Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate RR42_RS04535 RR42_RS04535 cysteine synthase
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__Cup4G11:RR42_RS04535 Length = 300 Score = 229 bits (583), Expect = 1e-64 Identities = 137/303 (45%), Positives = 182/303 (60%), Gaps = 20/303 (6%) Query: 7 ISELIGGTPLVRLNSVVPDGAGT-----VAAKVEYLNPGGSSKDRIAVKMIEAAEASGQL 61 I + IG TPLV+L + P GAG + K+E NP GS KDR AV MI AE+ G++ Sbjct: 6 IEDTIGNTPLVQLQRI-PGGAGAPRGNVILGKLEGNNPAGSVKDRPAVSMIARAESRGRI 64 Query: 62 KPGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVP 121 KPG T++E TSGNTG+ LA+ A RGYK V + P+ +S ++R + AYGAE+++ P Sbjct: 65 KPGDTLIEATSGNTGIALAMAAAIRGYKMVLIMPEDLSMERRQSMAAYGAEIILTPV--- 121 Query: 122 PHDPASYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIG 181 ++D + RD G DQ+ANP+ P +HY TTGPEIW DTEG++THFV+ +G Sbjct: 122 KGGMEYARDLADSMERDGRGVIL-DQFANPDNPLAHYETTGPEIWLDTEGRITHFVSAMG 180 Query: 182 TGGTITGAGRYLKEVSGGRVRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVP 240 T GTITG RYLKE + G ++IVGA P EGS G P E + P YDP Sbjct: 181 TTGTITGVSRYLKEQNAG-IQIVGAQPAEGSRIPGIRKWP-------EAYMPKIYDPKFI 232 Query: 241 DEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRG 300 D VS D+ M RR+AREE + G S A+ AL++AEE +A IV ++ D G Sbjct: 233 DRTEPVSQGDAEHMARRMAREEGIFCGISAAGALCVALRIAEEV-ENATIVFVVCDRGDR 291 Query: 301 YMS 303 Y+S Sbjct: 292 YLS 294 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: 417 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 464 Length of database: 300 Length adjustment: 30 Effective length of query: 434 Effective length of database: 270 Effective search space: 117180 Effective search space used: 117180 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: 49 (23.5 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