Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate GFF2323 PGA1_c23540 O-succinylhomoserine sulfhydrylase MetZ
Query= SwissProt::P9WGB5 (406 letters) >FitnessBrowser__Phaeo:GFF2323 Length = 396 Score = 394 bits (1011), Expect = e-114 Identities = 204/385 (52%), Positives = 270/385 (70%), Gaps = 6/385 (1%) Query: 24 VRGGMLRSGFEETAEAMYLTSGYVYGSAAVAEKSFAGE-LDHYVYSRYGNPTVSVFEERL 82 V GG RS + E +EA+YLT G+VY +A AE F D ++Y+RYGNPTV++FEER+ Sbjct: 12 VHGGTRRSQYNEVSEAIYLTQGFVYDTAEQAEARFIETGPDEFIYARYGNPTVAMFEERI 71 Query: 83 RLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQTVF 142 +EGA AFATASGMAAV +L ++L AGD +V+A++LFGSC + IL R+GV+ F Sbjct: 72 AALEGAEDAFATASGMAAVNGALTSILKAGDHVVSAKALFGSCLYILENILTRYGVEVTF 131 Query: 143 VDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLDNVFATPLL 202 VDG DL W AL T+AVFFE+ SNP ++DIAAV ELAHA GA VV+DNVF+TP+ Sbjct: 132 VDGTDLDAWRAALRPDTKAVFFESMSNPTLEVIDIAAVAELAHAVGATVVVDNVFSTPVF 191 Query: 203 QQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAMSAFNAWVL 262 G DVV+YS TKHIDGQGRVLGG ILG R++I G V+ M+HTG ++S FNAW L Sbjct: 192 SNAIEQGADVVIYSATKHIDGQGRVLGGVILGTRDFIRGTVEPYMKHTGGSLSPFNAWTL 251 Query: 263 LKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQMSG-GGTVV 321 LKGLET+++RV +A +A+ L+GHP++ + YP L H Q+ L +RQ+ G GGTV+ Sbjct: 252 LKGLETISLRVNAQAETALELAQALSGHPALSRLMYPGLEDHAQHALVQRQLGGKGGTVL 311 Query: 322 TFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEGRAAIGLG 381 + L +D AF L+ + + ISNNLGDAKS+ THPATTTH+ + E ++ +G+ Sbjct: 312 SLDLKGGKDA----AFRFLNALTIPVISNNLGDAKSIATHPATTTHQRLSEELKSELGIT 367 Query: 382 DGVVRISVGLEDTDDLIADIDRALS 406 G+VR SVGLED DLIAD+ +AL+ Sbjct: 368 PGLVRFSVGLEDAGDLIADLTQALA 392 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: 465 Number of extensions: 22 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: 396 Length adjustment: 31 Effective length of query: 375 Effective length of database: 365 Effective search space: 136875 Effective search space used: 136875 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