Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate 8501944 DvMF_2658 cysteine synthase (RefSeq)
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Miya:8501944 Length = 310 Score = 229 bits (585), Expect = 5e-65 Identities = 124/301 (41%), Positives = 176/301 (58%), Gaps = 10/301 (3%) Query: 5 NILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPGS 64 ++ E +G TPLVR+N ++ ++ AKLE NP SVKDRIAL MI+ A G+L PG Sbjct: 6 DMTELVGRTPLVRLNRVSEGCAAEVVAKLEFNNPCASVKDRIALAMIDGAMERGELAPGG 65 Query: 65 TIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDGA 124 ++E TSGNTG+GLA + V+G +++ M E +S ER+ +++ FGA ++LT G GA Sbjct: 66 LLVEPTSGNTGVGLAFVAAVRGLTLVLTMPESMSNERKALLRGFGARLVLTPASKGMRGA 125 Query: 125 IRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTLM 184 I + +V E PG QF N N + H KTTAEEIWA T G V FVA VGT GT+ Sbjct: 126 IEEAERIVAETPGAVM-LGQFVNPDNPLVHRKTTAEEIWADTDGKVDAFVAGVGTGGTVT 184 Query: 185 GVGKNLREKNPEIKIIEAQPTKGHYIQG-------LKSMEEAIVPAIYQADKIDEHILIE 237 G G+ LRE NP+IK+ +P + + G ++ + VP + DE I + Sbjct: 185 GTGRRLRELNPDIKVFAVEPDESPVLSGGAPGPHPIQGIGAGFVPPVLDTKVYDEIIRVP 244 Query: 238 SEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSG--VIVVLFADRGEKYLSTKL 295 ++A AR ++ +EGI G+SSGA AA +A + + +V + D GE+YLST L Sbjct: 245 GKDALVTARRLLREEGILCGVSSGANAFAAMAVARRPEMAGKRVVFVVCDTGERYLSTPL 304 Query: 296 F 296 F Sbjct: 305 F 305 Lambda K H 0.315 0.133 0.367 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: 294 Number of extensions: 18 Number of successful extensions: 4 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: 299 Length of database: 310 Length adjustment: 27 Effective length of query: 272 Effective length of database: 283 Effective search space: 76976 Effective search space used: 76976 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: 42 (22.0 bits) S2: 48 (23.1 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