Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate PfGW456L13_3394 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= reanno::Marino:GFF2751 (415 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394 Length = 391 Score = 312 bits (799), Expect = 1e-89 Identities = 194/413 (46%), Positives = 251/413 (60%), Gaps = 29/413 (7%) Query: 7 LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66 +KD IVDA+RTPIG++ G+LS VRAD LG++ I L ER D+ + +DDV++G Q Sbjct: 1 MKDIVIVDAVRTPIGKFRGSLSGVRADHLGSLVISRLLERV-DVSPTLVDDVIFGNVTQI 59 Query: 67 GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126 GE + ++AR +LL AG PV V G TI+R CGSG AV A AI G +++AGG E+M Sbjct: 60 GEQSANIARTALLGAGWPVTVAGLTIDRKCGSGEVAVHMAVGAIAAGAADIVVAGGAENM 119 Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186 SR P MG EI GW + ++Y + S E AE +A + +SR+ Sbjct: 120 SRVP--MGS-------NREIHGAAFGW-----MAAQRYELTSQGEAAERMADKWALSRDA 165 Query: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPL-----VVDTDEH-PRETSLEKL 240 D FA S QR AAA G E PV + ++ L V+ DE R+TS EKL Sbjct: 166 LDDFAFASHQRAAAACDAGYFDNETIPVVVEELREKELSEPAGVLRHDETIRRDTSREKL 225 Query: 241 ASLPTPFR-ENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRI 299 ++L T FR + G +TAGN+S ++DGA ALLL AD K+ LK RARVVA T G +P + Sbjct: 226 STLKTSFRPDTGRITAGNSSQISDGAAALLLMSADTAKKLGLKARARVVAFTTVGSDPTL 285 Query: 300 MGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIA 359 M GP AT+KVLA AGL + D+D+ E+NEAFA+ LA ++ G+P +N NGGAIA Sbjct: 286 MLTGPIAATQKVLAKAGLSINDIDLFEVNEAFASVPLAWMQETGVPH--SKLNVNGGAIA 343 Query: 360 LGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERMD 412 LGHPLG SGARL+TT LNELERR RY L +C G G A IIER+D Sbjct: 344 LGHPLGASGARLMTTMLNELERR-----GGRYGLQAICCAGGMGTATIIERLD 391 Lambda K H 0.318 0.133 0.382 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: 420 Number of extensions: 25 Number of successful extensions: 7 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: 415 Length of database: 391 Length adjustment: 31 Effective length of query: 384 Effective length of database: 360 Effective search space: 138240 Effective search space used: 138240 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: 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