Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012282805.1 HM1_RS07785 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000019165.1:WP_012282805.1 Length = 377 Score = 385 bits (988), Expect = e-111 Identities = 204/375 (54%), Positives = 254/375 (67%), Gaps = 16/375 (4%) Query: 4 HVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIAN 63 H+++ LAQ GN D TG VS PIY S +RH +GESTGFDY R+ NPTRQ++E+ IA Sbjct: 2 HIDSLLAQGGNGKDAGTGAVSFPIYQSATFRHPALGESTGFDYSRSGNPTRQVLEELIAK 61 Query: 64 LENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDF 123 LE G RGLAFSSG+AAI +++LF GD LI+ DLYGGTYRL E ++ +GLT Y + Sbjct: 62 LEGGRRGLAFSSGLAAITAVISLFGPGDHLILCEDLYGGTYRLLEQVFRPWGLTADYVNT 121 Query: 124 SDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRP 183 SD + + + +T TKA+F+ETPTNP M+ D+ I RI + GLLLIVDNTF +P LQRP Sbjct: 122 SDPEQVNAAVTSRTKAIFIETPTNPTMKITDLREIRRICDDGGLLLIVDNTFISPYLQRP 181 Query: 184 LELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRG 243 +E GADIVIHS TKYLGGHND++AGL V E LG+++ +QNA GAVL PFDSWLL+RG Sbjct: 182 IECGADIVIHSGTKYLGGHNDVVAGLAVAAREDLGDKLAFYQNASGAVLGPFDSWLLVRG 241 Query: 244 MKTLSLRMRQHQANAQELAAFLEEQEEISDVLY----------------PGKGGMLSFRL 287 MKTL LR+ + Q NA +A +L + V Y G GGM+SF L Sbjct: 242 MKTLGLRLDRAQENASAIARWLASHPAVDQVYYIGLDNHPGREVHFQQASGPGGMISFTL 301 Query: 288 QKEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVG 347 V L ++ I FAESLGGVES +T+PA QTH DIPE+IR GV + LLR SVG Sbjct: 302 HDAGKVPEVLSRIQLISFAESLGGVESLLTFPARQTHGDIPEDIRRRCGVTDCLLRLSVG 361 Query: 348 IEHAEDLKEDLKQAL 362 IE+ DL +DL QAL Sbjct: 362 IENVHDLIDDLAQAL 376 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: 398 Number of extensions: 11 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: 377 Length adjustment: 30 Effective length of query: 343 Effective length of database: 347 Effective search space: 119021 Effective search space used: 119021 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