Alignments for a candidate for gatB in Chlorobium limicola DSM 245

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Chlorobium limicola DSM 245

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_012467175.1 CLIM_RS11485 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B

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



>NCBI__GCF_000020465.1:WP_012467175.1
          Length = 475

 Score =  454 bits (1167), Expect = e-132
 Identities = 231/470 (49%), Positives = 314/470 (66%), Gaps = 2/470 (0%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M +E V+GLEVH +L T SK F    T FG  ANT    + L  PG LPVLN+  VE A+
Sbjct: 1   MKYELVVGLEVHCQLNTNSKAFCGCSTRFGNPANTNVCPVCLALPGALPVLNRRVVEDAV 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120
           K  +A  C IA  +   RKNYFYPD PK YQISQF++PI   G + I+VG   + I + R
Sbjct: 61  KLGLATGCSIAPSSILARKNYFYPDLPKGYQISQFEEPICTEGMLRIDVGDGCRDIRLIR 120

Query: 121 LHLEEDAGKLTHTGDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGV 180
           +H+EEDAGK  H     + +D NR G PL+EIVS PDIRT  EA AYL+K++ I++Y G+
Sbjct: 121 IHIEEDAGKSIHDIGDDTYIDVNRCGVPLLEIVSYPDIRTSREASAYLQKMRQIVKYLGI 180

Query: 181 SDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGF 240
           SD  MEEGSLRCDAN+S+R  G EE+GT+TE+KN+NSF  V+K +E+E +R   ++  G 
Sbjct: 181 SDGNMEEGSLRCDANVSVRLFGAEEYGTRTEIKNMNSFKNVEKAIEYEMQRHIDIIDGGG 240

Query: 241 FIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDER 300
            I QETR +D    +T  MR KE + DYRYFP+PDLV + +D E  ER++  +PE P++R
Sbjct: 241 TIVQETRLWDADKGETRSMRGKEFAHDYRYFPDPDLVPVLVDQEMLERIRLELPEFPEDR 300

Query: 301 RKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKEL 360
            +R++ E G   YDA VLT+ +E+AD+FE T+    +AK ASNW+MGEV   L  +  ++
Sbjct: 301 ERRFVSEYGIPPYDAGVLTVEREIADYFERTLTVCGDAKAASNWVMGEVMRTLKEKYLDI 360

Query: 361 ADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKG-GDAEKIVKEKGLVQISDEGVL 419
            + A++PE L G+I LI KG IS+ IAK+VF EL++ G   AE+IV  +GL Q+SD G +
Sbjct: 361 KEFAISPERLGGLIGLIGKGAISNTIAKQVF-ELMQTGEASAEEIVDREGLAQVSDTGAI 419

Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKIL 469
            + V E L+ NP+ + D++ GK +  GF VGQ M   KG+ANP +VN +L
Sbjct: 420 ERTVDEILEANPKQLADYREGKTKLFGFFVGQCMARMKGKANPQVVNDVL 469


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: 19
Number of successful extensions: 1
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: 475
Length adjustment: 33
Effective length of query: 443
Effective length of database: 442
Effective search space:   195806
Effective search space used:   195806
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_012467175.1 CLIM_RS11485 (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.9415.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-179  583.8   0.0   1.3e-179  583.7   0.0    1.0  1  lcl|NCBI__GCF_000020465.1:WP_012467175.1  CLIM_RS11485 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020465.1:WP_012467175.1  CLIM_RS11485 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 !  583.7   0.0  1.3e-179  1.3e-179       2     480 ..       1     473 [.       1     474 [. 0.99

  Alignments for each domain:
  == domain 1  score: 583.7 bits;  conditional E-value: 1.3e-179
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               ++yelv+GlEvH+qlnt+sK Fc cs+++ + + Ntnvcpvcl+lPGalPvlN+++v+ A+kl+la+++
  lcl|NCBI__GCF_000020465.1:WP_012467175.1   1 MKYELVVGLEVHCQLNTNSKAFCGCSTRFGN-PANTNVCPVCLALPGALPVLNRRVVEDAVKLGLATGC 68 
                                               68*****************************.99*********************************** PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesd 139
                                                 +++ s+ +RK+YfYpDlPkgyqi+q++ Pi+++G+l+i++ ++ + i++ r+h+EeD+gks +   d
  lcl|NCBI__GCF_000020465.1:WP_012467175.1  69 S-IAPSSILARKNYFYPDLPKGYQISQFEEPICTEGMLRIDVGDGCRDIRLIRIHIEEDAGKSIHDIGD 136
                                               *.668************************************************************9776 PP

                                 TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208
                                                   +++D NR+gvPLlEiV+ Pd++++ ea a+l+k+rqi++yl+isdg++eeGs+R+D+Nvs+rl G
  lcl|NCBI__GCF_000020465.1:WP_012467175.1 137 ---DTYIDVNRCGVPLLEIVSYPDIRTSREASAYLQKMRQIVKYLGISDGNMEEGSLRCDANVSVRLFG 202
                                               ...69**************************************************************** PP

                                 TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277
                                                e+ gtr EiKN+ns+k++ekaieyE++R ++++  g +++qetr +d  k  t s+R Ke ++DYRYf
  lcl|NCBI__GCF_000020465.1:WP_012467175.1 203 AEEYGTRTEIKNMNSFKNVEKAIEYEMQRHIDIIDGGGTIVQETRLWDADKGETRSMRGKEFAHDYRYF 271
                                               ********************************************************************* PP

                                 TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346
                                               p+Pdl+p+ +d+e++++ ++ +lpe+Pe +  r+++eyg+  +da vl+ ++e++d+fe   ++ +++k
  lcl|NCBI__GCF_000020465.1:WP_012467175.1 272 PDPDLVPVLVDQEMLER-IRLELPEFPEDRERRFVSEYGIPPYDAGVLTVEREIADYFERTLTVCGDAK 339
                                               *************9999.*************************************************** PP

                                 TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415
                                               +a nW++ e++++L++k ++++e++++pe l  li li +g is+++ak+++e + + + +++++++++
  lcl|NCBI__GCF_000020465.1:WP_012467175.1 340 AASNWVMGEVMRTLKEKYLDIKEFAISPERLGGLIGLIGKGAISNTIAKQVFELMQTGEASAEEIVDRE 408
                                               ********************************************************************* PP

                                 TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               gl q+sd+ ++ + v+e+++ npk++ +y++gk k+++f+vGq m + kg+a+p+ v+ +lk +l
  lcl|NCBI__GCF_000020465.1:WP_012467175.1 409 GLAQVSDTGAIERTVDEILEANPKQLADYREGKTKLFGFFVGQCMARMKGKANPQVVNDVLKSRL 473
                                               **************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (475 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: 9.76
//
[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