Alignments for a candidate for gatB in Calditerrivibrio nitroreducens DSM 19672

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Calditerrivibrio nitroreducens DSM 19672

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_013451171.1 CALNI_RS05245 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B

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



>NCBI__GCF_000183405.1:WP_013451171.1
          Length = 478

 Score =  483 bits (1242), Expect = e-141
 Identities = 245/473 (51%), Positives = 333/473 (70%), Gaps = 4/473 (0%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M FE VIGLEVHV+L T +KIF S PT FG E NT    + LG PGVLPVLN++ VE+ +
Sbjct: 1   MKFEPVIGLEVHVQLNTNTKIFCSCPTTFGEEPNTNVCPVCLGMPGVLPVLNEKVVEYTV 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120
           KA +ALNC+I   + F RKNYFYPD PK YQISQF+ PI  +G+++I+     KRIGITR
Sbjct: 61  KAGLALNCKIQQKSVFARKNYFYPDLPKNYQISQFELPICLDGFVDIDTENGVKRIGITR 120

Query: 121 LHLEEDAGKLTHTGD----GYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQ 176
           +H+EEDAGKL H  +      S VD+NR GTPL+EIVSEPD+R+ EEA AYLEKLK I++
Sbjct: 121 IHMEEDAGKLIHGENLGNPNSSYVDYNRTGTPLMEIVSEPDMRSSEEAKAYLEKLKLILE 180

Query: 177 YTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVL 236
           YTGVSDC ME+GSLRCDAN+S+RPIGQ+EFGTK E+KN+NSF  VQK +++E +RQ   +
Sbjct: 181 YTGVSDCSMEKGSLRCDANVSVRPIGQKEFGTKVEIKNMNSFKNVQKAIDYEIRRQISEI 240

Query: 237 LSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPEL 296
            SG  I QETR +D     TI MR KE S DYRYFP+PDLV + +  +  + +K ++PE+
Sbjct: 241 ESGNIIVQETRLWDPEKGITISMRSKEESHDYRYFPDPDLVPVVVTKDMIDSIKKTLPEM 300

Query: 297 PDERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAE 356
           PD+   + I +     YDA VL  +KE++DFF ET +     K  SNW+  E+   +N +
Sbjct: 301 PDKVLAKLISDYNLPEYDASVLVSSKELSDFFFETSKLTKNYKAISNWIQTEIMRVMNEK 360

Query: 357 QKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDE 416
              + +V ++P  L+ +I L+++  IS KIAK +F +++++     ++VKEKGLVQI+DE
Sbjct: 361 DCLINEVGISPAHLSELITLVDENVISLKIAKSLFDDILKEKRSPRELVKEKGLVQIADE 420

Query: 417 GVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKIL 469
           G L ++V + L    + +E +KNG+ + IGF VGQIMK +KG+ANP +VN++L
Sbjct: 421 GALEEVVKKVLSACSKEVERYKNGETKLIGFFVGQIMKETKGKANPKIVNELL 473


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: 665
Number of extensions: 23
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: 476
Length of database: 478
Length adjustment: 33
Effective length of query: 443
Effective length of database: 445
Effective search space:   197135
Effective search space used:   197135
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_013451171.1 CALNI_RS05245 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
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.9676.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-192  626.4   3.3   1.6e-192  626.2   3.3    1.0  1  lcl|NCBI__GCF_000183405.1:WP_013451171.1  CALNI_RS05245 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183405.1:WP_013451171.1  CALNI_RS05245 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  626.2   3.3  1.6e-192  1.6e-192       2     480 ..       1     477 [.       1     478 [] 0.99

  Alignments for each domain:
  == domain 1  score: 626.2 bits;  conditional E-value: 1.6e-192
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +++e viGlEvHvqlnt++K+Fc+c++ + e +pNtnvcpvclg+PG+lPvlN+++v+  +k +laln+
  lcl|NCBI__GCF_000183405.1:WP_013451171.1   1 MKFEPVIGLEVHVQLNTNTKIFCSCPTTFGE-EPNTNVCPVCLGMPGVLPVLNEKVVEYTVKAGLALNC 68 
                                               57999**************************.************************************* PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesd 139
                                               k ++++svF+RK+YfYpDlPk+yqi+q++lPi+ dG ++i++e++ k+igi+r+h+EeD+gk+ + e+ 
  lcl|NCBI__GCF_000183405.1:WP_013451171.1  69 K-IQQKSVFARKNYFYPDLPKNYQISQFELPICLDGFVDIDTENGVKRIGITRIHMEEDAGKLIHGENL 136
                                               *.557************************************************************8775 PP

                                 TIGR00133 140 k.dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk 207
                                                 ++ s+vD+NR+g+PL+EiV++Pd++s++ea+a+l+kl+ il+y+++sd+ +e+Gs+R+D+Nvs+r+ 
  lcl|NCBI__GCF_000183405.1:WP_013451171.1 137 GnPNSSYVDYNRTGTPLMEIVSEPDMRSSEEAKAYLEKLKLILEYTGVSDCSMEKGSLRCDANVSVRPI 205
                                               449****************************************************************** PP

                                 TIGR00133 208 GqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRY 276
                                               Gq+++gt+vEiKN+ns+k+++kai+yEi Rq+ ++++g+ ++qetr +d +k it+s+R+Kees+DYRY
  lcl|NCBI__GCF_000183405.1:WP_013451171.1 206 GQKEFGTKVEIKNMNSFKNVQKAIDYEIRRQISEIESGNIIVQETRLWDPEKGITISMRSKEESHDYRY 274
                                               ********************************************************************* PP

                                 TIGR00133 277 fpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep 345
                                               fp+Pdl+p++++++++++ ++++lpe+P++  ++l ++y+l e+da vlvs +el d f e +kl+k+ 
  lcl|NCBI__GCF_000183405.1:WP_013451171.1 275 FPDPDLVPVVVTKDMIDS-IKKTLPEMPDKVLAKLISDYNLPEYDASVLVSSKELSDFFFETSKLTKNY 342
                                               *****************9.9************************************************* PP

                                 TIGR00133 346 klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliek 414
                                               k+  nWi +e+++++n+k++ ++e+ ++p +l eli l++e++is k+ak+l++ +l++k++p++l+++
  lcl|NCBI__GCF_000183405.1:WP_013451171.1 343 KAISNWIQTEIMRVMNEKDCLINEVGISPAHLSELITLVDENVISLKIAKSLFDDILKEKRSPRELVKE 411
                                               ********************************************************************* PP

                                 TIGR00133 415 lgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               +gl+qi de +l ++v++v++   keve+yk+g  k+++f+vGq+mk+tkg+a+pk v++ll +ll
  lcl|NCBI__GCF_000183405.1:WP_013451171.1 412 KGLVQIADEGALEEVVKKVLSACSKEVERYKNGETKLIGFFVGQIMKETKGKANPKIVNELLTKLL 477
                                               **************************************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (478 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.22
//
[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