Alignments for a candidate for gatB in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Pseudomonas putida KT2440

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate PP_0930 PP_0930 Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__Putida:PP_0930
          Length = 481

 Score =  460 bits (1183), Expect = e-134
 Identities = 231/480 (48%), 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   MQWEVVIGLEIHTQLATQSKIFSGSATTFGSEPNTQASLVDLGMPGVLPVLNEQAVRMAC 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
              +A++ EI   + F RKNYFYPD PK YQISQ D PI   G++DI + DG  KRIG+T
Sbjct: 61  MFGLAIDAEIGKRNVFARKNYFYPDLPKGYQISQMDLPIVGKGHLDIALEDGTIKRIGVT 120

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

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

Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297
           GG++ QETR +D +  +T  MR KE ++DYRYFP+PD++P+ I+D++ E +R  +PELP 
Sbjct: 241 GGKVVQETRLYDPNKDETRSMRSKEEANDYRYFPDPDLLPVVIEDSFLETIRAGLPELPP 300

Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQV 357
           ++  ++  + GL AYDA+VL  ++E +D+FE  ++ G D KL +NW+M  +   LNK  V
Sbjct: 301 QKVERFQTQYGLSAYDANVLASSREQADYFEEVVKIGGDAKLAANWVMVELGSLLNKLGV 360

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

Query: 418 LLKFVNEALDNNEQSVEDYKNG----KGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473
           + K ++E L  N + VE Y+      +GK  GF VGQ MKASKG+ANP  VNQLLK +L+
Sbjct: 421 IDKMLDEMLAANAEQVEQYRAADEAKRGKMFGFFVGQAMKASKGKANPGQVNQLLKAKLE 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: 641
Number of extensions: 28
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 PP_0930 PP_0930 (Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase 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.26307.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-173  562.1   0.0   5.1e-173  561.9   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0930  PP_0930 Aspartyl/glutamyl-tRNA(A


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0930  PP_0930 Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  561.9   0.0  5.1e-173  5.1e-173       2     480 ..       1     479 [.       1     480 [. 0.98

  Alignments for each domain:
  == domain 1  score: 561.9 bits;  conditional E-value: 5.1e-173
                           TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsev 76 
                                         +++e+viGlE+H+ql t+sK+F+ + + + + +pNt+ + v+lg+PG+lPvlN++av++A + +la++++i  + 
  lcl|FitnessBrowser__Putida:PP_0930   1 MQWEVVIGLEIHTQLATQSKIFSGSATTFGS-EPNTQASLVDLGMPGVLPVLNEQAVRMACMFGLAIDAEIG-KR 73 
                                         5789***************************.**************************************55.69 PP

                           TIGR00133  77 svFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvDfNR 150
                                          vF+RK+YfYpDlPkgyqi+q dlPi+ +G+l+i le++  k+ig++r hlEeD+gks ++    +  + +D+NR
  lcl|FitnessBrowser__Putida:PP_0930  74 NVFARKNYFYPDLPKGYQISQMDLPIVGKGHLDIALEDGTiKRIGVTRAHLEEDAGKSLHEDF--SGSTGIDLNR 146
                                         9***********************************99888*******************954..67999***** PP

                           TIGR00133 151 sgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNlnslk 225
                                         +g+PLlEiV++Pd++sakea+a++k +++++ryl+i dg++ eGs+R+D+Nvsir+kGq+++gtr EiKN+ns++
  lcl|FitnessBrowser__Putida:PP_0930 147 AGTPLLEIVSEPDMRSAKEAVAYVKAIHALVRYLGICDGNMAEGSLRCDCNVSIRPKGQTEFGTRCEIKNVNSFR 221
                                         *************************************************************************** PP

                           TIGR00133 226 siekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekveekl 300
                                          ie+ai+ Ei+Rq++l+++g +v+qetr +d +k  t s+R+Kee++DYRYfp+Pdl p++i+++++++ +++ l
  lcl|FitnessBrowser__Putida:PP_0930 222 FIERAINSEIQRQIDLIEDGGKVVQETRLYDPNKDETRSMRSKEEANDYRYFPDPDLLPVVIEDSFLET-IRAGL 295
                                         *****************************************************************9988.***** PP

                           TIGR00133 301 pelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaeallkpe 375
                                         pelP +k +r++++ygls++da+vl s +e +d+feevvk  +++kla+nW++ el + Lnk  +++ +a +++ 
  lcl|FitnessBrowser__Putida:PP_0930 296 PELPPQKVERFQTQYGLSAYDANVLASSREQADYFEEVVKIGGDAKLAANWVMVELGSLLNKLGVEIDQAPVSAA 370
                                         *************************************************************************** PP

                           TIGR00133 376 elaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenpkevekyk....s 446
                                         +l  ++  i++++is+k+ak+++e +   ++d++++ie +gl q++d+ ++ k+++e+++ n+++ve+y+    +
  lcl|FitnessBrowser__Putida:PP_0930 371 QLGGMLLRIRDNTISGKIAKTVFEAMAAGEGDADSIIESKGLKQVTDTGAIDKMLDEMLAANAEQVEQYRaadeA 445
                                         *********************************************************************988877 PP

                           TIGR00133 447 gkekalkflvGqvmkktkgradpkevekllkell 480
                                         ++ k+++f+vGq+mk +kg+a+p +v++llk +l
  lcl|FitnessBrowser__Putida:PP_0930 446 KRGKMFGFFVGQAMKASKGKANPGQVNQLLKAKL 479
                                         8899***************************988 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.45
//
[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