Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate 3607478 Dshi_0891 cysteine synthase A (RefSeq)
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Dino:3607478 Length = 360 Score = 212 bits (539), Expect = 1e-59 Identities = 129/329 (39%), Positives = 183/329 (55%), Gaps = 42/329 (12%) Query: 3 YDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHP 62 YD++L+T+GNTP++RIN+L P V++Y K E FNP SVKDR+AL +IE AE G L P Sbjct: 17 YDSVLDTVGNTPVIRINNLAPEG-VELYVKAEFFNPAASVKDRLALNIIEAAERAGTLKP 75 Query: 63 GSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTD 122 G T++EATSGNTGIGLAM+ KGY ++I M+E SIERRK+++ GA+++LT + Sbjct: 76 GQTVVEATSGNTGIGLAMVCAQKGYPLVITMAESFSIERRKLMRLLGAKVVLTPRAEKGF 135 Query: 123 GAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKG-TVTHFVAAVGTSG 181 G RK EL + N +F +QF N H TTA+EI +G + + V GT G Sbjct: 136 GMYRKAVELAEAN--GWFLASQFETAANAEMHENTTAQEILGDFEGCKLDYIVTGYGTGG 193 Query: 182 TLMGVGKNLREKNPEIKIIEAQPTKG--------------------------HYIQGL-- 213 T+ G+G+ LR+ PE KII +P H IQG Sbjct: 194 TVTGLGRVLRKARPETKIILTEPANAQLLGSGIAQDRDPNGAPAVSHSAFEPHPIQGWTP 253 Query: 214 ----KSMEEAIVPAIYQADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQK 269 K ++E+I Y D + + + A AR + A+EGI G+S G+ + + Sbjct: 254 DFIPKVLQESIDQGFY-----DALLPVAGADGIAWARRLAAEEGILTGISGGSTFAISHE 308 Query: 270 LAEKIDSG-VIVVLFADRGEKYLSTKLFD 297 +A+ G VI+ + D GE+YLST LF+ Sbjct: 309 VAKTAPEGSVILCMLPDTGERYLSTPLFE 337 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: 305 Number of extensions: 19 Number of successful extensions: 6 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: 360 Length adjustment: 28 Effective length of query: 271 Effective length of database: 332 Effective search space: 89972 Effective search space used: 89972 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: 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