Alignments for a candidate for gatB in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Thiomicrospira cyclica ALM1

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_013835791.1 THICY_RS06340 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000214825.1:WP_013835791.1
          Length = 477

 Score =  453 bits (1165), Expect = e-132
 Identities = 237/477 (49%), Positives = 324/477 (67%), Gaps = 4/477 (0%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           MN+E VIGLE+H +L  +SKIFS++PT +GAE NTQ +V+DL  PGVLPVLN  AVE A+
Sbjct: 1   MNWEVVIGLEIHAQLACESKIFSNAPTAYGAEPNTQANVVDLAIPGVLPVLNARAVELAV 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120
           +  +A+  EI   + F RKNYFYPD+PKAYQISQF+ PI   G I IEV G+ K IGITR
Sbjct: 61  RFGLAVGAEIGQTSVFARKNYFYPDSPKAYQISQFELPIVGKGEITIEVDGQQKTIGITR 120

Query: 121 LHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179
            HLEEDAGK  H    G + +D NR GTPL+EIVSEPD+R+  EA AY + +  ++Q+  
Sbjct: 121 AHLEEDAGKSLHEDFQGLTGIDLNRAGTPLLEIVSEPDMRSAAEAVAYAKAIHELVQFLE 180

Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSG 239
           + D  M+EGS R D N+SLR  G E FGT+TELKN+NSF F++K L +E  R  ++L +G
Sbjct: 181 IGDGNMQEGSFRVDVNVSLRQPG-EAFGTRTELKNINSFKFIEKALAYEIDRHIEILEAG 239

Query: 240 FFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDE 299
             I QETR YD    +T  MR KE ++DYRYFP+PDL+ + + DE    +KA++PELP +
Sbjct: 240 GEIVQETRLYDPERDETRSMRSKEEANDYRYFPDPDLLPVVVSDEQLAAIKAALPELPGQ 299

Query: 300 RRKRYIEELGFAAYDAMVLTLTKEMADFFEETV-QKGAE-AKQASNWLMGEVSAYLNAEQ 357
            R R+ ++ G +AYDA +LT +   A +F+  V Q GAE AK A+NW+ GE++  LN   
Sbjct: 300 MRVRFEQDYGLSAYDAQLLTASAANARYFDALVAQLGAEQAKLAANWMNGELAKSLNKAD 359

Query: 358 KELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEG 417
             L +  +  + LAG++  I   T+S K+AK+VF+ +    G A++I+  KGL QI+D G
Sbjct: 360 LSLEESPIAADALAGLLIRIVDNTVSGKLAKQVFEAMWAGEGSADQIIDAKGLKQITDSG 419

Query: 418 VLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIK 474
            + K+V E L  N + +E +K G+++  GF VGQ+MK SKGQANP  VN +L E++K
Sbjct: 420 AIEKIVDEVLAANAKQVEAYKGGQEKMFGFFVGQVMKLSKGQANPAQVNDLLQEKLK 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: 623
Number of extensions: 33
Number of successful extensions: 4
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: 477
Length adjustment: 33
Effective length of query: 443
Effective length of database: 444
Effective search space:   196692
Effective search space used:   196692
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_013835791.1 THICY_RS06340 (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.22642.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.2e-171  555.0   0.0     7e-171  554.9   0.0    1.0  1  lcl|NCBI__GCF_000214825.1:WP_013835791.1  THICY_RS06340 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214825.1:WP_013835791.1  THICY_RS06340 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 !  554.9   0.0    7e-171    7e-171       2     480 ..       1     475 [.       1     476 [. 0.97

  Alignments for each domain:
  == domain 1  score: 554.9 bits;  conditional E-value: 7e-171
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +++e+viGlE+H ql  +sK+F+++++ +   +pNt+ + v+l++PG+lPvlN +av+ A+  +la+++
  lcl|NCBI__GCF_000214825.1:WP_013835791.1   1 MNWEVVIGLEIHAQLACESKIFSNAPTAYGA-EPNTQANVVDLAIPGVLPVLNARAVELAVRFGLAVGA 68 
                                               6899*************************99.************************************* PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesd 139
                                               +i  ++svF+RK+YfYpD Pk+yqi+q++lPi+ +G+++ie+++++k+igi+r hlEeD+gks ++   
  lcl|NCBI__GCF_000214825.1:WP_013835791.1  69 EI-GQTSVFARKNYFYPDSPKAYQISQFELPIVGKGEITIEVDGQQKTIGITRAHLEEDAGKSLHEDF- 135
                                               *5.57************************************************************944. PP

                                 TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208
                                                +  + +D+NR+g+PLlEiV++Pd++sa ea+a+ k +++++++lei dg+++eGs+RvDvNvs+r   
  lcl|NCBI__GCF_000214825.1:WP_013835791.1 136 -QGLTGIDLNRAGTPLLEIVSEPDMRSAAEAVAYAKAIHELVQFLEIGDGNMQEGSFRVDVNVSLRQP- 202
                                               .58999************************************************************55. PP

                                 TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277
                                                e++gtr E+KN+ns+k ieka+ yEi R +++l+ g e++qetr +d ++  t s+R+Kee++DYRYf
  lcl|NCBI__GCF_000214825.1:WP_013835791.1 203 GEAFGTRTELKNINSFKFIEKALAYEIDRHIEILEAGGEIVQETRLYDPERDETRSMRSKEEANDYRYF 271
                                               5789***************************************************************** PP

                                 TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep. 345
                                               p+Pdl p+++++e++   +++ lpelP ++r r++++ygls++da++l++ +  +++f+ +v  ++ + 
  lcl|NCBI__GCF_000214825.1:WP_013835791.1 272 PDPDLLPVVVSDEQLAA-IKAALPELPGQMRVRFEQDYGLSAYDAQLLTASAANARYFDALVAQLGAEq 339
                                               *************9999.9****************************************9988765544 PP

                                 TIGR00133 346 .klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklie 413
                                                kla+nW+  el+++Lnk ++sl+e+ +++++la l+  i ++++s+k ak+++e +   +++++++i+
  lcl|NCBI__GCF_000214825.1:WP_013835791.1 340 aKLAANWMNGELAKSLNKADLSLEESPIAADALAGLLIRIVDNTVSGKLAKQVFEAMWAGEGSADQIID 408
                                               69******************************************************************* PP

                                 TIGR00133 414 klgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               ++gl qi+d  ++ kiv+ev++ n+k+ve yk g+ek+++f+vGqvmk +kg+a+p++v+ ll+e+l
  lcl|NCBI__GCF_000214825.1:WP_013835791.1 409 AKGLKQITDSGAIEKIVDEVLAANAKQVEAYKGGQEKMFGFFVGQVMKLSKGQANPAQVNDLLQEKL 475
                                               *****************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (477 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: 00:00:00.02
# Mc/sec: 10.62
//
[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