Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Echvi_1734 Echvi_1734 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__Cola:Echvi_1734 Length = 369 Score = 232 bits (591), Expect = 1e-65 Identities = 142/379 (37%), Positives = 204/379 (53%), Gaps = 33/379 (8%) Query: 6 ETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLE 65 ET G + V PI LST + H Y R++NP R +E+ +A LE Sbjct: 4 ETLAIHGGEKKSAPHRAVVQPITLSTTFEHH----EESLIYSRSQNPNRMALEELLAQLE 59 Query: 66 NGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWK-KYGLTFHYDDFS 124 G+ AFSSG AA + G ++ SD+Y G + +K K +TF D S Sbjct: 60 KGSAAAAFSSGNAAGMAVFQALPLGSHIVAPSDMYHGLKKQLVELFKDKLEVTF--TDLS 117 Query: 125 DEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPL 184 D + L I PNTK +++ETP+NP+++ +DI + ++ KE + ++ DNTF TPV Q PL Sbjct: 118 DPENLEKAIQPNTKLLWIETPSNPMLKISDIRRLTKMAKEDDIRVVCDNTFATPVFQNPL 177 Query: 185 ELGADIVIHSATKYLGGHNDLLAG-LVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRG 243 ELGAD+V+HSATKY GGH+D+L G L+ K + +++ Q GAVL PFD +LL+R Sbjct: 178 ELGADLVMHSATKYFGGHSDILGGALITKKSDEFWKQIVNVQQTGGAVLSPFDCYLLVRS 237 Query: 244 MKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRL 287 +KTL+ RMR H +A +A FL++ ++ V YPG GG+LSF + Sbjct: 238 IKTLAYRMRGHAEHAGMIATFLDQHPKVERVFYPGLTAHPGHDVAKSQMTGFGGILSFLV 297 Query: 288 Q-KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSV 346 + K E + + +LK A SLGGVES I A D L+R SV Sbjct: 298 KGKPEDADKLISSLKYYTNATSLGGVESLIERRAAVEGPDTKTP--------QNLIRLSV 349 Query: 347 GIEHAEDLKEDLKQALCQV 365 G+EH +DL ED+++A + Sbjct: 350 GLEHLDDLLEDMEKAFYSI 368 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: 394 Number of extensions: 27 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: 369 Length adjustment: 30 Effective length of query: 343 Effective length of database: 339 Effective search space: 116277 Effective search space used: 116277 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: 49 (23.5 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