Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate PP_3280 PP_3280 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Putida:PP_3280 Length = 406 Score = 243 bits (621), Expect = 5e-69 Identities = 163/409 (39%), Positives = 224/409 (54%), Gaps = 31/409 (7%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQG 61 +A+I+ RTPIG+ Y GAL++ L ++ ++R +D K ++DV+ G A Q G Sbjct: 8 DALIIDAVRTPIGR-YAGALSSVRADDLAAIPLKALIQRHPELDWKAIDDVIFGCANQAG 66 Query: 62 ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121 N+A A L AGLP+ GTTI+R C SGL AI AAR++ + + GG ES+S Sbjct: 67 EDNRNVAHMASLLAGLPLEVPGTTINRLCGSGLDAIGNAARALRCGEAGLMLAGGVESMS 126 Query: 122 ---LVQNDKMNTF-------------HAVDPALEAIKGDVYMAMLDTAETVAKRYGISRE 165 V F V+P ++A G +M +TAE VA+++GISR Sbjct: 127 RAPFVMGKSEQAFGRAAELFDTTIGWRFVNPLMKAAYG--IDSMPETAENVAEQFGISRA 184 Query: 166 RQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPET 225 QD ++L SQ + AAAQ G+ EI P+ + + G + DE PR +T Sbjct: 185 DQDAFALRSQHKAAAAQARGRLAREIVPVE-----IPQRKGPAK----VVEHDEHPRGDT 235 Query: 226 TAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGC 285 T E LA L EG ++TAGNAS ++DGA A ++ S A GLK G GM G Sbjct: 236 TLEQLARLGTPFREGGSVTAGNASGVNDGACALLLASSAAARRHGLKARGRIVGMAVAGV 295 Query: 286 EPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNVNG 343 EP MGIGPV A ++L GL++ D+ + ELNEAFA Q L +LG+ D ++N NG Sbjct: 296 EPRLMGIGPVPATRKVLALTGLALADLDVIELNEAFAAQGLAVLRELGLADDDPRVNRNG 355 Query: 344 GAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 GAI++GHP GMSGARL AL E +YA+ TMC+G G G A + E Sbjct: 356 GAIALGHPLGMSGARLVTTALHELEETAGRYALCTMCIGVGQGIAMIIE 404 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: 416 Number of extensions: 22 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: 406 Length adjustment: 31 Effective length of query: 364 Effective length of database: 375 Effective search space: 136500 Effective search space used: 136500 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