Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate Synpcc7942_0370 Synpcc7942_0370 O-acetylhomoserine/O-acetylserine sulfhydrylase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__SynE:Synpcc7942_0370 Length = 434 Score = 247 bits (631), Expect = 4e-70 Identities = 151/426 (35%), Positives = 236/426 (55%), Gaps = 25/426 (5%) Query: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 T LH+ ++ GS PI+ + ++ +EDA A +F K G Y R NPT LE Sbjct: 7 TLALHAGQKPDPTTGSRAVPIYQTTSYVFEDAEHAANLFALKAFGNIYTRLMNPTTDVLE 66 Query: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAK 129 ++ + G + ++G AAI + + G +++S+ L+G T +L+ T+ G + Sbjct: 67 QRLAALHGGTGAVATSSGQAAIFYAIAAITSAGQNIISTTNLYGGTINLFRHTLKRFGIE 126 Query: 130 VSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTS 189 V VD++D +V AAI NTRLV+ E+I NP+ V D + I + + GI ++VDNT++ Sbjct: 127 VRFVDSSDASSVAAAIDENTRLVYTESIGNPKGNVDDFEAIAAIAHDSGIPFIVDNTVSP 186 Query: 190 PYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT--RYPHIA---------- 237 P LF P GA +VV SLTK GGHG +LGG + + G+F W ++P IA Sbjct: 187 PPLFNPLEHGADVVVLSLTKLAGGHGTSLGGIVIEKGDFPWNNGKFPEIAGPDPSYHGVN 246 Query: 238 -----ENYKKNPAPQWGMA---QIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECK 289 N+ + AP G+A +IR LRD G +L P A + +G ET+ LR ER + Sbjct: 247 FWDAFGNHPEAVAP--GLAYVLKIRTGLLRDIGATLSPFNAQQVLLGVETLPLRAERHVR 304 Query: 290 NALALAQMLQADERVAAVYYPGLESHPQH-ALSKALFRSFGSLMSFELKDGIDCFD-YLN 347 NA A+A+ L+ V V YPGL SHP + + L G+++ F ++ G++ +++ Sbjct: 305 NAQAVAEWLERHPLVTWVNYPGLPSHPDYDRAQRYLPNGAGAILGFGVQGGLEAGKRFIS 364 Query: 348 RLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADF 407 ++LA +N+ D +TLVI A T ++ E +A+ G++ +R+SVGLE DD++AD Sbjct: 365 AVKLASNLANVLDAKTLVIHPASTTHQQLSPEEQAAAGVSPDFVRLSVGLEHLDDILADL 424 Query: 408 RQALDA 413 QAL A Sbjct: 425 DQALQA 430 Lambda K H 0.319 0.134 0.391 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: 440 Number of extensions: 20 Number of successful extensions: 4 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: 413 Length of database: 434 Length adjustment: 32 Effective length of query: 381 Effective length of database: 402 Effective search space: 153162 Effective search space used: 153162 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: 51 (24.3 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