Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_004300924.1 C665_RS04210 acetyl-CoA C-acyltransferase
Query= BRENDA::B7XEI5 (396 letters) >NCBI__GCF_000310185.1:WP_004300924.1 Length = 427 Score = 236 bits (601), Expect = 1e-66 Identities = 160/429 (37%), Positives = 229/429 (53%), Gaps = 43/429 (10%) Query: 6 KGVFIVGAKRTPFGTFGGVFRNTSATELQTIAATAALKEANVAPDQVDTVTVGQVMSGTQ 65 K ++IV RTPF +A++L T A +A L APDQ+D V +G + Sbjct: 3 KPIYIVDGARTPFLKAKNAPGPFTASDLATAAGSALLMRQPFAPDQLDEVILG--CASPS 60 Query: 66 TDGIYTPRHAALKAGIPQEKPVLGINRLCGSGFQSVINGAQDILTGAAKVSLAGGVENMS 125 D + R AL+ G + P + R C SG Q++ + ++ G +++ LAGGV+ +S Sbjct: 61 ADEVNIGRVVALRLGCGNKVPGWTVMRNCASGMQAIDSAIANLQCGRSQLVLAGGVDALS 120 Query: 126 QAP--FAVRGVRF----------GTTLGLNYAFE-------DTLWAGLTDSYCGLPMGMT 166 AP F+ + VR+ G L + F + GLTD G MG T Sbjct: 121 HAPLLFSEKMVRWLAGWYAARSTGDRLAMLRTFRLGHLAPVIGIMKGLTDPIVGQLMGQT 180 Query: 167 AEKLGAQYSITRDEVDNFALQSQQRWKTSNDAGVFKAEIEPVTLTIKRKQVSVAVDEHPR 226 E L ++ ITR+++D FA++S +R DAG + EI P+ I R A D+ R Sbjct: 181 GENLAWKFGITREDMDAFAVESHRRVCAGQDAGHYAEEIVPL---IDRDGQVYAADDGVR 237 Query: 227 PQTTLEGLKKLPPVF-KKEGLVTAGTASGISDGAGAIVLASEEAAK--GLKPLARLVGWS 283 +++ L KL P F +K G VT G +S I+DGA +VLAS+EA + GL+PL R+V Sbjct: 238 RDSSMANLAKLKPFFDRKYGRVTPGNSSQITDGAAWLVLASQEAVERHGLQPLGRIVDSQ 297 Query: 284 VVGVDPSIMGVGPVPAIQNLLKATNMTLNDVDLIEINEAFCAQTLACAKALK-------- 335 G+ P MG+GPV A +L+ + +D+D E+NEAF AQ +AC +A Sbjct: 298 WAGLAPDQMGLGPVHATMPILQRHGLAPDDLDAWELNEAFAAQVIACLRAFADDDYCRTH 357 Query: 336 --------LDMNKLNVNGGATALGHPLGASGSRITAHLVHELRRRGLKRAIGSACIGGGQ 387 D +LNV+GGA ALGHP+GASG+RI HL+ LRR+G R + S CIGGGQ Sbjct: 358 FGVDAPGAPDAARLNVDGGAVALGHPVGASGARIVLHLLEVLRRKGGGRGLASICIGGGQ 417 Query: 388 GIALMVEAV 396 G A++VE V Sbjct: 418 GGAMLVETV 426 Lambda K H 0.317 0.133 0.382 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: 455 Number of extensions: 27 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: 396 Length of database: 427 Length adjustment: 31 Effective length of query: 365 Effective length of database: 396 Effective search space: 144540 Effective search space used: 144540 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: 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