Alignments for a candidate for metB in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for metB in Shewanella oneidensis MR-1

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate 203140 SO4056 cystathionine gamma-synthase (NCBI ptt file)

Query= SwissProt::P00935
         (386 letters)



>FitnessBrowser__MR1:203140
          Length = 393

 Score =  462 bits (1188), Expect = e-135
 Identities = 235/380 (61%), Positives = 286/380 (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 DQTDNQALAQAIAQQPKMVWIETPSNPLLRVVDIEAIAKASHGVGALVVVDNTFLSPILQ 188

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

Query: 243 RGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSF 302
           RGLRTL  R+   QRNAQ IV+ L   P+V K+Y+P L ++ GH IAA+QQKGFGAMLSF
Sbjct: 249 RGLRTLAVRIREHQRNAQRIVELLSNSPVVSKVYYPGLADHPGHAIAAKQQKGFGAMLSF 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: 14
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 203140 SO4056 (cystathionine gamma-synthase (NCBI ptt file))
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.24411.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.5e-212  691.2   0.0   1.8e-212  690.9   0.0    1.0  1  lcl|FitnessBrowser__MR1:203140  SO4056 cystathionine gamma-synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203140  SO4056 cystathionine gamma-synthase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  690.9   0.0  1.8e-212  1.8e-212       2     382 .]      10     389 ..       9     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 690.9 bits;  conditional E-value: 1.8e-212
                       TIGR02080   2 rkkatiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadavvtssGmsaie 80 
                                     r+ at+avr+G+esd+qygavvpPiylst+y+f+g+++pr++dysrsgnPtr++l +ala+lekGa++vvt++Gm+ai+
  lcl|FitnessBrowser__MR1:203140  10 RQLATLAVRQGIESDTQYGAVVPPIYLSTNYAFDGHKNPREFDYSRSGNPTRSILGDALAKLEKGATGVVTCTGMAAIT 88 
                                     6889*************************************************************************** PP

                       TIGR02080  81 llviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpklvlietPsnPllrvvdiaklc 159
                                     l++ +ll+pddllv+PhdcyGG+yrl+++lakkg++k+++vdq+d++al++a+a++pk+v+ietPsnPllrvvdi++++
  lcl|FitnessBrowser__MR1:203140  89 LVT-TLLGPDDLLVVPHDCYGGSYRLFTNLAKKGQFKLLVVDQTDNQALAQAIAQQPKMVWIETPSNPLLRVVDIEAIA 166
                                     *99.9************************************************************************** PP

                       TIGR02080 160 klakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaGaviakdkqlaeelawwanalGvtgaafdsy 238
                                     k+++ +ga+vvvdntflsPilq+Pl lGad+v+hs+tky+nGhsdv++Gaviakd+q+ e+l+ww+n+lG+tg+afdsy
  lcl|FitnessBrowser__MR1:203140 167 KASHGVGALVVVDNTFLSPILQQPLLLGADIVIHSTTKYINGHSDVVGGAVIAKDPQIGETLHWWSNTLGLTGSAFDSY 245
                                     ******************************************************************************* PP

                       TIGR02080 239 lllrGlrtlaarvreqernakkiveylqkqplvkkvyypglpdhagheiaakqqkGfGallsfelkGgeeevkkflkkl 317
                                     ++lrGlrtla+r+re++rna++ive+l+++p+v+kvyypgl+dh+gh+iaakqqkGfGa+lsfelkGge+ev +fl++l
  lcl|FitnessBrowser__MR1:203140 246 QTLRGLRTLAVRIREHQRNAQRIVELLSNSPVVSKVYYPGLADHPGHAIAAKQQKGFGAMLSFELKGGEAEVVAFLDAL 324
                                     ******************************************************************************* PP

                       TIGR02080 318 klftlaeslGGvesliahpatmthaamekeareeaGikdellrlsvGledaddliadleqalaav 382
                                     +lf++aeslGGvesl+a+patmth+ame++ar+eaGikd+llrlsvG+edaddl+ad++++laav
  lcl|FitnessBrowser__MR1:203140 325 SLFSVAESLGGVESLVAVPATMTHRAMEPQARFEAGIKDTLLRLSVGIEDADDLVADIQAGLAAV 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.44
//
[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