Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_010440841.1 G7G_RS0109505 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000192475.1:WP_010440841.1 Length = 390 Score = 283 bits (725), Expect = 5e-81 Identities = 171/401 (42%), Positives = 238/401 (59%), Gaps = 12/401 (2%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M +V I A RTP+G F G GV A DL ++A ++ A D VDEV GC A Sbjct: 1 MNEVVIAGAARTPMGGFQGMFDGVTAADLGGAAIRAALKGAGA---DTVDEVLMGCVLPA 57 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 G+ + AR A AGL E +P TLN++C SGM A AF IA G + +AGG+ESM Sbjct: 58 GQ-GQAPARQAGFAAGLGEEVPATTLNKMCGSGMKAAMIAFDQIALGHTQTMVAGGMESM 116 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 + AP+++ K G + F++ L + M A++ A+ YQ +R Sbjct: 117 TNAPYLLPKMRGGARIG---HGQVVDHMFLDGLEDAYDKGRLMGTFAEDCAESYQFTREA 173 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTL-EALTKLKP 239 QD +ALRS A +AQ F +EI V I +KGE +++ DE +P++ E + LKP Sbjct: 174 QDEYALRSLSNALSAQENNAFDQEITSVSIQTRKGEVVLDADE--QPQSARPEKIPTLKP 231 Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299 D TVTA N+S ++DGAAAL+LASAE +K LT RAR+LG AS AP + PV Sbjct: 232 AFREDGTVTAANSSSISDGAAALVLASAEEAEKQNLTVRARILGHASHAQAPGLFTTAPV 291 Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359 PA +KL +R+G D D+ E+NEAFA +A + E+G++ + VN NGGA ALGHP+G Sbjct: 292 PAAQKLLDRIGWKKEDVDLWEVNEAFAVVPMAFMHEMGLSREI--VNVNGGACALGHPIG 349 Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 SGAR+++T L+ LEK ++G+A +C+G G+G A+AIERV Sbjct: 350 ASGARIMVTLLNALEKRDLKRGVAAICIGGGEGTAIAIERV 390 Lambda K H 0.318 0.134 0.383 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: 368 Number of extensions: 12 Number of successful extensions: 6 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: 400 Length of database: 390 Length adjustment: 31 Effective length of query: 369 Effective length of database: 359 Effective search space: 132471 Effective search space used: 132471 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 24 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