Align cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate 8501944 DvMF_2658 cysteine synthase (RefSeq)
Query= BRENDA::Q2V0C9 (504 letters) >FitnessBrowser__Miya:8501944 Length = 310 Score = 249 bits (636), Expect = 1e-70 Identities = 137/310 (44%), Positives = 194/310 (62%), Gaps = 12/310 (3%) Query: 34 KIMPDILTAIGQTPLIKLNNIPKSYGIKCEIYAKCEFLNPGGSVKDRIAYRMIQDAEDKG 93 +I D+ +G+TPL++LN + S G E+ AK EF NP SVKDRIA MI A ++G Sbjct: 2 EIARDMTELVGRTPLVRLNRV--SEGCAAEVVAKLEFNNPCASVKDRIALAMIDGAMERG 59 Query: 94 LLKPGCTIIEPTSGNTGIGLAMAAAVRGYKCIIVMPEKMSDEKISTLYALGAKIIRTPTE 153 L PG ++EPTSGNTG+GLA AAVRG ++ MPE MS+E+ + L GA+++ TP Sbjct: 60 ELAPGGLLVEPTSGNTGVGLAFVAAVRGLTLVLTMPESMSNERKALLRGFGARLVLTPAS 119 Query: 154 ASWHSPEAHISVAQKLQKEIPNSIILDQYTNPGNPLAHYDQTAIEIWKQCEGKIDYLVAG 213 I A+++ E P +++L Q+ NP NPL H TA EIW +GK+D VAG Sbjct: 120 KGMRGA---IEEAERIVAETPGAVMLGQFVNPDNPLVHRKTTAEEIWADTDGKVDAFVAG 176 Query: 214 AGTGGTISGIGRKLKELSPNIKIIAVDPKGSILDPSSDSQNEVGFYEVEGIGYDFIPTVL 273 GTGGT++G GR+L+EL+P+IK+ AV+P S + S G + ++GIG F+P VL Sbjct: 177 VGTGGTVTGTGRRLRELNPDIKVFAVEPDESPV----LSGGAPGPHPIQGIGAGFVPPVL 232 Query: 274 DRNVIDKWIKTEDNESLNAARMLIRQEGLLCGGSSGAALIAALKIAKDIPE--EKRMVII 331 D V D+ I+ ++L AR L+R+EG+LCG SSGA AA+ +A+ PE KR+V + Sbjct: 233 DTKVYDEIIRVPGKDALVTARRLLREEGILCGVSSGANAFAAMAVARR-PEMAGKRVVFV 291 Query: 332 LPDGIRNYLT 341 + D YL+ Sbjct: 292 VCDTGERYLS 301 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: 322 Number of extensions: 23 Number of successful extensions: 5 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: 504 Length of database: 310 Length adjustment: 31 Effective length of query: 473 Effective length of database: 279 Effective search space: 131967 Effective search space used: 131967 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