Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate AZOBR_RS08650 AZOBR_RS08650 cystathionine beta-lyase
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__azobra:AZOBR_RS08650 Length = 392 Score = 159 bits (402), Expect = 1e-43 Identities = 118/390 (30%), Positives = 183/390 (46%), Gaps = 36/390 (9%) Query: 6 ETKLAQIGNRSDEVTGTVSAPIY-----LSTAYRHRGIGESTGFD---YVRTKNPTRQLV 57 +T L G E G V+ P+Y L G+ FD Y R PT Sbjct: 7 DTVLGHAGRSPRENHGIVNPPVYHCSTVLFPTLEDLEAGDHAPFDRINYGRIGTPTTLAF 66 Query: 58 EDAIANLENGARGLAFSSGMAAIQTIMALF-KSGDELIVSSDLYGGTYRLFENEWKKYGL 116 E AI LE R + SG+ AI T + F K+GD ++++ YG T R + YG+ Sbjct: 67 EQAITELEGAYRSVNTGSGLNAIATALFAFTKTGDHVLITDSAYGPTRRFANDTLVPYGV 126 Query: 117 TFHYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFY 176 Y D + + + PNT VF+E+P + + D+ IA K G +++DNT+ Sbjct: 127 EVEYFDPTIGAGITRLLKPNTSVVFLESPGSLTFEVQDVPAIAAAAKTVGATVMIDNTWA 186 Query: 177 TPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFD 236 TP+ +PL G D+ IHSATKY+ GH D + G++ +E + + G P D Sbjct: 187 TPLFFQPLRHGVDVSIHSATKYIVGHADAMLGVISCANEAQWLAVKKAATRTGTCAGPDD 246 Query: 237 SWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPG----------------KG 280 +L +RG++TLS+R++QH+A+A LA +L +Q E++ +L+P Sbjct: 247 IYLGLRGLRTLSVRLKQHEASALALAEWLSKQPEVTRILHPAFPDCPGHELWKRDIGRSS 306 Query: 281 GMLSFRLQ--KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVC 338 G+ S + + ++ L +L+ S GG ES I PA P IR A Sbjct: 307 GLFSIVMNTVPKPALSAMLNSLELFGLGYSWGGFESLI-LPAR------PAAIRTATRWT 359 Query: 339 N--RLLRFSVGIEHAEDLKEDLKQALCQVK 366 + +LR G+E +DL DL A +++ Sbjct: 360 DPGTMLRLHAGLEDVDDLIRDLDGAFARLR 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: 313 Number of extensions: 13 Number of successful extensions: 3 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