Align O-acetylhomoserine (thiol)-lyase; EC 2.5.1.49 (characterized)
to candidate Echvi_3411 Echvi_3411 OAH/OAS sulfhydrylase
Query= CharProtDB::CH_122447 (437 letters) >FitnessBrowser__Cola:Echvi_3411 Length = 436 Score = 559 bits (1440), Expect = e-164 Identities = 281/435 (64%), Positives = 339/435 (77%), Gaps = 11/435 (2%) Query: 1 MSDPSPKRFETLQLHAGQEPDPATNSRAVPIYATTSYTFNDSAHGARLFGLKEFGNIYSR 60 MSD + K FETLQLHAG EPD TNSRAVPIY T+SY FN + HGA LFGLKEFGNIY+R Sbjct: 1 MSDHNFK-FETLQLHAGHEPDSNTNSRAVPIYQTSSYVFNSAEHGANLFGLKEFGNIYTR 59 Query: 61 IMNPTVDVFEKRIAALEGGVAAVAASSGQAAQFMAISALAHAGDNIVSTSNLYGGTYNQF 120 IMNPT DVFEKR+AALEGGVAA+A SSGQAAQF+A+S + GDN V++ LYGGTYNQF Sbjct: 60 IMNPTNDVFEKRMAALEGGVAALAVSSGQAAQFIALSNILENGDNFVTSPFLYGGTYNQF 119 Query: 121 KVLFPRLGITTKFVQGDKAEDIAAAIDDRTKAVYVETIGNPRYNVPDFEVIAKVAHEKGI 180 KV F RLGI+ +F +KAED+ IDDRTKA+YVETIGNP +NVPDFE ++ ++ + I Sbjct: 120 KVSFKRLGISARFASSEKAEDMEKLIDDRTKALYVETIGNPGFNVPDFEALSALSKKHDI 179 Query: 181 PLVVDNTFGAGGYFVRPIEHGADIVVHSATKWIGGHGTTIGGVVVDSGKFDWGKNAARFP 240 PLVVDNTFGAGGY RP+ HGA IVV SATKWIGGHGT+IGG++VD G ++WG +FP Sbjct: 180 PLVVDNTFGAGGYLFRPLAHGAHIVVASATKWIGGHGTSIGGIIVDGGNYNWGN--GKFP 237 Query: 241 QFTQPSEGYHGLNFWETFGP--------IAFAIRVRVEILRDLGSALNPFAAQQLILGLE 292 QF++PSEGYHGLNFWE FG IAF+IR RVE LRD G A++PF + L+ GLE Sbjct: 238 QFSEPSEGYHGLNFWEVFGEGNPLGLPNIAFSIRARVEGLRDFGPAISPFNSFLLLQGLE 297 Query: 293 TLSLRAERHASNALALANWLKKNDHVSWVSYVGLEEHSSHEVAKKYLKRGFGGVLSFGVK 352 TLSLRAER NAL LA WL+ + V+ VSY GLE H H +AKKYLK+GFGGVL+F VK Sbjct: 298 TLSLRAERTVENALTLAKWLENHPQVATVSYPGLESHGHHTLAKKYLKKGFGGVLTFEVK 357 Query: 353 GEAAVGSQVVDNFKLISNLANVGDSKTLAIHPWSTTHEQLTDQERIDSGVTEDAIRISVG 412 G G ++VD+ +LIS+LANVGD+KTL I P +TTH+QL+++E+ +GVT +RIS+G Sbjct: 358 GGKEAGEKLVDSLQLISHLANVGDAKTLIIQPSATTHQQLSEKEQAAAGVTPGMLRISLG 417 Query: 413 TEHIDDIIADFEQSF 427 EHIDDI AD EQ+F Sbjct: 418 IEHIDDICADLEQAF 432 Lambda K H 0.318 0.134 0.394 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: 607 Number of extensions: 23 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: 437 Length of database: 436 Length adjustment: 32 Effective length of query: 405 Effective length of database: 404 Effective search space: 163620 Effective search space used: 163620 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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