Align O-ureido-L-serine synthase; Cysteine synthase homolog DscD; O-acetylserine sulfhydrylase; EC 2.6.99.3; EC 2.5.1.47 (characterized)
to candidate 3607478 Dshi_0891 cysteine synthase A (RefSeq)
Query= SwissProt::D2Z027 (324 letters) >FitnessBrowser__Dino:3607478 Length = 360 Score = 306 bits (784), Expect = 5e-88 Identities = 162/329 (49%), Positives = 212/329 (64%), Gaps = 20/329 (6%) Query: 4 FNSILDTIGRTPIVRLQRMAPEHTSVYVKVESFNPGGSVKDRLALSVVLDAEAKGLLKPG 63 ++S+LDT+G TP++R+ +APE +YVK E FNP SVKDRLAL+++ AE G LKPG Sbjct: 17 YDSVLDTVGNTPVIRINNLAPEGVELYVKAEFFNPAASVKDRLALNIIEAAERAGTLKPG 76 Query: 64 DTIVECTSGNVGIALAMVAAARGYRFVAVMGDTYSVERRKLIRAYGGKLVLFPGHLGSKG 123 T+VE TSGN GI LAMV A +GY V M +++S+ERRKL+R G K+VL P G Sbjct: 77 QTVVEATSGNTGIGLAMVCAQKGYPLVITMAESFSIERRKLMRLLGAKVVLTPRAEKGFG 136 Query: 124 GNLIADELAEKYGWFRARQFDNPANPSYHRETTASEILADFAGKRLDHFVTGFGTTGTLT 183 A ELAE GWF A QF+ AN H TTA EIL DF G +LD+ VTG+GT GT+T Sbjct: 137 MYRKAVELAEANGWFLASQFETAANAEMHENTTAQEILGDFEGCKLDYIVTGYGTGGTVT 196 Query: 184 GVGQMLRVARPEVRVVALEPSNAAMLARG----------------EWSPHQIQGLAPNFV 227 G+G++LR ARPE +++ EP+NA +L G + PH IQG P+F+ Sbjct: 197 GLGRVLRKARPETKIILTEPANAQLLGSGIAQDRDPNGAPAVSHSAFEPHPIQGWTPDFI 256 Query: 228 PGVLDRSV----IDDLVTMDEVTARDTSRRLAAEEGIFAGISAGATVATALSIAEHAPEG 283 P VL S+ D L+ + +RRLAAEEGI GIS G+T A + +A+ APEG Sbjct: 257 PKVLQESIDQGFYDALLPVAGADGIAWARRLAAEEGILTGISGGSTFAISHEVAKTAPEG 316 Query: 284 TVLLAMLPDTGERYLSTFLFDGVDEGSDD 312 +V+L MLPDTGERYLST LF+G+ E ++ Sbjct: 317 SVILCMLPDTGERYLSTPLFEGIVEDMNE 345 Lambda K H 0.319 0.136 0.395 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: 326 Number of extensions: 16 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: 324 Length of database: 360 Length adjustment: 29 Effective length of query: 295 Effective length of database: 331 Effective search space: 97645 Effective search space used: 97645 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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