Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate HSERO_RS01265 HSERO_RS01265 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__HerbieS:HSERO_RS01265 Length = 398 Score = 296 bits (757), Expect = 9e-85 Identities = 180/398 (45%), Positives = 238/398 (59%), Gaps = 8/398 (2%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQ 59 + +A IV+ RTPIGKA RG T LL AI+ AV + G+DPK +ED ++G + Sbjct: 5 LQDAYIVAATRTPIGKAPRGMFKNTRPDDLLVRAIQSAVAQVPGLDPKLIEDAIVGCSFP 64 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 +GA G N+AR A+L AGLP T G TI+R CASG+ AIA+AA + ++ + G ES Sbjct: 65 EGAQGLNMARNAVLLAGLPNTIGGVTINRYCASGITAIAMAADRIRVGEADVMIAAGAES 124 Query: 120 ISLVQNDKMNTFHAVDPALEAIKGD-VYMA--MLDTAETVAKRYGISRERQDEYSLESQR 176 +S+V M FH + A K + V MA M TAE VA+++ +SRE QDE+SL S + Sbjct: 125 MSMVP---MMGFHP-SININAFKDENVGMAYGMGLTAEKVAQQWKVSREAQDEFSLASHQ 180 Query: 177 RTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAV 236 + AAQ+ G+F DE+ + ATG + K T+S DEGPR ++ LA LK V Sbjct: 181 KAIAAQEAGEFADEMTSFEIVERFPNLATGEIDVKTRTVSLDEGPRADSNLAALAKLKPV 240 Query: 237 RGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVF 296 ++TAGN+SQ SDGA A +I+S+K L PL F G P+ MGIGP Sbjct: 241 FAAKGSVTAGNSSQTSDGAGALIIVSEKILKQFNLTPLARFVSFAVRGVPPEIMGIGPKE 300 Query: 297 AVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSG 356 A+P LK GL+ D I ELNEAFA Q L LG+DP K+N GGAI++GHP G +G Sbjct: 301 AIPAALKAGGLTQDQIDWIELNEAFAAQALAVIGDLGLDPSKVNPMGGAIALGHPLGATG 360 Query: 357 ARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 A A + RR+ KY +VTMCVG GMG+AG+FE V Sbjct: 361 AIRAATTIHALRRKNLKYGMVTMCVGTGMGAAGIFERV 398 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: 395 Number of extensions: 20 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: 398 Length adjustment: 31 Effective length of query: 364 Effective length of database: 367 Effective search space: 133588 Effective search space used: 133588 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