GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metB in Shewanella loihica PV-4

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate 5208004 Shew_0520 O-succinylhomoserine (thiol)-lyase (RefSeq)

Query= SwissProt::P00935
         (386 letters)



>FitnessBrowser__PV4:5208004
          Length = 388

 Score =  461 bits (1186), Expect = e-134
 Identities = 235/381 (61%), Positives = 286/381 (75%), Gaps = 1/381 (0%)

Query: 3   RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALA 62
           RK AT AVR G+  D Q+G VVPPI+LS+ Y+F G  +PRA DYSR GNPTR ++  A+A
Sbjct: 4   RKLATAAVRRGIESDTQHGAVVPPIYLSTNYSFEGHQQPRAFDYSRSGNPTRSILGDAIA 63

Query: 63  ELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFV 122
           ELE GA  V+T TGM+AI LVT++ L P DLLV PHDCYGGSYRLF +LAK+G +++L V
Sbjct: 64  ELEQGATGVVTCTGMAAITLVTSL-LGPEDLLVVPHDCYGGSYRLFTNLAKKGAFKLLVV 122

Query: 123 DQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQ 182
           DQ DE+AL  AL + PK+V +E+PSNPLLRVVDI  I   + +VGA  VVDNTFLSP LQ
Sbjct: 123 DQTDERALEQALTQSPKMVWLETPSNPLLRVVDIEAIAQASHKVGAQVVVDNTFLSPVLQ 182

Query: 183 NPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLL 242
            PL LGAD+V+HS TKY+NGHSDVV G V+AKDP+V   L WW+N +G+TG AFDSYL L
Sbjct: 183 QPLQLGADIVVHSTTKYINGHSDVVGGAVVAKDPEVGELLHWWSNTLGLTGSAFDSYLTL 242

Query: 243 RGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSF 302
           RGLRTL  R+   Q NAQ ++  L     V+K+Y+P L E+ GHEIAARQQKGFGAMLSF
Sbjct: 243 RGLRTLAVRIREHQANAQKVLALLCDHKAVEKVYYPGLAEHPGHEIAARQQKGFGAMLSF 302

Query: 303 ELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRI 362
           EL G E  L  FL  L  F++AESLGGVESL++  ATMTH  M P+AR  AG+ +TL+R+
Sbjct: 303 ELKGGESALVAFLDALQYFSVAESLGGVESLVAVPATMTHRAMDPDARREAGVKDTLIRL 362

Query: 363 STGIEDGEDLIADLENGFRAA 383
           S GIEDGEDL+AD+  G  AA
Sbjct: 363 SVGIEDGEDLVADILAGLEAA 383


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: 431
Number of extensions: 10
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: 388
Length adjustment: 30
Effective length of query: 356
Effective length of database: 358
Effective search space:   127448
Effective search space used:   127448
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 5208004 Shew_0520 (O-succinylhomoserine (thiol)-lyase (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.1526387.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                    -----------
   6.6e-200  649.6   0.0   7.8e-200  649.3   0.0    1.0  1  FitnessBrowser__PV4:5208004  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__PV4:5208004  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  649.3   0.0  7.8e-200  7.8e-200       2     381 ..       4     382 ..       3     383 .. 0.99

  Alignments for each domain:
  == domain 1  score: 649.3 bits;  conditional E-value: 7.8e-200
                    TIGR02080   2 rkkatiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadavvtssGmsaiellv 83 
                                  rk at avr+G+esd+q+gavvpPiylst+y+f+g+++pra+dysrsgnPtr++l +a+aele+Ga++vvt++Gm+ai+l++
  FitnessBrowser__PV4:5208004   4 RKLATAAVRRGIESDTQHGAVVPPIYLSTNYSFEGHQQPRAFDYSRSGNPTRSILGDAIAELEQGATGVVTCTGMAAITLVT 85 
                                  6899****************************************************************************99 PP

                    TIGR02080  84 iallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpklvlietPsnPllrvvdiaklcklakaa 165
                                   +ll+p+dllv+PhdcyGG+yrl+++lakkg +k+++vdq+de+ale+al++ pk+v++etPsnPllrvvdi++++++++++
  FitnessBrowser__PV4:5208004  86 -SLLGPEDLLVVPHDCYGGSYRLFTNLAKKGAFKLLVVDQTDERALEQALTQSPKMVWLETPSNPLLRVVDIEAIAQASHKV 166
                                  .********************************************************************************* PP

                    TIGR02080 166 gavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaGaviakdkqlaeelawwanalGvtgaafdsylllrGlrtl 247
                                  ga vvvdntflsP+lq+Pl+lGad+v+hs+tky+nGhsdv++Gav+akd+++ e l+ww+n+lG+tg+afdsyl+lrGlrtl
  FitnessBrowser__PV4:5208004 167 GAQVVVDNTFLSPVLQQPLQLGADIVVHSTTKYINGHSDVVGGAVVAKDPEVGELLHWWSNTLGLTGSAFDSYLTLRGLRTL 248
                                  ********************************************************************************** PP

                    TIGR02080 248 aarvreqernakkiveylqkqplvkkvyypglpdhagheiaakqqkGfGallsfelkGgeeevkkflkklklftlaeslGGv 329
                                  a+r+re++ na+k++++l ++ +v+kvyypgl++h+gheiaa+qqkGfGa+lsfelkGge+++ +fl++l+ f++aeslGGv
  FitnessBrowser__PV4:5208004 249 AVRIREHQANAQKVLALLCDHKAVEKVYYPGLAEHPGHEIAARQQKGFGAMLSFELKGGESALVAFLDALQYFSVAESLGGV 330
                                  ********************************************************************************** PP

                    TIGR02080 330 esliahpatmthaamekeareeaGikdellrlsvGledaddliadleqalaa 381
                                  esl+a+patmth+am+++ar eaG+kd+l+rlsvG+ed++dl+ad+ ++l+a
  FitnessBrowser__PV4:5208004 331 ESLVAVPATMTHRAMDPDARREAGVKDTLIRLSVGIEDGEDLVADILAGLEA 382
                                  **********************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (382 nodes)
Target sequences:                          1  (388 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: 13.28
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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