Alignments for a candidate for astC in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for astC in Pseudomonas simiae WCS417

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF4238 PS417_21710 acetylornithine aminotransferase

Query= reanno::WCS417:GFF4238
         (406 letters)



>FitnessBrowser__WCS417:GFF4238
          Length = 406

 Score =  806 bits (2083), Expect = 0.0
 Identities = 406/406 (100%), Positives = 406/406 (100%)

Query: 1   MSVEQAPVQRADFDQVMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAH 60
           MSVEQAPVQRADFDQVMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAH
Sbjct: 1   MSVEQAPVQRADFDQVMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAH 60

Query: 61  PALVGALTEQAHKLWHVSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLAR 120
           PALVGALTEQAHKLWHVSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLAR
Sbjct: 61  PALVGALTEQAHKLWHVSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLAR 120

Query: 121 RVAFDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALK 180
           RVAFDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALK
Sbjct: 121 RVAFDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALK 180

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFA 240
           AAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFA
Sbjct: 181 AAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFA 240

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           YQHYGVTPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVID
Sbjct: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVID 300

Query: 301 VINTPEVLAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNA 360
           VINTPEVLAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNA
Sbjct: 301 VINTPEVLAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNA 360

Query: 361 AEKENLMILQAGPDVVRFAPSLVVEDADIKEGLDRFERAVKALTQA 406
           AEKENLMILQAGPDVVRFAPSLVVEDADIKEGLDRFERAVKALTQA
Sbjct: 361 AEKENLMILQAGPDVVRFAPSLVVEDADIKEGLDRFERAVKALTQA 406


Lambda     K      H
   0.320    0.137    0.400 

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: 718
Number of extensions: 11
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: 406
Length of database: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate GFF4238 PS417_21710 (acetylornithine aminotransferase)
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

# 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.carbon/TIGR03246.hmm
# target sequence database:        /tmp/gapView.8945.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03246  [M=397]
Accession:   TIGR03246
Description: arg_catab_astC: succinylornithine transaminase family
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.8e-219  714.5   1.5     2e-219  714.3   1.5    1.0  1  lcl|FitnessBrowser__WCS417:GFF4238  PS417_21710 acetylornithine amin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4238  PS417_21710 acetylornithine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.3   1.5    2e-219    2e-219       1     396 [.       8     403 ..       8     404 .. 1.00

  Alignments for each domain:
  == domain 1  score: 714.3 bits;  conditional E-value: 2e-219
                           TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngyt 75 
                                         v+r++fd+vmvp+yapa+fipvrgeGsrvwdq+g+e+idfaGGiavn lGhahp+lv al+eqa+klwh++n++t
  lcl|FitnessBrowser__WCS417:GFF4238   8 VQRADFDQVMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVSNVFT 82 
                                         79************************************************************************* PP

                           TIGR03246  76 nepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqaky 150
                                         nep+lrla+kl+datfa++vffcnsGaeaneaa+klar+va+d++g+ek+ei+a  nsfhGrtlftv vGGq+ky
  lcl|FitnessBrowser__WCS417:GFF4238  83 NEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKY 157
                                         *************************************************************************** PP

                           TIGR03246 151 sedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGv 225
                                         s++f+p+++gi+h++yndl+alka++sdktcav++epiqGegGv+pa+ a+l+g+r+lcd+ nall+fdevqtG+
  lcl|FitnessBrowser__WCS417:GFF4238 158 SDGFGPKITGITHVPYNDLDALKAAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGM 232
                                         *************************************************************************** PP

                           TIGR03246 226 GrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntael 300
                                         Gr G+l+ay++yGvtpdiltsak+lGgGfpi a+ltte+lak+l vGthGttyGGnplacavae+v+d++nt+e+
  lcl|FitnessBrowser__WCS417:GFF4238 233 GRSGHLFAYQHYGVTPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEV 307
                                         *************************************************************************** PP

                           TIGR03246 301 leGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapsl 375
                                         l+Gv+++h+lf ++le+i+++y +f+e+rG+Gll+G+vl+++++Gkakd+ naa++e +++l+aGpdvvrfapsl
  lcl|FitnessBrowser__WCS417:GFF4238 308 LAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAAEKENLMILQAGPDVVRFAPSL 382
                                         *************************************************************************** PP

                           TIGR03246 376 vieeeeikeGlarlekavekl 396
                                         v+e+++ikeGl+r+e+av+ l
  lcl|FitnessBrowser__WCS417:GFF4238 383 VVEDADIKEGLDRFERAVKAL 403
                                         ******************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (406 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.63
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources