Alignments for a candidate for gatB in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Pseudomonas fluorescens FW300-N2E3

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate AO353_05265 AO353_05265 glutamyl-tRNA amidotransferase

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05265
          Length = 481

 Score =  459 bits (1180), Expect = e-133
 Identities = 226/480 (47%), Positives = 328/480 (68%), Gaps = 7/480 (1%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +E VIGLE+H +L T SK+FS S   FG+EPN+  +++DL  PGVLPV+N+ AV  A+
Sbjct: 1   MQWEVVIGLEIHTQLATQSKIFSGSATTFGSEPNTQASLVDLGMPGVLPVLNQEAVRMAV 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
              +A++ EI   + F RKNYFYPD PK YQISQ + PI   G++DI + DG  KR+GIT
Sbjct: 61  MFGLAIDAEIGQHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIPLEDGTVKRVGIT 120

Query: 120 RLHMEEDAGKSTHK--GEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYT 177
           R H+EEDAGKS H+     + +DLNR GTPL+EIVSEPD+RS KEA AY++ + ++++Y 
Sbjct: 121 RAHLEEDAGKSLHEEFNGATGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKAIHALVRYL 180

Query: 178 GVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLS 237
           G+ D  M EGSLRCD N+S+RP GQ +FGT+ E+KN+NSF ++ K +  E +RQ E +  
Sbjct: 181 GICDGNMAEGSLRCDCNVSIRPKGQVEFGTRCEIKNVNSFRFIEKAINTEVRRQIELIED 240

Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297
           GG++ Q+TR +D +  +T  MR KE ++DYRYFP+PD++P+ I+D++   +R T+PELP 
Sbjct: 241 GGKVIQQTRLYDPNKDETRAMRSKEEANDYRYFPDPDLLPVVIEDSFLNDIRATLPELPP 300

Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQV 357
           +++ ++  + GL  YDA VL  ++E +D+FE  +    D KL +NW+M  +   LNK  +
Sbjct: 301 QKRERFQEQFGLSVYDASVLASSREQADYFEKVVSIAGDAKLAANWVMVELGSLLNKQGL 360

Query: 358 ELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEAT 417
           E+ +  ++ E L GM+  I+D T+S KIAK VF  +A   G+A +I++  GL Q++D   
Sbjct: 361 EIDEAPVSAEQLGGMLLRIKDNTISGKIAKTVFEAMANGEGSADEIIDKRGLKQVTDSGA 420

Query: 418 LLKFVNEALDNNEQSVEDYKNG----KGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473
           +   ++E L  N + VE Y+      +GK  GF VGQ MKASKG+ANPQ VN+LLK +L+
Sbjct: 421 ISAVLDEMLAANAEQVEQYRAADEAKRGKMFGFFVGQAMKASKGKANPQQVNELLKSKLE 480


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: 636
Number of extensions: 21
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: 481
Length adjustment: 34
Effective length of query: 441
Effective length of database: 447
Effective search space:   197127
Effective search space used:   197127
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 AO353_05265 AO353_05265 (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.3683951.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.5e-174  565.4   0.0     5e-174  565.2   0.0    1.0  1  FitnessBrowser__pseudo3_N2E3:AO353_05265  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo3_N2E3:AO353_05265  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.2   0.0    5e-174    5e-174       2     480 ..       1     479 [.       1     480 [. 0.98

  Alignments for each domain:
  == domain 1  score: 565.2 bits;  conditional E-value: 5e-174
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +++e+viGlE+H+ql t+sK+F+ + + + + +pNt+ + v+lg+PG+lPvlN+eav++A++ +la+++
  FitnessBrowser__pseudo3_N2E3:AO353_05265   1 MQWEVVIGLEIHTQLATQSKIFSGSATTFGS-EPNTQASLVDLGMPGVLPVLNQEAVRMAVMFGLAIDA 68 
                                               5789***************************.************************************* PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykes 138
                                               +i  +  vF+RK+YfYpDlPkgyqi+q +lPi+ +G+l+i le++  k++gi+r hlEeD+gks ++e 
  FitnessBrowser__pseudo3_N2E3:AO353_05265  69 EIG-QHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIPLEDGTvKRVGITRAHLEEDAGKSLHEEF 136
                                               *55.79***********************************999878********************77 PP

                                 TIGR00133 139 dkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk 207
                                               +    + +D+NR+g+PLlEiV++Pd++sakea+a++k +++++ryl+i dg++ eGs+R+D+Nvsir+k
  FitnessBrowser__pseudo3_N2E3:AO353_05265 137 N--GATGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKAIHALVRYLGICDGNMAEGSLRCDCNVSIRPK 203
                                               5..7999************************************************************** PP

                                 TIGR00133 208 GqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRY 276
                                               Gq ++gtr EiKN+ns++ iekai+ E+ Rq++l+++g +v q+tr +d +k  t ++R+Kee++DYRY
  FitnessBrowser__pseudo3_N2E3:AO353_05265 204 GQVEFGTRCEIKNVNSFRFIEKAINTEVRRQIELIEDGGKVIQQTRLYDPNKDETRAMRSKEEANDYRY 272
                                               ********************************************************************* PP

                                 TIGR00133 277 fpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep 345
                                               fp+Pdl p++i+++++++ ++++lpelP +kr+r+++++gls +da vl s +e +d+fe+vv+ ++++
  FitnessBrowser__pseudo3_N2E3:AO353_05265 273 FPDPDLLPVVIEDSFLND-IRATLPELPPQKRERFQEQFGLSVYDASVLASSREQADYFEKVVSIAGDA 340
                                               **************9999.************************************************** PP

                                 TIGR00133 346 klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliek 414
                                               kla+nW++ el + Lnk+ +++ ea +++e+l  ++  ik+++is+k+ak+++e + + +++++++i+k
  FitnessBrowser__pseudo3_N2E3:AO353_05265 341 KLAANWVMVELGSLLNKQGLEIDEAPVSAEQLGGMLLRIKDNTISGKIAKTVFEAMANGEGSADEIIDK 409
                                               ********************************************************************* PP

                                 TIGR00133 415 lgliqisdekelvkiveevikenpkevekyk....sgkekalkflvGqvmkktkgradpkevekllkel 479
                                               +gl q++d  ++ ++++e+++ n+++ve+y+    +++ k+++f+vGq+mk +kg+a+p++v++llk +
  FitnessBrowser__pseudo3_N2E3:AO353_05265 410 RGLKQVTDSGAISAVLDEMLAANAEQVEQYRaadeAKRGKMFGFFVGQAMKASKGKANPQQVNELLKSK 478
                                               ******************************9888778899***************************98 PP

                                 TIGR00133 480 l 480
                                               l
  FitnessBrowser__pseudo3_N2E3:AO353_05265 479 L 479
                                               8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (481 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 32.02
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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