHELVRYLEIC 184

Query: 182 DCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGFF 241
           D  M+EGS RCDAN+S+RP GQ EFGT+ E+KN+NSF FV+K + HE +RQ  V+  G  
Sbjct: 185 DGNMQEGSFRCDANVSVRPKGQAEFGTRAEIKNINSFKFVEKAINHEIERQIDVIEGGGK 244

Query: 242 IQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDERR 301
           + QETR YD    +T  MR KE ++DYRYFP+PDL+ + I++  K+ ++A++PELP+ ++
Sbjct: 245 VVQETRLYDANKDETRSMRSKEEANDYRYFPDPDLLPVEIEESLKDEIRATLPELPEAKK 304

Query: 302 KRYIEELGFAAYDAMVLTLTKEMADFFEETVQ-KGAEAKQASNWLMGEVSAYLNAEQKEL 360
            R++E+       A  LT ++E+ADF+E+ V+  G EAK   NWL G+V   LN    E+
Sbjct: 305 LRFLEQYSLDVESAATLTSSRELADFYEQVVELSGGEAKLVGNWLTGDVLGALNKAGLEI 364

Query: 361 ADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVLL 420
           ++  ++ E LAG++K I   TIS K AK+VF +L      A++I++++GL QI+D G + 
Sbjct: 365 SNCPVSAERLAGLLKRIADNTISGKTAKQVFDKLWNSDVSADEIIEKEGLKQITDTGAIE 424

Query: 421 KLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIK 474
            +V + +  NP  +E ++ GKD+A+  LVGQIMK ++G+ANP  VNK+L+ ++K
Sbjct: 425 AIVDKVIAANPVPVEQYRAGKDKALMALVGQIMKQTQGKANPGEVNKMLIAKLK 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: 606
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: 479
Length adjustment: 34
Effective length of query: 442
Effective length of database: 445
Effective search space:   196690
Effective search space used:   196690
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_013817764.1 METME_RS05375 (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.27050.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-183  595.2   0.0   4.8e-183  595.0   0.0    1.0  1  lcl|NCBI__GCF_000214665.1:WP_013817764.1  METME_RS05375 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214665.1:WP_013817764.1  METME_RS05375 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 !  595.0   0.0  4.8e-183  4.8e-183       3     480 ..       4     477 ..       2     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 595.0 bits;  conditional E-value: 4.8e-183
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               e+e+viGlE+H+ql tksK+F+ +s+ +   +pNt+ c+v+lglPG+lPvlNk+av+kA++ +la++++
  lcl|NCBI__GCF_000214665.1:WP_013817764.1   4 EWEAVIGLEIHTQLSTKSKIFSGASTAYGA-EPNTQACAVDLGLPGVLPVLNKDAVRKAVTFGLAIDAQ 71 
                                               789*************************99.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140
                                                +++ svF+RK+YfYpDlPkgyqi+q++lPi+ +G+l+ie+++  k+igi+r hlEeD+gks ++    
  lcl|NCBI__GCF_000214665.1:WP_013817764.1  72 -IAPHSVFARKNYFYPDLPKGYQISQFELPIVGNGHLDIEVDGVTKRIGITRAHLEEDAGKSLHEDF-- 137
                                               .668************************************************************944.. PP

                                 TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209
                                               +  + +D+NR+g+PLlEiV++Pd++sakea+a+++kl++++rylei dg+++eGs+R+D+Nvs+r+kGq
  lcl|NCBI__GCF_000214665.1:WP_013817764.1 138 HGLTGIDLNRAGTPLLEIVSEPDMRSAKEAVAYMRKLHELVRYLEICDGNMQEGSFRCDANVSVRPKGQ 206
                                               58999**************************************************************** PP

                                 TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278
                                                ++gtr+EiKN+ns+k +ekai++EieRq+++++ g +v+qetr +d +k  t s+R+Kee++DYRYfp
  lcl|NCBI__GCF_000214665.1:WP_013817764.1 207 AEFGTRAEIKNINSFKFVEKAINHEIERQIDVIEGGGKVVQETRLYDANKDETRSMRSKEEANDYRYFP 275
                                               ********************************************************************* PP

                                 TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklik.epk 346
                                               +Pdl p+ei+e++ +e ++++lpelPeak+ r+ ++y l+ e a +l+s +el+d +e+vv+l++ e+k
  lcl|NCBI__GCF_000214665.1:WP_013817764.1 276 DPDLLPVEIEESLKDE-IRATLPELPEAKKLRFLEQYSLDVESAATLTSSRELADFYEQVVELSGgEAK 343
                                               ************8665.********************************************98761569 PP

                                 TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415
                                               l+ nW++ ++lg Lnk  ++++++ +++e la l+k i +++is+k+ak+++++l +   +++++iek+
  lcl|NCBI__GCF_000214665.1:WP_013817764.1 344 LVGNWLTGDVLGALNKAGLEISNCPVSAERLAGLLKRIADNTISGKTAKQVFDKLWNSDVSADEIIEKE 412
                                               ********************************************************************* PP

                                 TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               gl qi+d+ ++ +iv++vi+ np  ve+y++gk+kal  lvGq+mk+t+g+a+p ev+k+l  +l
  lcl|NCBI__GCF_000214665.1:WP_013817764.1 413 GLKQITDTGAIEAIVDKVIAANPVPVEQYRAGKDKALMALVGQIMKQTQGKANPGEVNKMLIAKL 477
                                               ***********************************************************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (479 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.09
//
[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