Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate N515DRAFT_4363 N515DRAFT_4363 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__Dyella79:N515DRAFT_4363 Length = 399 Score = 286 bits (731), Expect = 9e-82 Identities = 151/376 (40%), Positives = 219/376 (58%), Gaps = 17/376 (4%) Query: 7 TKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLEN 66 T + G SD G V P++LST Y G+G +DY R+ NPTR L+ +A+A LE Sbjct: 12 TCAVRAGIESDTQHGAVVPPLHLSTNYAFEGLGGKRAYDYSRSGNPTRDLLGNALAELEQ 71 Query: 67 GARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSDE 126 GA + +SGMAA+ + L +G ++ + D YGGT+RL + KK T + D +D Sbjct: 72 GAGAVVTASGMAAVALALELVPAGGRVLAAHDCYGGTWRLLDAWAKKGRFTLEFADLTDR 131 Query: 127 DCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLEL 186 L + + V+VETP+NPL++ D+ H+A+ G L++VDNTF +P LQ+PL L Sbjct: 132 VALAAGLASKPSLVWVETPSNPLLRITDVRHVAQAAHAAGALVVVDNTFLSPALQQPLVL 191 Query: 187 GADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKT 246 GAD+V+HS TKY+ GH+D++ G VV +D+ + +++ N G PFDS+L +RG++T Sbjct: 192 GADVVVHSTTKYINGHSDVVGGAVVARDQAVADQLKWWGNCNGLTGAPFDSFLTLRGLRT 251 Query: 247 LSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRLQKE 290 LS+R+RQHQ NAQ +A L+ + V YPG G MLSF L+ + Sbjct: 252 LSVRLRQHQENAQRIATLLDGHAAVRKVYYPGLESHPGHALAARQQAGFGAMLSFELEGD 311 Query: 291 -EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGIE 349 + F+ LK AESLGGVES + +PA+ TH + E R G+ + LLR SVGIE Sbjct: 312 VAQIEAFVNELKYFSLAESLGGVESLVAHPASMTHASMAPEARRTAGIADSLLRISVGIE 371 Query: 350 HAEDLKEDLKQALCQV 365 +DL D+ L +V Sbjct: 372 DGDDLVRDVDAGLARV 387 Lambda K H 0.319 0.135 0.392 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: 365 Number of extensions: 17 Number of successful extensions: 2 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: 373 Length of database: 399 Length adjustment: 30 Effective length of query: 343 Effective length of database: 369 Effective search space: 126567 Effective search space used: 126567 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: 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