Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 5208004 Shew_0520 O-succinylhomoserine (thiol)-lyase (RefSeq)
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__PV4:5208004 Length = 388 Score = 293 bits (750), Expect = 5e-84 Identities = 166/378 (43%), Positives = 226/378 (59%), Gaps = 17/378 (4%) Query: 2 SQHVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAI 61 ++ + T + G SD G V PIYLST Y G + FDY R+ NPTR ++ DAI Sbjct: 3 ARKLATAAVRRGIESDTQHGAVVPPIYLSTNYSFEGHQQPRAFDYSRSGNPTRSILGDAI 62 Query: 62 ANLENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYD 121 A LE GA G+ +GMAAI + +L D L+V D YGG+YRLF N KK Sbjct: 63 AELEQGATGVVTCTGMAAITLVTSLLGPEDLLVVPHDCYGGSYRLFTNLAKKGAFKLLVV 122 Query: 122 DFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQ 181 D +DE L +T + K V++ETP+NPL++ DIE IA+ + + G ++VDNTF +PVLQ Sbjct: 123 DQTDERALEQALTQSPKMVWLETPSNPLLRVVDIEAIAQASHKVGAQVVVDNTFLSPVLQ 182 Query: 182 RPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLM 241 +PL+LGADIV+HS TKY+ GH+D++ G VV KD +GE + N +G FDS+L + Sbjct: 183 QPLQLGADIVVHSTTKYINGHSDVVGGAVVAKDPEVGELLHWWSNTLGLTGSAFDSYLTL 242 Query: 242 RGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSF 285 RG++TL++R+R+HQANAQ++ A L + + + V YPG G MLSF Sbjct: 243 RGLRTLAVRIREHQANAQKVLALLCDHKAVEKVYYPGLAEHPGHEIAARQQKGFGAMLSF 302 Query: 286 RLQ-KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRF 344 L+ E + FL AL+ AESLGGVES + PAT TH + + R GV + L+R Sbjct: 303 ELKGGESALVAFLDALQYFSVAESLGGVESLVAVPATMTHRAMDPDARREAGVKDTLIRL 362 Query: 345 SVGIEHAEDLKEDLKQAL 362 SVGIE EDL D+ L Sbjct: 363 SVGIEDGEDLVADILAGL 380 Lambda K H 0.319 0.135 0.392 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: 353 Number of extensions: 13 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: 373 Length of database: 388 Length adjustment: 30 Effective length of query: 343 Effective length of database: 358 Effective search space: 122794 Effective search space used: 122794 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)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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