Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate HSERO_RS20660 HSERO_RS20660 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__HerbieS:HSERO_RS20660 Length = 401 Score = 238 bits (608), Expect = 2e-67 Identities = 161/411 (39%), Positives = 222/411 (54%), Gaps = 31/411 (7%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQG 61 EA+I RTP G+ Y GAL A L I ++R G+D VED++ G A Q G Sbjct: 2 EALICDAIRTPFGR-YGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAG 60 Query: 62 ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121 N+AR A L AGLP+ G+T++R C S L A+ +AAR++ V++ + GG ES++ Sbjct: 61 EDNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMT 120 Query: 122 ---LVQNDKMNTF-------------HAVDPALEAIKGDVYMAMLDTAETVAKRYGISRE 165 V + F V+P ++A G +M +TAE VA + I+R Sbjct: 121 RAPFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYG--IDSMPETAENVATDFQINRA 178 Query: 166 RQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPET 225 QD ++L SQ+R AAAQ G F EIAP++ D + ++ DE PRP+T Sbjct: 179 DQDAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDP---------LVVTTDEHPRPDT 229 Query: 226 TAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGC 285 T LA LK V T+TAGNAS ++DGA A ++ S K A LKP GM + G Sbjct: 230 TLATLAKLKGVVRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGV 289 Query: 286 EPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNVNG 343 P MG GP AV ++L + GL++ + + ELNEAFA Q L LG+ D +N NG Sbjct: 290 APRIMGFGPAPAVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNG 349 Query: 344 GAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 GAI++GHP G SGARL A+ + R +YA+ TMC+G G G A + E V Sbjct: 350 GAIAIGHPLGASGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 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: 26 Number of successful extensions: 4 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