Align cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate BWI76_RS20685 BWI76_RS20685 cysteine synthase B
Query= BRENDA::Q2V0C9 (504 letters) >FitnessBrowser__Koxy:BWI76_RS20685 Length = 303 Score = 191 bits (485), Expect = 3e-53 Identities = 110/305 (36%), Positives = 171/305 (56%), Gaps = 19/305 (6%) Query: 43 IGQTPLIKLNNIPKSYGIKCEIYAKCEFLNPGGSVKDRIAYRMIQDAEDKGLLKPGCTII 102 IG TPL+KL + G EI+ K E NP GSVKDR A MI +AE +G +KPG +I Sbjct: 8 IGNTPLVKLQRMGPDNG--SEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGDVLI 65 Query: 103 EPTSGNTGIGLAMAAAVRGYKCIIVMPEKMSDEKISTLYALGAKIIRTPTEASWH-SPEA 161 E TSGNTGI LAM AA++GY+ ++MP+ MS E+ + + A GA++I E + + Sbjct: 66 EATSGNTGIALAMIAALKGYQMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGARDL 125 Query: 162 HISVAQKLQKEIPNSIILDQYTNPGNPLAHYDQTAIEIWKQCEGKIDYLVAGAGTGGTIS 221 +++AQ+ + + +LDQ+ NP NP AHY T EIW+Q +G+I + V+ GT GTI+ Sbjct: 126 ALAMAQRGEGK-----LLDQFNNPDNPYAHYTTTGPEIWRQTDGRITHFVSSMGTTGTIT 180 Query: 222 GIGRKLKELSPNIKIIAVDPKGSILDPSSDSQNEVGFYEVEGIGYDFIPTVLDRNVIDKW 281 G+ R L+E + I+ + P+ P + +++P + + ++D Sbjct: 181 GVSRFLREQDKAVSIVGLQPEEGSSIPG-----------IRRWPAEYMPGIFNAQLVDVV 229 Query: 282 IKTEDNESLNAARMLIRQEGLLCGGSSGAALIAALKIAKDIPEEKRMVIILPDGIRNYLT 341 + ++ N RML +EG+ CG SSG A++ AL++A++ P + I+ G R T Sbjct: 230 LDIHQQDAENTMRMLAVKEGIFCGVSSGGAVVGALRVARENPGAVVVAIVCDRGDRYLST 289 Query: 342 KFVSE 346 E Sbjct: 290 GVFGE 294 Lambda K H 0.318 0.135 0.404 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: 321 Number of extensions: 24 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: 504 Length of database: 303 Length adjustment: 30 Effective length of query: 474 Effective length of database: 273 Effective search space: 129402 Effective search space used: 129402 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: 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