Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate GFF4108 PS417_21045 cysteine synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__WCS417:GFF4108 Length = 304 Score = 184 bits (468), Expect = 2e-51 Identities = 110/304 (36%), Positives = 173/304 (56%), Gaps = 17/304 (5%) Query: 1 MIYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKL 60 M++++IL+ IG TP+VR+ + + +++YAKLE NP GS K RIAL MI AE G L Sbjct: 1 MLHNSILDVIGQTPIVRLAQFSEDLGIEVYAKLESLNPGGSHKARIALGMILDAERRGVL 60 Query: 61 --HPGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKK 118 G TIIE + GNTGIGL M G V GY V++V+ + S E++K+++ +GA+++L+D + Sbjct: 61 IRDSGQTIIEPSGGNTGIGLVMAGNVLGYKVVLVIPDNYSPEKQKLLRLYGAKVVLSDSR 120 Query: 119 LGTDGAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIW-AQTKGTVTHFVAAV 177 LG + K EL ENP Y NQ N N H TTA EI A + +FV + Sbjct: 121 LGNNSHGEKCMELQLENP-SYVMLNQQRNGANPQTHRDTTAPEILRAFGEKRADYFVCGI 179 Query: 178 GTSGTLMGVGKNLREKNPEIKIIEAQPTK---------GHYIQGLKSMEEAIVPAIYQAD 228 GT G + G+G+ L+ PE++++ +P + H+IQGL ++P+I D Sbjct: 180 GTGGHITGIGETLKTAWPELRVMGVEPEECDLLKNQHAPHHIQGLSI---GLIPSILNLD 236 Query: 229 KIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKI-DSGVIVVLFADRG 287 ID + + ++ + I+ + I +G+SS A M+A +LA ++ V++ + D Sbjct: 237 VIDGMLKVSRQDCIDMMKRIMRTDAISLGLSSAANMVAIARLAPELPPETVVLTMVYDNA 296 Query: 288 EKYL 291 + YL Sbjct: 297 DSYL 300 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: 215 Number of extensions: 10 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: 304 Length adjustment: 27 Effective length of query: 272 Effective length of database: 277 Effective search space: 75344 Effective search space used: 75344 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