Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 7026472 Shewana3_3614 cystathionine gamma-synthase (RefSeq)
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__ANA3:7026472 Length = 393 Score = 288 bits (738), Expect = 1e-82 Identities = 165/380 (43%), Positives = 218/380 (57%), Gaps = 17/380 (4%) Query: 3 QHVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIA 62 + + T + G SD G V PIYLST Y G FDY R+ NPTR ++ DA+A Sbjct: 10 RQLATLAVRQGIESDTQYGAVVPPIYLSTNYAFDGHKNPREFDYSRSGNPTRSILGDALA 69 Query: 63 NLENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDD 122 LE GA G+ +GMAAI + L D L+V D YGG+YRLF N KK D Sbjct: 70 KLEKGATGVVTCTGMAAITLVTTLLGPDDLLVVPHDCYGGSYRLFTNLAKKGQFKLLVVD 129 Query: 123 FSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQR 182 +D L I K V++ETP+NPL++ DIE IA+ + G L++VDNTF +P+LQ+ Sbjct: 130 QTDAQALEQAIAQQPKMVWIETPSNPLLRVVDIEAIAKASHAVGALVVVDNTFLSPILQQ 189 Query: 183 PLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMR 242 PL LGADIVIHS TKY+ GH+D++ G V+ KD +LGE + N +G FDS+ +R Sbjct: 190 PLLLGADIVIHSTTKYINGHSDVVGGAVIAKDPQLGETLHWWSNTLGLTGSAFDSYQTLR 249 Query: 243 GMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFR 286 G++TL++R+R+HQ+NAQ + L +S V YPG G MLSF Sbjct: 250 GLRTLAVRIREHQSNAQRIVDVLTSSPVVSKVYYPGLADHPGHAIAAKQQKGFGAMLSFE 309 Query: 287 LQ-KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFS 345 L+ E V FL AL AESLGGVES + PAT TH + + R G+ + LLR S Sbjct: 310 LKGGEAEVVAFLDALSLFSVAESLGGVESLVAVPATMTHRAMEPQARFEAGIKDTLLRLS 369 Query: 346 VGIEHAEDLKEDLKQALCQV 365 VGIE A+DL D++ L V Sbjct: 370 VGIEDADDLVADIQAGLAAV 389 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: 354 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: 373 Length of database: 393 Length adjustment: 30 Effective length of query: 343 Effective length of database: 363 Effective search space: 124509 Effective search space used: 124509 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