Alignments for a candidate for gatB in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Cupriavidus basilensis 4G11

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate RR42_RS00605 RR42_RS00605 glutamyl-tRNA amidotransferase

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__Cup4G11:RR42_RS00605
          Length = 486

 Score =  443 bits (1140), Expect = e-129
 Identities = 232/484 (47%), Positives = 325/484 (67%), Gaps = 12/484 (2%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +E VIGLE H +L T SK+FS +   FGA PN+  + +DLA PGVLPV+N+ AV+ A+
Sbjct: 1   MQWEVVIGLETHTQLSTASKIFSGTSTAFGAAPNTQASPVDLALPGVLPVLNRGAVERAI 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGET-----KR 115
           +  +A+   IA  S F RKNYFYPD PK YQISQ++ P+ + G I I+V+G+      K 
Sbjct: 61  QFGLAIGATIAPRSIFARKNYFYPDLPKGYQISQYELPVVQGGSISIQVEGKKGETYEKT 120

Query: 116 IGITRLHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSI 173
           + +TR H+EEDAGKS H+    +  +DLNR GTPL+EIV+EPD+RS  EA AY + L ++
Sbjct: 121 VQLTRAHLEEDAGKSLHEDFAGMTGIDLNRAGTPLLEIVTEPDMRSSAEAVAYAKALHAL 180

Query: 174 IQYTGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEE 233
           + + G+ D  M+EGS RCDAN+S+RPYG  K GT+ E+KNLNSF ++++ ++YE + Q  
Sbjct: 181 VMWLGICDGNMQEGSFRCDANVSVRPYGSPKLGTRREIKNLNSFRFLQQAIDYEVQWQIA 240

Query: 234 ELLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIP 293
           E+  G EI Q T  FD  TG+T  MR KE + DYRYFP+PD++PL ID AW ERV+  +P
Sbjct: 241 EIEDGREIQQATVLFDPDTGETRAMRTKEDAHDYRYFPDPDLLPLEIDAAWIERVKSALP 300

Query: 294 ELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHG--ADVKLTSNWLMGGVNEY 351
           ELP   +A+ V++ GL AYDA VLT +K ++++FE+ +     A+ K  +NWLMG V+  
Sbjct: 301 ELPVAMQARLVSQYGLSAYDASVLTASKSLANYFEAVVAEAGTANAKPAANWLMGDVSSL 360

Query: 352 LNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKK-VFPELAA--KGGNAKQIMEDNG 408
           LN+  + L    + P  LA ++  I DGT+S+  AKK VFP + A   G +A  I+   G
Sbjct: 361 LNREGIALEAAPVKPAQLAKLLVRIADGTVSNNTAKKDVFPAMWAGEAGADADAIIAAKG 420

Query: 409 LVQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLL 468
           L Q+SD   L K +++ L  N +SVE+++ GK KA   LVGQ MKA+KG+ NP  VN+LL
Sbjct: 421 LKQMSDSGELEKIIDDVLAANAKSVEEFRAGKEKAFNALVGQAMKATKGKGNPAQVNELL 480

Query: 469 KQEL 472
           K++L
Sbjct: 481 KRKL 484


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: 577
Number of extensions: 22
Number of successful extensions: 5
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: 486
Length adjustment: 34
Effective length of query: 441
Effective length of database: 452
Effective search space:   199332
Effective search space used:   199332
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 RR42_RS00605 RR42_RS00605 (glutamyl-tRNA amidotransferase)
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.32209.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-167  541.7   0.0   7.6e-167  541.5   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS00605  RR42_RS00605 glutamyl-tRNA amido


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS00605  RR42_RS00605 glutamyl-tRNA amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  541.5   0.0  7.6e-167  7.6e-167       2     480 ..       1     484 [.       1     485 [. 0.97

  Alignments for each domain:
  == domain 1  score: 541.5 bits;  conditional E-value: 7.6e-167
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +++e+viGlE+H+ql t+sK+F+ +s+ +    pNt+ +pv+l+lPG+lPvlN+ av+ A++ +la+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS00605   1 MQWEVVIGLETHTQLSTASKIFSGTSTAFGA-APNTQASPVDLALPGVLPVLNRGAVERAIQFGLAIGA 68 
                                               5789*************************99.9************************************ PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.....keigierlhlEeDtgksq 134
                                                 +++ s+F+RK+YfYpDlPkgyqi+q++lP++++G+++i++e+k+     k+++++r hlEeD+gks 
  lcl|FitnessBrowser__Cup4G11:RR42_RS00605  69 T-IAPRSIFARKNYFYPDLPKGYQISQYELPVVQGGSISIQVEGKKgetyeKTVQLTRAHLEEDAGKSL 136
                                               *.668**************************************99999999****************** PP

                                 TIGR00133 135 ykesdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvs 203
                                               ++    + ++ +D+NR+g+PLlEiVt+Pd++s+ ea+a+ k l++++ +l+i dg+++eGs+R+D+Nvs
  lcl|FitnessBrowser__Cup4G11:RR42_RS00605 137 HED--FAGMTGIDLNRAGTPLLEIVTEPDMRSSAEAVAYAKALHALVMWLGICDGNMQEGSFRCDANVS 203
                                               *94..4789************************************************************ PP

                                 TIGR00133 204 irlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeese 272
                                               +r+ G+ k gtr EiKNlns++ +++ai+yE++ q++++++g+e++q+t  fd  +  t ++R Ke+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS00605 204 VRPYGSPKLGTRREIKNLNSFRFLQQAIDYEVQWQIAEIEDGREIQQATVLFDPDTGETRAMRTKEDAH 272
                                               ********************************************************************* PP

                                 TIGR00133 273 DYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvkl 341
                                               DYRYfp+Pdl p+eid  ++++ v+  lpelP a+++rl+++ygls++da vl++ ++l+++fe vv  
  lcl|FitnessBrowser__Cup4G11:RR42_RS00605 273 DYRYFPDPDLLPLEIDAAWIER-VKSALPELPVAMQARLVSQYGLSAYDASVLTASKSLANYFEAVVAE 340
                                               *********************9.*******************************************998 PP

                                 TIGR00133 342 ikep..klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksak.elleellen..k 405
                                               ++++  k a+nW++ ++ + Ln++ i l++a +kp +la+l+  i +g++s+ +ak +++  +     +
  lcl|FitnessBrowser__Cup4G11:RR42_RS00605 341 AGTAnaKPAANWLMGDVSSLLNREGIALEAAPVKPAQLAKLLVRIADGTVSNNTAKkDVFPAMWAGeaG 409
                                               87665699*******************************************998862588888755669 PP

                                 TIGR00133 406 kdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevek 474
                                                d++++i ++gl q+sd  el ki+++v++ n+k+ve++++gkeka++ lvGq+mk tkg+ +p++v++
  lcl|FitnessBrowser__Cup4G11:RR42_RS00605 410 ADADAIIAAKGLKQMSDSGELEKIIDDVLAANAKSVEEFRAGKEKAFNALVGQAMKATKGKGNPAQVNE 478
                                               9******************************************************************** PP

                                 TIGR00133 475 llkell 480
                                               llk +l
  lcl|FitnessBrowser__Cup4G11:RR42_RS00605 479 LLKRKL 484
                                               ***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (486 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: 7.44
//
[ok]

This GapMind analysis is from Apr 09 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