Align propanoyl-CoA C-acyltransferase (EC 2.3.1.176) (characterized)
to candidate WP_011868149.1 MMARC5_RS01930 acetyl-CoA acetyltransferase
Query= BRENDA::P22307 (547 letters) >NCBI__GCF_000016125.1:WP_011868149.1 Length = 392 Score = 184 bits (466), Expect = 7e-51 Identities = 130/403 (32%), Positives = 198/403 (49%), Gaps = 30/403 (7%) Query: 11 LRRVFVVGVGMTKFVKPGAENSRDYPDLAEEAGKKALADAQIPYSAVDQACVGYVFGDST 70 ++ V ++G G TKF + E+ R L EAG KA+ DA + +D VG + G Sbjct: 1 MKDVAIIGYGQTKFGELWEESFRS---LIVEAGTKAIIDANVDGDDIDAMYVGTMSGGLF 57 Query: 71 CGQR----AIYHSLGMTGIPIINVNNNCATGSTALFMARQLIQGGVAECVLALGFEKMSK 126 GQ I G+ IP V CA+GS AL A I G + VL G EKM+ Sbjct: 58 VGQEHTASLIADYAGLNPIPCTRVEAACASGSLALRSAFLSIASGAHDVVLVGGVEKMTD 117 Query: 127 GSLGIKFSDRTIPTDKHVDLLINKYGLSAHPVAPQMFGYAGKEHMEKYGTKIEHFAKIGW 186 SD T D ++ P ++ K +M++YG +E + Sbjct: 118 ------VSDATSAIATASD---QEWEAFVGATFPSLYAMMAKRYMKEYGLTLEQLSSWSA 168 Query: 187 KNHKHSVNNPYSQFQDEYSLDEVMASKEVFDFLTILQCCPTSDGAAAAILASEAFVQKYG 246 H+++V+N Y+QF+ + ++D++M + V D LT+L C P SDGA+A I+ Y Sbjct: 169 IAHENAVHNNYAQFRSKITIDQIMRASPVADPLTLLHCSPVSDGASALIVCDAEKATDYA 228 Query: 247 LQSKAVEILAQEMMTDLPSSFEEKSIIKMVGFDMSKEAARKCYEKSGLTPNDIDVIELHD 306 + + + I A +D + + M + +K A++K YE +G+ + +DV E+HD Sbjct: 229 PKDEIIYIKASTQASDTIALQDRND---MTTLNAAKVASKKAYEIAGINASQVDVAEVHD 285 Query: 307 CFSTNELLTYEALGLCPEGQGATLVDRG-----DNTYGGKWVINPSGGLISKGHPLGATG 361 CF+ N L+ E LG C +G+ +V+ G D+++ +NPSGGL + GH LGATG Sbjct: 286 CFAINGLVLTEDLGFCKKGEAGKVVEAGKTRIDDDSF---VTVNPSGGLKAAGHALGATG 342 Query: 362 LAQCAELCWQLR--GEAGKRQVPGAK-VALQHNLGIGGAVVVT 401 + Q EL WQL+ E RQV A+ N+G G V T Sbjct: 343 IRQVGELYWQLKQDKECKDRQVTIENGYAISANVGGTGGTVCT 385 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: 460 Number of extensions: 24 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: 547 Length of database: 392 Length adjustment: 33 Effective length of query: 514 Effective length of database: 359 Effective search space: 184526 Effective search space used: 184526 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