GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B 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.aa/TIGR03246.hmm
# target sequence database:        /tmp/gapView.6605.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.06
//
[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:

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:

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:

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:

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