Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 6937867 Sama_2008 cystathionine beta-lyase (RefSeq)
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__SB2B:6937867 Length = 401 Score = 171 bits (434), Expect = 2e-47 Identities = 120/391 (30%), Positives = 191/391 (48%), Gaps = 37/391 (9%) Query: 7 TKLAQIGNRSDEVTGTVSAPIYLSTAY--------RHRGIGESTG-FDYVRTKNPTRQLV 57 TK+ +G G ++ P++ ++ RH + G Y R PT Sbjct: 10 TKIVSLGREKKYSKGVINPPVFRASTIVFDTMEEMRHAAKNKHNGEMFYGRRGTPTHFGF 69 Query: 58 EDAIANLENGARGLAFSSGMAAIQ-TIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGL 116 + AIA LE GA + SG AAI +++A ++GD L++ +Y T L + K YG+ Sbjct: 70 QAAIAELEGGAGTALYPSGAAAISASLLAFLQAGDHLLMVDSVYEPTRDLCDKVLKGYGI 129 Query: 117 TFHYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFY 176 Y D + + I PNT+ +FVE+P + M+ D+ +ARI EHGL++I+DNT+ Sbjct: 130 ETTYYDPLIGAGIEALIRPNTRVLFVESPGSITMEVQDVPTLARIAHEHGLVVILDNTWA 189 Query: 177 TPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFD 236 +P+ RP ELG D+ I +ATKY+ GH+D++ G + +++ +H +G P D Sbjct: 190 SPINSRPFELGVDVSIQAATKYIVGHSDVMMGTATASPQ-YWDKLREHSYLLGQTTSPDD 248 Query: 237 SWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYP----------------GKG 280 +L RG++TL +RM QH+ NA +A +L+ + E+ + +P G Sbjct: 249 VYLAARGLRTLGVRMAQHEKNALAVANWLKTRPEVDHLRHPAFEECPGHEFFKRDFSGSN 308 Query: 281 GMLSFRLQK--EEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIAN--G 336 G+ SF L++ + V ++ + S GG ES I T H IR A Sbjct: 309 GLFSFVLKRGTVDAVTAMVEGMSHFKMGFSWGGFESLI-LGVTGIH-----NIRSATRWD 362 Query: 337 VCNRLLRFSVGIEHAEDLKEDLKQALCQVKE 367 L+R +G+E EDL EDL + E Sbjct: 363 SSKPLIRVHIGLEDPEDLIEDLSAGFVRFNE 393 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: 349 Number of extensions: 17 Number of successful extensions: 5 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: 401 Length adjustment: 30 Effective length of query: 343 Effective length of database: 371 Effective search space: 127253 Effective search space used: 127253 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