Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate SMc01666 SMc01666 methionine gamma-lyase
Query= SwissProt::P9WGB5 (406 letters) >FitnessBrowser__Smeli:SMc01666 Length = 427 Score = 192 bits (488), Expect = 2e-53 Identities = 129/395 (32%), Positives = 207/395 (52%), Gaps = 37/395 (9%) Query: 40 MYLTSGYVYGSAAVAEKSF----------AGELDHYVYSRYGNPTVSVFEERLRLIEGAP 89 ++LTS +V+ SA F AG VYSR+ +P + E+RL + E A Sbjct: 40 IFLTSTFVFHSAEEGRDFFDFVSGRREPPAGVGAGLVYSRFNHPNSEIVEDRLAIFERAE 99 Query: 90 AAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQTV-FVDGDDL 148 A +SGM+A+ T+L A + GD ++ ++ L+G + ++ GV V F DG D Sbjct: 100 AGALFSSGMSAIATTLLAFVRPGDSILHSQPLYGGTETLLAKTFLNLGVSAVGFADGTDE 159 Query: 149 SQW----ERALSVP-TQAVFFETPSNPMQSLVDIAAVTELAHAAGAK------VVLDNVF 197 + E A+S + ETP+NP SLVD+A V +A G + V DN Sbjct: 160 AAVNAAAEEAMSKGRVSVILIETPANPTNSLVDVALVRRIAERIGERQAHRPIVACDNTL 219 Query: 198 ATPLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAMSAF 257 P+ Q G D+ +YS TK++ G ++ GA+LG + I V+ L G + Sbjct: 220 LGPVFQHPIEHGADLSLYSLTKYVGGHSDLIAGAVLGSKALIR-QVKALRGSIGTQLDPH 278 Query: 258 NAWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSH----PQYDLAKRQ 313 + W++ + LETL++R++ +N +A+ +AEFL HP V R YLP H P + Q Sbjct: 279 SCWMIGRSLETLSVRMEKANDNARIVAEFLRDHPKVE--RIHYLPFHDADTPVGRVFATQ 336 Query: 314 MSGGGTVVTFALDCPEDVA--KQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMG 371 +G G+ +F D+A ++ AF L+ +++ ++ +LG +SL +HPA TH + Sbjct: 337 CTGAGSTFSF------DIAGGQEAAFRFLNALQIFKLAVSLGGTESLASHPAAMTHSGVP 390 Query: 372 PEGRAAIGLGDGVVRISVGLEDTDDLIADIDRALS 406 E RA IG+ + +R+S+G+E DDL+AD+ AL+ Sbjct: 391 IEVRARIGVLESTIRLSIGIEHPDDLVADVANALT 425 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: 457 Number of extensions: 35 Number of successful extensions: 5 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: 427 Length adjustment: 31 Effective length of query: 375 Effective length of database: 396 Effective search space: 148500 Effective search space used: 148500 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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