Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate 351451 BT1923 O-acetylhomoserine (thiol)-lyase (NCBI ptt file)
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__Btheta:351451 Length = 426 Score = 209 bits (532), Expect = 1e-58 Identities = 131/402 (32%), Positives = 220/402 (54%), Gaps = 20/402 (4%) Query: 30 PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89 PI+ S TF Y+ + Q+A +F + GY Y R NPT A+ KI +E G + + ++G Sbjct: 27 PIYQSTTFKYDTSEQMARLFDLEDSGYFYTRLQNPTNDAVAAKIAALEGGVAAMLTSSGQ 86 Query: 90 AAIGAIVQGLLREGDHVVSSAFLFGNTNSLW-MTVGAQGAKVSMV--DATDVKNVEAAIT 146 AA + + + GDH V S+ ++G T +L+ +T+ G V+ V DA++ + + AA Sbjct: 87 AANFYAIFNICQAGDHFVCSSAIYGGTFNLFGVTMKKLGIDVTFVNPDASE-EEISAAFQ 145 Query: 147 ANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNS 206 NT+ +F ETI+NP +V D+++ + G+ +VDNT +P RP GA ++V+S Sbjct: 146 PNTKALFGETISNPSLEVLDIEKFARIAHSHGVPLIVDNTFPTPINCRPFEWGADIIVHS 205 Query: 207 LTKSIGGHGNALGGALTDTGEFDW----TRYPHIAE--------NYKKNPAPQWGMAQIR 254 TK + GH ++GG + D+G FDW ++P + Y K + + Sbjct: 206 TTKYMDGHATSVGGCIVDSGNFDWDAHADKFPGLCTPDESYHGLTYTKAFGKGAYITKAT 265 Query: 255 AKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLES 314 A+ +RD G P+ + + +G ET+ LR + C+NA +A+ L +E+VA V Y GL Sbjct: 266 AQLMRDLGSIQSPQNSFLLNLGLETLHLRMPQHCRNAQKVAEYLSKNEKVAWVNYCGLPD 325 Query: 315 HPQHALS-KALFRSFGSLMSFELKDGID-CFDYLNRLRLAIPTSNLGDTRTLVI-PVAHT 371 + +AL+ K + ++SF LK G D +++ L +++ D R+ V+ P +HT Sbjct: 326 NKYYALAQKYMPNGSCGVISFGLKGGRDVSIKFMDSLEFIAIVTHVADARSCVLHPASHT 385 Query: 372 IFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 ++ E+ G+ LIR+SVG+E+ DD++AD QAL+A Sbjct: 386 -HRQLSDEQLMEAGVRPDLIRLSVGIENADDIIADIEQALNA 426 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: 406 Number of extensions: 21 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: 426 Length adjustment: 32 Effective length of query: 381 Effective length of database: 394 Effective search space: 150114 Effective search space used: 150114 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