Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate BWI76_RS00785 BWI76_RS00785 cystathionine gamma-synthase
Query= SwissProt::P9WGB5 (406 letters) >FitnessBrowser__Koxy:BWI76_RS00785 Length = 386 Score = 212 bits (539), Expect = 2e-59 Identities = 130/387 (33%), Positives = 208/387 (53%), Gaps = 17/387 (4%) Query: 19 QATVGVRGGMLRSG-FEETAEAMYLTSGYVYGSAAVAEKSFAG--ELDHYVYSRYGNPTV 75 QAT+ VR G+ + ++L+S Y +F G E + YSR GNPT Sbjct: 5 QATIAVRSGLNDDEQYGCVVPPIHLSSTY----------NFTGFNEPRAHDYSRRGNPTR 54 Query: 76 SVFEERLRLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPR 135 V + L +EG A T +GM+A+ L GD LVA +G + + + R Sbjct: 55 DVVQRALAELEGGAGAVLTNTGMSAILLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKR 114 Query: 136 WGVQTVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLDN 195 + +FVD +D AL+ + V E+PSNP+ +VDIA + LA AGA V+DN Sbjct: 115 GCYRVLFVDQNDEQALSAALAEKPKLVLVESPSNPLLRVVDIAKICGLAREAGAVSVVDN 174 Query: 196 VFATPLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAMS 255 F +P LQ LG D+V++S TK+++G V+ G ++ + + G Sbjct: 175 TFLSPALQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPATVTELAWWANNIGVTGG 234 Query: 256 AFNAWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQMS 315 AF++++LL+GL TL+ R++ + +A I ++L P V+ + +P LP + +++A RQ Sbjct: 235 AFDSYLLLRGLRTLSPRMEVAQRNALAIVDYLKTQPLVKKLYHPSLPENQGHEIAARQQK 294 Query: 316 GGGTVVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEGR 375 G G +++F LD E ++ L + L ++ +LG +SL++H AT TH M PE R Sbjct: 295 GFGAMLSFELDGDEQTLRR----FLSGLSLFTLAESLGGVESLISHAATMTHAGMAPEAR 350 Query: 376 AAIGLGDGVVRISVGLEDTDDLIADID 402 AA G+ + ++RIS G+ED +DLIAD++ Sbjct: 351 AAAGISETLLRISTGIEDGEDLIADLE 377 Lambda K H 0.319 0.135 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: 371 Number of extensions: 18 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: 406 Length of database: 386 Length adjustment: 31 Effective length of query: 375 Effective length of database: 355 Effective search space: 133125 Effective search space used: 133125 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 (21.8 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