Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 6939073 Sama_3171 cystathionine gamma-synthase (RefSeq)
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__SB2B:6939073 Length = 386 Score = 286 bits (732), Expect = 7e-82 Identities = 162/370 (43%), Positives = 220/370 (59%), Gaps = 17/370 (4%) Query: 13 GNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLENGARGLA 72 G SD G V PIYLST Y G FDY R+ NPTR ++ +A+A LE GA G+ Sbjct: 14 GIESDTQHGAVVPPIYLSTNYSFDGHKNPRKFDYSRSGNPTRCILGEALAELEQGATGII 73 Query: 73 FSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSDEDCLRSK 132 +GMAAI + +L D L+V D YGG+YRLF N KK D +D+ L + Sbjct: 74 TCTGMAAITLVTSLLGPDDLLVVPHDCYGGSYRLFTNLAKKGAFKLAVVDQTDDAALAAV 133 Query: 133 ITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLELGADIVI 192 I + V++ETP+NPL++ DI+ I+ + E G L++VDNTF +P+LQ+PL LGADIVI Sbjct: 134 IAQKPRMVWLETPSNPLLRVVDIQAISDASHEVGALVVVDNTFLSPILQQPLLLGADIVI 193 Query: 193 HSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKTLSLRMR 252 HS TKY+ GH+D++ G V+ +D LGE + N +G FDS+L +RG++TL++R+R Sbjct: 194 HSTTKYINGHSDVVGGAVIARDAELGETLHWWSNTLGLTGSAFDSYLTLRGIRTLAVRVR 253 Query: 253 QHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRL-QKEEWVNP 295 +HQ+NAQ + L+ ++S V YPG G MLSF L E+ + Sbjct: 254 EHQSNAQRIVDVLKNSPQVSKVYYPGLADHPGHDIAARQQKGFGAMLSFELVGGEKELVA 313 Query: 296 FLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGIEHAEDLK 355 FL AL+ AESLGGVES + PAT TH + E R G+ + LLR SVGIE AEDL Sbjct: 314 FLDALQHFSVAESLGGVESLVAVPATMTHRAMVPEARAEAGIKDTLLRLSVGIEDAEDLV 373 Query: 356 EDLKQALCQV 365 D++ L V Sbjct: 374 ADIQAGLAAV 383 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: 351 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: 386 Length adjustment: 30 Effective length of query: 343 Effective length of database: 356 Effective search space: 122108 Effective search space used: 122108 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