Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate 15519 b1397 acetyl-CoA acetyltransferase (NCBI)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Keio:15519 Length = 401 Score = 263 bits (673), Expect = 5e-75 Identities = 174/413 (42%), Positives = 233/413 (56%), Gaps = 31/413 (7%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAI-EHAVKRAGIDPKEVEDVVMGAAMQ 59 M EA I RTPIG+ Y GAL++ L + E V+ +D + ++DV++G A Q Sbjct: 1 MREAFICDGIRTPIGR-YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQ 59 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G N+AR A L AGLP + +GTTI+R C SGL A+ AAR++ ++ + GG ES Sbjct: 60 AGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVES 119 Query: 120 IS---LVQNDKMNTFHAVDPALEAIKGDVYM-----------AMLDTAETVAKRYGISRE 165 +S V + F + G ++ +M +TAE VA+ ISRE Sbjct: 120 MSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRE 179 Query: 166 RQDEYSLESQRRTAAAQQGGKFNDEIAPI--STKMGVVDKATGAVSFKDITLSQDEGPRP 223 QD ++L SQ+RTA AQ G +EI P+ K GVV + + DE RP Sbjct: 180 DQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTE-----------IQHDEHLRP 228 Query: 224 ETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSY 283 ETT E L GLKA ITAGNAS ++DGA+A +I S++ AAA+GL P M + Sbjct: 229 ETTLEQLRGLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATA 288 Query: 284 GCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNV 341 G EP MG+GPV A R+L+R GLS+ D+ + ELNEAFA Q L +LG+ D +N Sbjct: 289 GVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNP 348 Query: 342 NGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 NGGAI++GHP GMSGARLA A E RR +YA+ TMC+G G G A + E V Sbjct: 349 NGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 Lambda K H 0.316 0.134 0.378 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: 390 Number of extensions: 18 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: 395 Length of database: 401 Length adjustment: 31 Effective length of query: 364 Effective length of database: 370 Effective search space: 134680 Effective search space used: 134680 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 17 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