Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 3607593 Dshi_1002 Cystathionine gamma-synthase (RefSeq)
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__Dino:3607593 Length = 380 Score = 204 bits (520), Expect = 2e-57 Identities = 143/383 (37%), Positives = 198/383 (51%), Gaps = 35/383 (9%) Query: 4 HVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQL--VEDAI 61 H +T A G D +G V PI +T +R D + +++ + L VE + Sbjct: 8 HPDTLAAHGGGAVDTASGGVVPPIQPATTFRRGPDYAPLNPDNIYSRDDSEALRAVETLL 67 Query: 62 ANLENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYD 121 A LE GA LAF SGMAA + +G +++ S +Y GT + + + G+T Sbjct: 68 AALEGGAGALAFPSGMAATAAVFRTLPAGARVVLQSGIYWGTTKWVRDFCARRGVTLVEV 127 Query: 122 DFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQ 181 D +D L S T VFVETP+NP ++ DI A G LL+VD+T TPVL Sbjct: 128 DAADAHALGSACAAPTALVFVETPSNPWLKTVDIRAAAAAAHGAGALLVVDSTAATPVLT 187 Query: 182 RPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQH----QNAIGAVLPPFDS 237 RPL LGAD+V+HSATK L GH+D+LAG +V D G E + ++ GAVL PF++ Sbjct: 188 RPLGLGADLVMHSATKGLNGHSDVLAGALVTAD--AGHETWARIATDRHDAGAVLGPFEA 245 Query: 238 WLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK-----------------G 280 WLL+RGM+TL LR+ + A A ELA L ++DV YPG G Sbjct: 246 WLLLRGMRTLPLRVARMSATALELAQRLSTDTRVADVFYPGLPGHAGHDIAVAQMTGGFG 305 Query: 281 GMLSFRLQKE-EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCN 339 G++SF + + + + L+ A SLGGVES + + AT I +G+ Sbjct: 306 GLMSFLVHGDRQTALEVVGRLELFQRATSLGGVESLVEHRAT---------IEPDSGIPE 356 Query: 340 RLLRFSVGIEHAEDLKEDLKQAL 362 L+R SVGIE A DL DL +AL Sbjct: 357 TLVRLSVGIEDAGDLWADLDRAL 379 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: 347 Number of extensions: 17 Number of successful extensions: 3 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: 380 Length adjustment: 30 Effective length of query: 343 Effective length of database: 350 Effective search space: 120050 Effective search space used: 120050 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