Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate AO353_23295 AO353_23295 cystathionine beta-lyase
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23295 Length = 392 Score = 306 bits (785), Expect = 5e-88 Identities = 166/392 (42%), Positives = 240/392 (61%), Gaps = 27/392 (6%) Query: 1 MSQHVE--------TKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNP 52 MSQH E T++ G D TG + PIY ++ Y + G GFDY R+ NP Sbjct: 1 MSQHDENATPRAFATRVIHAGQTPDPTTGALMPPIYANSTYLQQSPGVHKGFDYGRSHNP 60 Query: 53 TRQLVEDAIANLENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWK 112 TR +E +A+LE G + AF+SG+AAI T++ L +G ++ +DLYGGT+RLF+ + Sbjct: 61 TRFALERCVADLEGGTQAFAFASGLAAISTVLELLDTGSHIVSGNDLYGGTFRLFDKVRR 120 Query: 113 KY-GLTFHYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIV 171 + G F + D +D + + +T+ V+VETP+NPL++ D+ +AR +E G++ + Sbjct: 121 RSAGHRFSFVDLTDLTAFEAALQDDTRMVWVETPSNPLLRITDLAAVARTCRERGIICVA 180 Query: 172 DNTFYTPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVV-KDERLGEEMFQHQNAIGA 230 DNTF +P +QRPLELG DIV+HS TKYL GH+D++ G+ VV ++ L E + QNA+GA Sbjct: 181 DNTFASPRIQRPLELGFDIVLHSTTKYLNGHSDVIGGIAVVGQNAELRERLGFLQNAVGA 240 Query: 231 VLPPFDSWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------- 279 + PFD++L +RG+KTL+LRM +H +NA ELA +L Q +++ V YPG Sbjct: 241 IAGPFDAFLTLRGVKTLALRMERHCSNALELARWLSHQPQVARVYYPGLPSHPQHELAQR 300 Query: 280 -----GGMLSFRLQKE-EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRI 333 GGM+S L + FL++++ AESLGGVES I +PA TH IP E R Sbjct: 301 QMHGFGGMISLDLDTDLAGAKRFLESVQIFALAESLGGVESLIEHPAIMTHASIPAETRA 360 Query: 334 ANGVCNRLLRFSVGIEHAEDLKEDLKQALCQV 365 G+ + L+R SVGIE EDL+ DL QAL Q+ Sbjct: 361 ELGIGDALIRLSVGIEDVEDLRADLAQALAQI 392 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: 373 Number of extensions: 19 Number of successful extensions: 4 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: 392 Length adjustment: 30 Effective length of query: 343 Effective length of database: 362 Effective search space: 124166 Effective search space used: 124166 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