Align propanoyl-CoA C-acyltransferase (EC 2.3.1.176) (characterized)
to candidate WP_011023935.1 MA_RS21100 acetyl-CoA acetyltransferase
Query= BRENDA::P22307 (547 letters) >NCBI__GCF_000007345.1:WP_011023935.1 Length = 390 Score = 211 bits (536), Expect = 5e-59 Identities = 135/397 (34%), Positives = 198/397 (49%), Gaps = 22/397 (5%) Query: 11 LRRVFVVGVGMTKFVKPGAENSRDYPDLAEEAGKKALADAQIPYSAVDQACVGYVFGDST 70 +R V ++GV TKF G R D+ EA L DA + +D +G + G Sbjct: 1 MRDVAIIGVKNTKF---GELWDRSLRDIIVEAAIGVLDDADVSGKEIDALYLGNMSGGRF 57 Query: 71 CGQRAI------YHSLGMT-GIPIINVNNNCATGSTALFMARQLIQGGVAECVLALGFEK 123 Q I Y L IP V CA+G AL A + G + V+A G EK Sbjct: 58 VDQEHIGALIADYSGLSKNLHIPATRVEAACASGGLALRQAIMAVASGYSNIVVAAGAEK 117 Query: 124 MSKGSLGIKFSDRTIPTDKHVDLLINKYGLSAHPVAPQMFGYAGKEHMEKYGTKIEHFAK 183 M+ S D+ + + A P ++ K HM +YGT E A+ Sbjct: 118 MTDVGTEEASSALAAAADREWEGM-------AGATFPGLYAMIAKLHMHRYGTTSEQLAE 170 Query: 184 IGWKNHKHSVNNPYSQFQDEYSLDEVMASKEVFDFLTILQCCPTSDGAAAAILASEAFVQ 243 + KNHK+ NP +Q+++E S+D+V+ S V D L I C P +DGA+A ++A Sbjct: 171 VAVKNHKNGSLNPIAQYKNEISVDDVLKSIMVADPLHIFDCSPITDGASALVVAPADIAH 230 Query: 244 KYGLQSKAVEILAQEMMTDLPSSFEEKSIIKMVGFDMSKEAARKCYEKSGLTPNDIDVIE 303 KY + I A +D + + + I + D + AA++ Y + LTP DID++E Sbjct: 231 KY--TDTPIYIKATAQASDTIALHDRRDITTL---DSTVMAAKRAYSMAKLTPEDIDLVE 285 Query: 304 LHDCFSTNELLTYEALGLCPEGQGATLVDRGDNTYGGKWVINPSGGLISKGHPLGATGLA 363 +HDCF+ E+ E LG +G+G + + G+ GG+ +N SGGL + GHP+GATG+ Sbjct: 286 VHDCFTIAEICAIEDLGFAEKGKGGIVTENGETAIGGRIPVNTSGGLKACGHPVGATGIK 345 Query: 364 QCAELCWQLRGEAGKRQVPGAKVALQHNLGIGGAVVV 400 Q E+ QLRG+AGKRQV GA+ + HN+G GA V Sbjct: 346 QAVEIVTQLRGDAGKRQVAGAEYGMTHNVGGSGATAV 382 Lambda K H 0.317 0.134 0.395 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: 483 Number of extensions: 22 Number of successful extensions: 3 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: 547 Length of database: 390 Length adjustment: 33 Effective length of query: 514 Effective length of database: 357 Effective search space: 183498 Effective search space used: 183498 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 (21.6 bits) S2: 51 (24.3 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