Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_187147762.1 HM1_RS07785 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000019165.1:WP_187147762.1 Length = 379 Score = 387 bits (994), Expect = e-112 Identities = 205/378 (54%), Positives = 256/378 (67%), Gaps = 16/378 (4%) Query: 1 MSQHVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDA 60 M+ H+++ LAQ GN D TG VS PIY S +RH +GESTGFDY R+ NPTRQ++E+ Sbjct: 1 MAMHIDSLLAQGGNGKDAGTGAVSFPIYQSATFRHPALGESTGFDYSRSGNPTRQVLEEL 60 Query: 61 IANLENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHY 120 IA LE G RGLAFSSG+AAI +++LF GD LI+ DLYGGTYRL E ++ +GLT Y Sbjct: 61 IAKLEGGRRGLAFSSGLAAITAVISLFGPGDHLILCEDLYGGTYRLLEQVFRPWGLTADY 120 Query: 121 DDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVL 180 + SD + + + +T TKA+F+ETPTNP M+ D+ I RI + GLLLIVDNTF +P L Sbjct: 121 VNTSDPEQVNAAVTSRTKAIFIETPTNPTMKITDLREIRRICDDGGLLLIVDNTFISPYL 180 Query: 181 QRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLL 240 QRP+E GADIVIHS TKYLGGHND++AGL V E LG+++ +QNA GAVL PFDSWLL Sbjct: 181 QRPIECGADIVIHSGTKYLGGHNDVVAGLAVAAREDLGDKLAFYQNASGAVLGPFDSWLL 240 Query: 241 MRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLY----------------PGKGGMLS 284 +RGMKTL LR+ + Q NA +A +L + V Y G GGM+S Sbjct: 241 VRGMKTLGLRLDRAQENASAIARWLASHPAVDQVYYIGLDNHPGREVHFQQASGPGGMIS 300 Query: 285 FRLQKEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRF 344 F L V L ++ I FAESLGGVES +T+PA QTH DIPE+IR GV + LLR Sbjct: 301 FTLHDAGKVPEVLSRIQLISFAESLGGVESLLTFPARQTHGDIPEDIRRRCGVTDCLLRL 360 Query: 345 SVGIEHAEDLKEDLKQAL 362 SVGIE+ DL +DL QAL Sbjct: 361 SVGIENVHDLIDDLAQAL 378 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: 399 Number of extensions: 12 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: 379 Length adjustment: 30 Effective length of query: 343 Effective length of database: 349 Effective search space: 119707 Effective search space used: 119707 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