Align Putative cystathionine beta-synthase MT1108; EC 4.2.1.22; Beta-thionase; Serine sulfhydrase (uncharacterized)
to candidate 16520 b2421 cysteine synthase B (O-acetylserine sulfhydrolase B) (NCBI)
Query= curated2:P9WP50 (464 letters) >FitnessBrowser__Keio:16520 Length = 303 Score = 204 bits (518), Expect = 4e-57 Identities = 117/298 (39%), Positives = 173/298 (58%), Gaps = 14/298 (4%) Query: 7 ISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGT 66 + + IG TPLV+L + PD V K+E NP GS KDR A+ MI AE G++KPG Sbjct: 4 LEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGDV 63 Query: 67 IVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPA 126 ++E TSGNTG+ LA++A +GY+ + PD +S+++R + AYGAE+++ Sbjct: 64 LIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELIL---VTKEQGME 120 Query: 127 SYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGTI 186 ++ + +G DQ+ NP+ P +HY TTGPEIW T G++THFV+ +GT GTI Sbjct: 121 GARDLALEMANRGEGKLL-DQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTI 179 Query: 187 TGAGRYLKEVSGGRVRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVPDEIIA 245 TG R+++E S V IVG P EGS G P ++ P ++ S+ DE++ Sbjct: 180 TGVSRFMREQS-KPVTIVGLQPEEGSSIPGIRRWP-------TEYLPGIFNASLVDEVLD 231 Query: 246 VSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGYMS 303 + D+ + R LA E + G S G AV AL+VA +A PDA++V ++ D G Y+S Sbjct: 232 IHQRDAENTMRELAVREGIFCGVSSGGAVAGALRVA-KANPDAVVVAIICDRGDRYLS 288 Lambda K H 0.316 0.135 0.398 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: 407 Number of extensions: 18 Number of successful extensions: 3 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: 464 Length of database: 303 Length adjustment: 30 Effective length of query: 434 Effective length of database: 273 Effective search space: 118482 Effective search space used: 118482 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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