Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate Ga0059261_2888 Ga0059261_2888 acetyl-CoA acetyltransferases
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Korea:Ga0059261_2888 Length = 393 Score = 317 bits (811), Expect = 5e-91 Identities = 189/404 (46%), Positives = 250/404 (61%), Gaps = 15/404 (3%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M++ LI+ VRT IG + GAL +V A DLGA+ + IAR + AV V+ G + Sbjct: 1 MSDVLILSGVRTAIGDFGGALKNVPAADLGALVIGEAIAR-AGIAADAVGHVVMGNVIPS 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 + +AR+AA+ AG+PV+VP T+NRLCGSGL A+ SAA+ + GE G+ +AGG E+M Sbjct: 60 TPSDAYLARVAAVRAGVPVAVPALTVNRLCGSGLQAIISAAQGIALGECGVAVAGGAENM 119 Query: 121 SRAPFVMGKSEQAFGRSA---EIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNIS 177 S+AP + + FG+ ++ D + + + F M TAENVAAQ I Sbjct: 120 SQAPHYVASAR--FGQKMGDIQMLDA------LTRTLSDPFDQVHMGVTAENVAAQCGID 171 Query: 178 RADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAK 237 RA QD A+ S + A AIA GR +IV VEI R G + + DEH R + TLE +A+ Sbjct: 172 RAAQDEAAVESHRRGARAIAEGRFRDQIVPVEIKSRGGTV-MFDTDEHVRAEVTLEDMAR 230 Query: 238 LGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGI 297 L F++ G+VTAGNASG+NDGA A++L S E AQR G K AR++G AGVEPR+MG+ Sbjct: 231 LRPAFQRDGTVTAGNASGINDGAAAVVLGSPEEAQRLGAKPLARILGWGHAGVEPRVMGL 290 Query: 298 GPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGH 357 GPV A L G+ L +DVIE NEAFAAQ AV +LG D E+ N NG I+LGH Sbjct: 291 GPVEAVPIALRRAGVTLDRIDVIESNEAFAAQACAVSAQLGF--DPEKTNVNGSGISLGH 348 Query: 358 PLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 P+G +GA L+EL+ GR L TMCIG GQGIAL+IER+ Sbjct: 349 PVGATGAINTVKLLYELQRSGGRLGLVTMCIGGGQGIALVIERL 392 Lambda K H 0.319 0.134 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: 489 Number of extensions: 22 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