Align cysteine synthase (EC 2.5.1.47); cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate WP_052285808.1 AZC_RS00140 cysteine synthase
Query= BRENDA::F9UT54 (303 letters) >NCBI__GCF_000010525.1:WP_052285808.1 Length = 378 Score = 95.5 bits (236), Expect = 2e-24 Identities = 85/287 (29%), Positives = 124/287 (43%), Gaps = 22/287 (7%) Query: 28 IYAKLEMFNPGGSIKDRLGAYLIEDGLQRGRVNAKTTIIEPTAGNTGIGLALATQAHHLR 87 IY K E +P GS+K RL L G+ G++ T++E ++G+T + A + L Sbjct: 63 IYLKDESSHPTGSLKHRLARSLFLFGVCNGQIREGITLVEASSGSTAVSEAYFARLLGLP 122 Query: 88 TILVVPEKFSMEKQVLMQALGAEIVHTPSEEGIKGAIRKAEALAATISNSYVPMQFKNPA 147 V+ S EK ++ G + +A ALA + YV QF N Sbjct: 123 FYAVMTRTTSPEKIADIEREGGRCHFVDDSSAVYA---EAAALAERLGGLYVD-QFTNAE 178 Query: 148 NPAAYY--HTLAPEILADM---PAPI-TAFVAGAGSGGTFAGVAAYLQAQDSATKAVVVE 201 + + +A I M P + T V GAG+GGT A + YL+ + AT+ V + Sbjct: 179 RVTDWRGNNNIAESIFQQMQGEPRSVPTWIVMGAGTGGTSATIGRYLRYRHHATRLCVAD 238 Query: 202 PEGSILNGG---------PAHAHRTEGIGVEFIPPFFDQVRIDQTLTIADNDAFAQVRHL 252 PEGS+ R EGIG + P F ID + + D + A +R L Sbjct: 239 PEGSVFYDAFRTGDRSLTSCPGSRIEGIGRPRVEPSFIPEVIDHMIRVPDAASIAAMRVL 298 Query: 253 ARDHGLLIGSSSGAALAASLQLATNLPANSH---IVTIFPDSSERYL 296 AR G +G S+G A A LA + +VT+ D ERYL Sbjct: 299 ARRLGRKVGPSTGTAFHALCMLAAEMMGRGETGSLVTLICDRGERYL 345 Lambda K H 0.317 0.133 0.378 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: 269 Number of extensions: 13 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: 303 Length of database: 378 Length adjustment: 28 Effective length of query: 275 Effective length of database: 350 Effective search space: 96250 Effective search space used: 96250 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 (21.7 bits) S2: 49 (23.5 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