Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_011320837.1 AVA_RS21060 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000204075.1:WP_011320837.1 Length = 378 Score = 348 bits (894), Expect = e-100 Identities = 181/374 (48%), Positives = 244/374 (65%), Gaps = 17/374 (4%) Query: 6 ETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLE 65 ETK G +SD TG V PIYL++ Y+ IG+ G++Y RT NPTR +E+A+A +E Sbjct: 4 ETKAIHEGQQSDPQTGAVIVPIYLTSTYQQEAIGQHKGYEYSRTGNPTRNALEEALAAIE 63 Query: 66 NGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSD 125 NG GLAF+SG+AA T+++L KS D ++ DLYGGTYRL E K +G+T Y D D Sbjct: 64 NGEYGLAFASGLAATTTVLSLLKSCDHIVAGDDLYGGTYRLLERVVKNWGVTTTYVDIDD 123 Query: 126 EDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLE 185 I PNTK ++VETPTNPL++ DI +A I +++ L+L+VDNTF +P QRPL+ Sbjct: 124 ISNFAKAIQPNTKLIWVETPTNPLLKIIDIAALANIAEQNNLILVVDNTFASPYFQRPLD 183 Query: 186 LGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMK 245 GADIV+HS TKYLGGH+D++ G VV +E+L E+ +QNAIGAV PFDSWL++RG+K Sbjct: 184 NGADIVVHSTTKYLGGHSDIIGGAVVTSNEQLYTELKFYQNAIGAVPSPFDSWLVLRGIK 243 Query: 246 TLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRLQK 289 TL++RMR+H+ NA LA FLE+ ++ V YPG GGM+S L+ Sbjct: 244 TLAVRMREHEKNALLLAQFLEQHPKVERVYYPGLPSHEQHQLAKSQMSGFGGMISLELKG 303 Query: 290 E-EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGI 348 + V F L+ AESLGGVES + YPA TH +P+E R G+ + L+R SVGI Sbjct: 304 DFADVEKFASRLQLFLLAESLGGVESLLCYPAKMTHGSLPQEERYKRGINDNLVRLSVGI 363 Query: 349 EHAEDLKEDLKQAL 362 E+ DL+ DL+ AL Sbjct: 364 ENVLDLQADLENAL 377 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: 387 Number of extensions: 16 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: 378 Length adjustment: 30 Effective length of query: 343 Effective length of database: 348 Effective search space: 119364 Effective search space used: 119364 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 10 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