GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metB in Shewanella sp. ANA-3

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate 7026472 Shewana3_3614 cystathionine gamma-synthase (RefSeq)

Query= SwissProt::P00935
         (386 letters)



>lcl|FitnessBrowser__ANA3:7026472 Shewana3_3614 cystathionine
           gamma-synthase (RefSeq)
          Length = 393

 Score =  458 bits (1179), Expect = e-133
 Identities = 234/380 (61%), Positives = 285/380 (75%), Gaps = 1/380 (0%)

Query: 3   RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALA 62
           R+ AT+AVR G+  D QYG VVPPI+LS+ Y F G   PR  DYSR GNPTR ++  ALA
Sbjct: 10  RQLATLAVRQGIESDTQYGAVVPPIYLSTNYAFDGHKNPREFDYSRSGNPTRSILGDALA 69

Query: 63  ELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFV 122
           +LE GA  V+T TGM+AI LVTT+ L P DLLV PHDCYGGSYRLF +LAK+G +++L V
Sbjct: 70  KLEKGATGVVTCTGMAAITLVTTL-LGPDDLLVVPHDCYGGSYRLFTNLAKKGQFKLLVV 128

Query: 123 DQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQ 182
           DQ D QAL  A+A++PK+V +E+PSNPLLRVVDI  I   +  VGA+ VVDNTFLSP LQ
Sbjct: 129 DQTDAQALEQAIAQQPKMVWIETPSNPLLRVVDIEAIAKASHAVGALVVVDNTFLSPILQ 188

Query: 183 NPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLL 242
            PL LGAD+V+HS TKY+NGHSDVV G VIAKDP +   L WW+N +G+TG AFDSY  L
Sbjct: 189 QPLLLGADIVIHSTTKYINGHSDVVGGAVIAKDPQLGETLHWWSNTLGLTGSAFDSYQTL 248

Query: 243 RGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSF 302
           RGLRTL  R+   Q NAQ IV  L + P+V K+Y+P L ++ GH IAA+QQKGFGAMLSF
Sbjct: 249 RGLRTLAVRIREHQSNAQRIVDVLTSSPVVSKVYYPGLADHPGHAIAAKQQKGFGAMLSF 308

Query: 303 ELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRI 362
           EL G E  +  FL  LSLF++AESLGGVESL++  ATMTH  M P+AR  AGI +TLLR+
Sbjct: 309 ELKGGEAEVVAFLDALSLFSVAESLGGVESLVAVPATMTHRAMEPQARFEAGIKDTLLRL 368

Query: 363 STGIEDGEDLIADLENGFRA 382
           S GIED +DL+AD++ G  A
Sbjct: 369 SVGIEDADDLVADIQAGLAA 388


Lambda     K      H
   0.319    0.136    0.394 

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: 456
Number of extensions: 15
Number of successful extensions: 2
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: 386
Length of database: 393
Length adjustment: 30
Effective length of query: 356
Effective length of database: 363
Effective search space:   129228
Effective search space used:   129228
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 7026472 Shewana3_3614 (cystathionine gamma-synthase (RefSeq))
to HMM TIGR02080 (metB: O-succinylhomoserine (thiol)-lyase (EC 2.5.1.48))

# 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/TIGR02080.hmm
# target sequence database:        /tmp/gapView.25400.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02080  [M=382]
Accession:   TIGR02080
Description: O_succ_thio_ly: O-succinylhomoserine (thiol)-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-211  688.0   0.1   1.6e-211  687.8   0.1    1.0  1  lcl|FitnessBrowser__ANA3:7026472  Shewana3_3614 cystathionine gamm


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026472  Shewana3_3614 cystathionine gamma-synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  687.8   0.1  1.6e-211  1.6e-211       2     382 .]      10     389 ..       9     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 687.8 bits;  conditional E-value: 1.6e-211
                         TIGR02080   2 rkkatiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadavvtssGmsa 78 
                                       r+ at+avr+G+esd+qygavvpPiylst+y+f+g+++pr++dysrsgnPtr++l +ala+lekGa++vvt++Gm+a
  lcl|FitnessBrowser__ANA3:7026472  10 RQLATLAVRQGIESDTQYGAVVPPIYLSTNYAFDGHKNPREFDYSRSGNPTRSILGDALAKLEKGATGVVTCTGMAA 86 
                                       6889************************************************************************* PP

                         TIGR02080  79 iellviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpklvlietPsnPllrvvdi 155
                                       i+l++ +ll+pddllv+PhdcyGG+yrl+++lakkg++k+++vdq+d++ale+a+a++pk+v+ietPsnPllrvvdi
  lcl|FitnessBrowser__ANA3:7026472  87 ITLVT-TLLGPDDLLVVPHDCYGGSYRLFTNLAKKGQFKLLVVDQTDAQALEQAIAQQPKMVWIETPSNPLLRVVDI 162
                                       ***99.9********************************************************************** PP

                         TIGR02080 156 aklcklakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaGaviakdkqlaeelawwanalGvtg 232
                                       ++++k+++a+ga+vvvdntflsPilq+Pl lGad+v+hs+tky+nGhsdv++Gaviakd+ql e+l+ww+n+lG+tg
  lcl|FitnessBrowser__ANA3:7026472 163 EAIAKASHAVGALVVVDNTFLSPILQQPLLLGADIVIHSTTKYINGHSDVVGGAVIAKDPQLGETLHWWSNTLGLTG 239
                                       ***************************************************************************** PP

                         TIGR02080 233 aafdsylllrGlrtlaarvreqernakkiveylqkqplvkkvyypglpdhagheiaakqqkGfGallsfelkGgeee 309
                                       +afdsy++lrGlrtla+r+re++ na++iv+ l+++p+v+kvyypgl+dh+gh+iaakqqkGfGa+lsfelkGge+e
  lcl|FitnessBrowser__ANA3:7026472 240 SAFDSYQTLRGLRTLAVRIREHQSNAQRIVDVLTSSPVVSKVYYPGLADHPGHAIAAKQQKGFGAMLSFELKGGEAE 316
                                       ***************************************************************************** PP

                         TIGR02080 310 vkkflkklklftlaeslGGvesliahpatmthaamekeareeaGikdellrlsvGledaddliadleqalaav 382
                                       v +fl++l+lf++aeslGGvesl+a+patmth+ame++ar+eaGikd+llrlsvG+edaddl+ad++++laav
  lcl|FitnessBrowser__ANA3:7026472 317 VVAFLDALSLFSVAESLGGVESLVAVPATMTHRAMEPQARFEAGIKDTLLRLSVGIEDADDLVADIQAGLAAV 389
                                       **********************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (382 nodes)
Target sequences:                          1  (393 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: 00:00:00.02
# Mc/sec: 7.10
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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