Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate Echvi_3705 Echvi_3705 acetyl-CoA acetyltransferases
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__Cola:Echvi_3705 Length = 393 Score = 241 bits (616), Expect = 2e-68 Identities = 144/410 (35%), Positives = 226/410 (55%), Gaps = 27/410 (6%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 M+E +I +RTP+G +GG LS + A +L A ++ L R ++ E +D+VI+G A Sbjct: 1 MKEVYIISAVRTPLGSFGGKLSGLTAVELGAQAIKGALGR-AQVTPEQVDEVIMGNVLSA 59 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 + AR A + AG+ V TT+N++C SG+ ++ FAA++I G D+++AGG+ESM Sbjct: 60 NL-GQAPARQAAIGAGIGYHVPCTTVNKVCASGMKSVMFAAQSIMTGQSDIIVAGGMESM 118 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPET---------AENVA 171 S P+ + KA G++F N D + E A+N A Sbjct: 119 SNVPYYIPKAR-------------FGYKFGNGEFVDGLAKDGLHEVYYNFPMGNCADNTA 165 Query: 172 ELLKISREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETT 231 + ISRE QD +A++S +R A+A + +E++PV K++KG + DE + Sbjct: 166 KEKNISREAQDEYAIQSYRRAAEAWKAQAFQDEVIPVTFKSRKGESITVDEDEEYQ-NVL 224 Query: 232 LEQLRGLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVE 291 E++ L+ F G +TA NAS +NDGAAAL++ S++ A A GL P A+I+ A A + Sbjct: 225 FEKIPSLRPVFDKEGTVTAANASTMNDGAAALVLMSKEKAEALGLQPVAKILGFADAATD 284 Query: 292 PRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGG 351 P P A + L+ AG+ +D E+NEAF+A AL +EL +P+D +N GG Sbjct: 285 PIWFTTAPALAIPKALKNAGIQAEAVDYYEINEAFSAVALANQQELNIPND--RLNVFGG 342 Query: 352 AIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 A++LGHPLG SGAR+ L ++ G+ + +C G G AM++E + Sbjct: 343 AVSLGHPLGASGARIMATLHSVLRQKGGKIGVAGICNGGGGASAMVIENL 392 Lambda K H 0.319 0.135 0.384 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: 370 Number of extensions: 20 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: 401 Length of database: 393 Length adjustment: 31 Effective length of query: 370 Effective length of database: 362 Effective search space: 133940 Effective search space used: 133940 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 Sep 17 2021. The underlying query database was built on Sep 17 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