Alignments for a candidate for gatB in Thiomicrospira microaerophila ASL8-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Thiomicrospira microaerophila ASL8-2

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_044410249.1 NA59_RS07220 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000934765.1:WP_044410249.1
          Length = 477

 Score =  460 bits (1184), Expect = e-134
 Identities = 234/476 (49%), Positives = 328/476 (68%), Gaps = 5/476 (1%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +ETVIGLE+H +L T SK+FS +   +GAEPNS   ++DLA PGVLPV+NKRA++  +
Sbjct: 1   MQWETVIGLEIHAQLATKSKIFSAASTAYGAEPNSQACLVDLAMPGVLPVLNKRALEMGI 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITR 120
              +A+N E+  +S F RKNYFYPD+PK YQISQFD P+   G I+IEV+GE K IG+TR
Sbjct: 61  AFGLAINAEVPKKSVFARKNYFYPDSPKGYQISQFDLPVVGKGQIEIEVNGEKKIIGVTR 120

Query: 121 LHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTG 178
            H+EEDAGKS H+  + +  +DLNR GTPL+EIVSEPD+RS  EA AY + +  ++Q+ G
Sbjct: 121 AHLEEDAGKSLHEDFHGMTGIDLNRSGTPLLEIVSEPDMRSAAEAIAYAKAIHELVQFIG 180

Query: 179 VSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSG 238
           + D  ++EGS R D N+S+R  G E +GT+ ELKN+NSF +V K + YE  R  + + SG
Sbjct: 181 ICDGNLQEGSFRMDVNVSIRRPG-EPYGTRTELKNINSFKFVEKAIAYEVDRHIDVIESG 239

Query: 239 GEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDE 298
           G I QETR +D    +T  MR KE ++DYRYFP+PD++P+ I D   E VRQ +PELP  
Sbjct: 240 GTIVQETRLYDADKDETRSMRAKEEANDYRYFPDPDLLPVMISDEDIEAVRQRLPELPAV 299

Query: 299 RKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGAD--VKLTSNWLMGGVNEYLNKNQ 356
            +A++V + GL  YDA++LT +K M+ +FE+ ++   D   KL +NW+ G + + LN+++
Sbjct: 300 LRARFVADYGLSDYDANLLTSSKAMAQYFETMLQTAGDAQAKLCANWMSGELAKSLNRDE 359

Query: 357 VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEA 416
           + +  + ++  +LAG++  I D T+S KIAK+VF  +    G+A Q++E  GL QI+D  
Sbjct: 360 LAIEASPISATDLAGLVVRIVDNTISGKIAKQVFEAMWQGEGSADQVIEAKGLKQITDSG 419

Query: 417 TLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
            + + V+E L  N Q VE YK G+ K  GF VGQ+MK SKGQANP  VN LLKQ+L
Sbjct: 420 AIEQIVDEVLAANSQQVEAYKGGQEKMFGFFVGQVMKLSKGQANPAQVNALLKQKL 475


Lambda     K      H
   0.313    0.133    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: 593
Number of extensions: 28
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: 475
Length of database: 477
Length adjustment: 33
Effective length of query: 442
Effective length of database: 444
Effective search space:   196248
Effective search space used:   196248
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_044410249.1 NA59_RS07220 (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.28704.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.7e-173  561.5   0.0   7.5e-173  561.4   0.0    1.0  1  lcl|NCBI__GCF_000934765.1:WP_044410249.1  NA59_RS07220 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000934765.1:WP_044410249.1  NA59_RS07220 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 !  561.4   0.0  7.5e-173  7.5e-173       3     480 ..       2     475 ..       1     476 [. 0.98

  Alignments for each domain:
  == domain 1  score: 561.4 bits;  conditional E-value: 7.5e-173
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               ++e viGlE+H ql tksK+F+ +s+ +   +pN++ c v+l++PG+lPvlNk+a+++ +  +la+n++
  lcl|NCBI__GCF_000934765.1:WP_044410249.1   2 QWETVIGLEIHAQLATKSKIFSAASTAYGA-EPNSQACLVDLAMPGVLPVLNKRALEMGIAFGLAINAE 69 
                                               7899************************99.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140
                                                v ++svF+RK+YfYpD Pkgyqi+q+dlP++ +G++eie+++++k ig++r hlEeD+gks ++    
  lcl|NCBI__GCF_000934765.1:WP_044410249.1  70 -VPKKSVFARKNYFYPDSPKGYQISQFDLPVVGKGQIEIEVNGEKKIIGVTRAHLEEDAGKSLHEDF-- 135
                                               .667************************************************************944.. PP

                                 TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209
                                               + ++ +D+NRsg+PLlEiV++Pd++sa ea a+ k +++++++++i dg+l+eGs+R+DvNvsir    
  lcl|NCBI__GCF_000934765.1:WP_044410249.1 136 HGMTGIDLNRSGTPLLEIVSEPDMRSAAEAIAYAKAIHELVQFIGICDGNLQEGSFRMDVNVSIRRP-G 203
                                               5899*************************************************************55.5 PP

                                 TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278
                                               e  gtr E+KN+ns+k +ekai yE+ R ++++++g +++qetr +d  k  t s+R Kee++DYRYfp
  lcl|NCBI__GCF_000934765.1:WP_044410249.1 204 EPYGTRTELKNINSFKFVEKAIAYEVDRHIDVIESGGTIVQETRLYDADKDETRSMRAKEEANDYRYFP 272
                                               6789***************************************************************** PP

                                 TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep.. 345
                                               +Pdl p+ i++e ++  v+++lpelP   r+r++ +ygls++da++l+s + ++++fe++ ++++++  
  lcl|NCBI__GCF_000934765.1:WP_044410249.1 273 DPDLLPVMISDEDIEA-VRQRLPELPAVLRARFVADYGLSDYDANLLTSSKAMAQYFETMLQTAGDAqa 340
                                               **************99.**********************************************998877 PP

                                 TIGR00133 346 klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliek 414
                                               kl +nW+  el+++Ln+ ++ ++++ +++++la l+  i +++is+k+ak+++e + + +++++++ie+
  lcl|NCBI__GCF_000934765.1:WP_044410249.1 341 KLCANWMSGELAKSLNRDELAIEASPISATDLAGLVVRIVDNTISGKIAKQVFEAMWQGEGSADQVIEA 409
                                               999****************************************************************** PP

                                 TIGR00133 415 lgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               +gl qi+d  ++ +iv+ev++ n ++ve yk g+ek+++f+vGqvmk +kg+a+p++v++llk++l
  lcl|NCBI__GCF_000934765.1:WP_044410249.1 410 KGLKQITDSGAIEQIVDEVLAANSQQVEAYKGGQEKMFGFFVGQVMKLSKGQANPAQVNALLKQKL 475
                                               ***************************************************************988 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.36
//
[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