Align Putative cystathionine beta-synthase MT1108; EC 4.2.1.22; Beta-thionase; Serine sulfhydrase (uncharacterized)
to candidate Echvi_0220 Echvi_0220 cysteine synthase B
Query= curated2:P9WP50 (464 letters) >FitnessBrowser__Cola:Echvi_0220 Length = 292 Score = 195 bits (495), Expect = 2e-54 Identities = 118/299 (39%), Positives = 166/299 (55%), Gaps = 13/299 (4%) Query: 9 ELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGTIV 68 ELIG TPLV L + + + K+E NPGGS KDR A MI+ A G LK G +V Sbjct: 5 ELIGNTPLVELEHIPTNPNVKIYCKLEGQNPGGSVKDRAAYSMIKRAMDRGDLKQGDRVV 64 Query: 69 EPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPASY 128 E TSGNTG+ LA++A+ G + + PD + ++ + AYGA+V++ P A Y Sbjct: 65 EATSGNTGIALAMIAKVLGVEMTLIMPDNSTRERVVSMEAYGAKVILTPAA----KTIEY 120 Query: 129 YSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGTITG 188 + +G + +Q+ANP+ +HY TGPEI DT G++THFV+ +GT GTI G Sbjct: 121 SRTLAEEMAKNEGYYILNQFANPDNYQAHYEGTGPEIMRDTNGEITHFVSAMGTTGTIMG 180 Query: 189 AGRYLKEVSGGRVRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVPDEIIAVS 247 RYLKE V+IVG P +GS G + +F P YD S D+II VS Sbjct: 181 VSRYLKEQKPA-VQIVGTQPTDGSSIPG-------IRRWSPEFLPKIYDASRVDQIIDVS 232 Query: 248 DSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGYMSKIF 306 ++ +MTRR+A+EE +L G S G A+ AA+K+AE ++ + G R S +F Sbjct: 233 QEEATEMTRRMAKEEGILAGMSSGGALHAAVKLAESLDSGVIVCITCDRGDRYLSSDLF 291 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: 356 Number of extensions: 12 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: 292 Length adjustment: 30 Effective length of query: 434 Effective length of database: 262 Effective search space: 113708 Effective search space used: 113708 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 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