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.
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:
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