Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_078428932.1 BK574_RS13250 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::P9WGB5 (406 letters) >NCBI__GCF_002019605.1:WP_078428932.1 Length = 401 Score = 217 bits (553), Expect = 4e-61 Identities = 117/347 (33%), Positives = 193/347 (55%), Gaps = 4/347 (1%) Query: 60 GELDHYVYSRYGNPTVSVFEERLRLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAAR 119 G ++Y R NPTV FE++L+L+E A AA + ++GMAA+ +L L GDR+V + Sbjct: 52 GRKKGHIYGRNTNPTVQAFEDKLKLLENAAAATSFSTGMAAISNTLYTFLRPGDRVVTIK 111 Query: 120 SLFGSCFVVCSEILPRWGVQTVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAA 179 +G + +E LP+ + F + + Q E ++ + ++ ETP+NP + DI Sbjct: 112 DTYGGTNKIFTEFLPQMDISISFCETGNHEQIETEVAKGCKILYLETPTNPTVKITDIKR 171 Query: 180 VTELAHAAGAKVVLDNVFATPLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYI 239 + + H AGA V++DN FATPL QQ LG D+V++S TK + G LGG + E Sbjct: 172 MAKAGHEAGAIVIVDNTFATPLNQQPLELGADIVLHSATKFLGGHADALGGVACSNNEEY 231 Query: 240 DGPVQKLMRHTGPAMSAFNAWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYP 299 + G M + A+++L+G++TL +RV+ +A ++A +L V V YP Sbjct: 232 IEKIYHYREINGATMDPWAAYLILRGMKTLELRVRRQEENALKLANYLKSEEIVESVFYP 291 Query: 300 YLPSHPQYDLAKRQMSGGGTVVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLV 359 L HP +D+AK+QM G G +++FA+ D K ++L + + + NLG ++ V Sbjct: 292 GLEEHPNHDIAKQQMVGFGGMLSFAVKGGIDTVK----KLLPNLTFANRAANLGAVETTV 347 Query: 360 THPATTTHRAMGPEGRAAIGLGDGVVRISVGLEDTDDLIADIDRALS 406 TT+H PE R A+G+ +G++R+S G+E+ +D+I D A + Sbjct: 348 GPARTTSHVECTPEERKAMGIPEGLIRVSCGIENAEDIINDFKEAFT 394 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: 355 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: 406 Length of database: 401 Length adjustment: 31 Effective length of query: 375 Effective length of database: 370 Effective search space: 138750 Effective search space used: 138750 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 10 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