Alignments for a candidate for gatB in Sulfurihydrogenibium subterraneum DSM 15120

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Sulfurihydrogenibium subterraneum DSM 15120

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_028950402.1 Q385_RS0103865 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000619805.1:WP_028950402.1
          Length = 482

 Score =  486 bits (1251), Expect = e-142
 Identities = 239/471 (50%), Positives = 336/471 (71%), Gaps = 1/471 (0%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           F+ VIGLE HV++ T +KMF      +GA PN+N   + LA+PG LPV+NK A+++A++A
Sbjct: 11  FDVVIGLETHVQMNTKTKMFCGCKVEYGAPPNTNICPVCLAHPGSLPVINKTAIEYAVKA 70

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITRLH 122
           A+ALN ++   S   RKNYFYPD PK YQISQ+D+P+  +GYI+I+++ E K+I I RLH
Sbjct: 71  ALALNCKVHNLSIMARKNYFYPDLPKGYQISQYDKPLATDGYIEIKLEDEFKKIRIHRLH 130

Query: 123 MEEDAGKSTHKGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGVSDV 182
           +EEDAGK+ H+G  S VDLNR GTPL+EIV+EPDI S +EA  YLEKLR+I++Y GVS+ 
Sbjct: 131 IEEDAGKTIHEGSKSYVDLNRAGTPLMEIVTEPDISSAEEARKYLEKLRNIMRYIGVSEA 190

Query: 183 KMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGGEIG 242
            ME+G LRCD NISL+P G  + GTK ELKN+NSF ++ K +EYE +RQ + L  G +I 
Sbjct: 191 DMEKGQLRCDVNISLKPKGASQLGTKVELKNINSFRFIVKAIEYEIERQAKLLKKGEKII 250

Query: 243 QETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDERKAK 302
           QETR FD  +GKT  MR KE + DYRYFP+PD++P+ + D+  E +++++PELPD++  +
Sbjct: 251 QETRLFDPDSGKTYTMRTKEEAHDYRYFPDPDLLPIVLKDSQIEEIKKSLPELPDQKYHR 310

Query: 303 YVNELGLPAYDAHVLTLTKEMSDFFESTIEH-GADVKLTSNWLMGGVNEYLNKNQVELLD 361
           Y+    LP YDA VLT  K ++++FE  I+H   + KL SNW++  +   LN+  +E+ +
Sbjct: 311 YIQSFNLPPYDAEVLTSDKNLANYFEEVIKHFSQNPKLVSNWILNELLGRLNEKGIEIEN 370

Query: 362 TKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLLKF 421
           + ++P + A +I LI DGT+S KIAK+VF      G + K I+E+ GL QIS+E  +   
Sbjct: 371 SPISPVSFAELISLIADGTISGKIAKEVFDIAFETGKSPKSIVEEKGLKQISNEDEIRSI 430

Query: 422 VNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
           V   L+ +   VE YK+G  K +GFLVGQIMK +KG+ANPQLVN++LK+EL
Sbjct: 431 VKAVLEKHPAEVEKYKSGNEKILGFLVGQIMKETKGKANPQLVNKILKEEL 481


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: 650
Number of extensions: 19
Number of successful extensions: 2
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: 482
Length adjustment: 34
Effective length of query: 441
Effective length of database: 448
Effective search space:   197568
Effective search space used:   197568
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_028950402.1 Q385_RS0103865 (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.19268.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-198  645.0   4.8   3.6e-198  644.9   4.8    1.0  1  lcl|NCBI__GCF_000619805.1:WP_028950402.1  Q385_RS0103865 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000619805.1:WP_028950402.1  Q385_RS0103865 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 !  644.9   4.8  3.6e-198  3.6e-198       3     480 ..      10     481 ..       8     482 .] 0.98

  Alignments for each domain:
  == domain 1  score: 644.9 bits;  conditional E-value: 3.6e-198
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               e+++viGlE+Hvq+ntk+K+Fc c+ e+   +pNtn+cpvcl+ PG+lPv+Nk a++ A+k alaln+k
  lcl|NCBI__GCF_000619805.1:WP_028950402.1  10 EFDVVIGLETHVQMNTKTKMFCGCKVEYGA-PPNTNICPVCLAHPGSLPVINKTAIEYAVKAALALNCK 77 
                                               89**************************99.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140
                                                v++ s+ +RK+YfYpDlPkgyqi+q+d+P+a+dG++ei+le++ k+i+i+rlh+EeD+gk+ +++s  
  lcl|NCBI__GCF_000619805.1:WP_028950402.1  78 -VHNLSIMARKNYFYPDLPKGYQISQYDKPLATDGYIEIKLEDEFKKIRIHRLHIEEDAGKTIHEGS-- 143
                                               .668*************************************************************77.. PP

                                 TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209
                                                  s+vD+NR+g+PL+EiVt+Pd++sa+ear++l+klr+i+ry+++s++d+e+G +R+DvN+s+++kG 
  lcl|NCBI__GCF_000619805.1:WP_028950402.1 144 --KSYVDLNRAGTPLMEIVTEPDISSAEEARKYLEKLRNIMRYIGVSEADMEKGQLRCDVNISLKPKGA 210
                                               ..59***************************************************************** PP

                                 TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278
                                               ++ gt+vE+KN+ns++ i kaieyEieRq kllkkge++ qetr fd  + +t ++R Kee++DYRYfp
  lcl|NCBI__GCF_000619805.1:WP_028950402.1 211 SQLGTKVELKNINSFRFIVKAIEYEIERQAKLLKKGEKIIQETRLFDPDSGKTYTMRTKEEAHDYRYFP 279
                                               ********************************************************************* PP

                                 TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep.k 346
                                               +Pdl pi++++++++e +++ lpelP++k +r+ + ++l  +da+vl+sd++l+++feev k  +++ k
  lcl|NCBI__GCF_000619805.1:WP_028950402.1 280 DPDLLPIVLKDSQIEE-IKKSLPELPDQKYHRYIQSFNLPPYDAEVLTSDKNLANYFEEVIKHFSQNpK 347
                                               ****************.9*****************************************998766544* PP

                                 TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415
                                               l+ nWil+ellg+Ln+k i+++++ ++p ++aeli li +g+is+k+ake+++  +e++k+pk+++e++
  lcl|NCBI__GCF_000619805.1:WP_028950402.1 348 LVSNWILNELLGRLNEKGIEIENSPISPVSFAELISLIADGTISGKIAKEVFDIAFETGKSPKSIVEEK 416
                                               ********************************************************************* PP

                                 TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               gl qis+e+e+ +iv++v++++p evekyksg ek+l+flvGq+mk+tkg+a+p+ v+k+lke l
  lcl|NCBI__GCF_000619805.1:WP_028950402.1 417 GLKQISNEDEIRSIVKAVLEKHPAEVEKYKSGNEKILGFLVGQIMKETKGKANPQLVNKILKEEL 481
                                               ***************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (482 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: 00:00:00.01
# Mc/sec: 12.29
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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