Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate H281DRAFT_04626 H281DRAFT_04626 acetyl-CoA acyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Burk376:H281DRAFT_04626 Length = 399 Score = 303 bits (776), Expect = 6e-87 Identities = 182/395 (46%), Positives = 237/395 (60%), Gaps = 5/395 (1%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQ 59 + +A IV+ +RTPIGKA RG T LL HAI AV + G+D K +ED ++G A+ Sbjct: 5 LQDAYIVAASRTPIGKAPRGMFRNTRPDELLVHAIRSAVAQVPGLDTKVIEDAIVGCAIP 64 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 + G N+AR L AGLP + G T++R CASGL A+A+AA + + + GG ES Sbjct: 65 EAEQGLNVARMGALLAGLPNSVGGVTVNRFCASGLTALAMAADRIRVGESDAMIAGGCES 124 Query: 120 ISLVQNDKMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYSLESQRR 177 +S+V M ++ P + DV +A M TAE VA+R+ ISRE QD +S+ES RR Sbjct: 125 MSMVP--MMGNKPSLSPHIFDRNEDVGIAYGMGLTAEKVAERWKISREAQDAFSVESHRR 182 Query: 178 TAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVR 237 AAQQ G+FNDEIA + D ATG V K ++ DEGPR +T+ EGLA L+ V Sbjct: 183 AIAAQQAGEFNDEIAAYTITERFPDLATGEVRVKTREVALDEGPRADTSLEGLAKLRTVF 242 Query: 238 GEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFA 297 ++TAGN+SQ SDGA A +++S+K L PL F G P+ MGIGP A Sbjct: 243 ANKGSVTAGNSSQTSDGAGALIVVSEKILKQFNLTPLARFVSFAVRGVPPEIMGIGPKEA 302 Query: 298 VPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGA 357 +P LK GL DDI ELNEAFA Q L LG+DP K+N GGAI++GHP G +GA Sbjct: 303 IPAALKAAGLKQDDIDWIELNEAFAAQSLAVIQDLGLDPSKINPLGGAIALGHPLGATGA 362 Query: 358 RLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 A + RRR KY +VTMCVG GMG+AG+ E Sbjct: 363 IRASTVVHGLRRRNYKYGMVTMCVGTGMGAAGIIE 397 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: 429 Number of extensions: 18 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: 395 Length of database: 399 Length adjustment: 31 Effective length of query: 364 Effective length of database: 368 Effective search space: 133952 Effective search space used: 133952 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