Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_110804635.1 C8J30_RS05090 acetyl-CoA C-acyltransferase family protein
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_003217355.1:WP_110804635.1 Length = 391 Score = 340 bits (872), Expect = 4e-98 Identities = 193/400 (48%), Positives = 257/400 (64%), Gaps = 9/400 (2%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M + I RT IG FGG+LAG DL + +A +E + + +Q+++V G Sbjct: 1 MTGIVILSGARTAIGAFGGSLAGFAPVDLGTIAARAALERS-GIAPEQINQVVMGHILNT 59 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 + V+R+A + AG+P P + +NRLC SG+ AI +A +A+ GE + A+AGGV+ M Sbjct: 60 EPRDMYVSRVAAIQAGIPVETPAMNVNRLCGSGVQAIVSAAQALMLGEGDFALAGGVDVM 119 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAP+++ A G K+ D ++ + L +G M TA+NVA + +SR D Sbjct: 120 SRAPYILPAARFG----QKMGDASVIDMMVGAL-SCPFGTGHMGVTAENVATECAISRED 174 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240 QD FAL SQ +AAAA AAG F +EIVPV IA +KG I + DEH + TTL+ L LKP Sbjct: 175 QDTFALESQTRAAAAIAAGAFKDEIVPVEIASRKGTVIFDTDEHPKA-TTLDKLAALKPA 233 Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300 +VTAGNASG+NDGA AL++A +A GL P AR+ G A GV P VMG+GP+P Sbjct: 234 FLKGGSVTAGNASGINDGAGALVIAREDAAVATGLKPLARIRGFAIAGVRPEVMGLGPIP 293 Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360 AVR L E+ G+ VSDFDVIE NEAFA+Q LAV R L + D +VNPNGGAIALGHP+G Sbjct: 294 AVRLLCEKTGLKVSDFDVIESNEAFAAQALAVSRALDL--DPTKVNPNGGAIALGHPVGA 351 Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 +GA L + L+ L ++GGR GL TMC+G GQG+ALAIER+ Sbjct: 352 TGAILTVKTLYHLRRTGGRLGLITMCIGGGQGIALAIERL 391 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: 437 Number of extensions: 25 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: 400 Length of database: 391 Length adjustment: 31 Effective length of query: 369 Effective length of database: 360 Effective search space: 132840 Effective search space used: 132840 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