Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate Dsui_0325 Dsui_0325 acetyl-CoA acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >FitnessBrowser__PS:Dsui_0325 Length = 432 Score = 241 bits (615), Expect = 3e-68 Identities = 168/432 (38%), Positives = 244/432 (56%), Gaps = 48/432 (11%) Query: 5 VYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGED 64 VY+ D RTP + A DLA +AL+ R P LDEV LGCA+ + D Sbjct: 10 VYVVDGARTPFLKAKNGPGPFSAADLAVQAGRALLARQPFAP-EDLDEVVLGCASPS-PD 67 Query: 65 NRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRA 124 N+ R+A L G + V G T+ R CASGM A+ +A I SG +ELV+AGGV+++SRA Sbjct: 68 EVNIGRVAALRLGCGNKVTGWTVMRNCASGMQALDSAMANIQSGRSELVLAGGVDALSRA 127 Query: 125 PYVMGKADSAFGRGQKIEDTTIGWR-----------FINPLMKAQYGVD------AMPET 167 P + A + G ++ T+G + +NP++ G+ M +T Sbjct: 128 PLLYNDAMVLWFAGM-MQMKTLGQKAGHFLKLRPSVLLNPVIGLMKGLTDPVVGLLMGQT 186 Query: 168 ADNVADDYKVSRADQDAFALRSQQ--LAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEH 225 A+N+A + +SR + DAF++RS Q +AGRA+ A EIVP+V G G TV D+ Sbjct: 187 AENLAWRFGISREEMDAFSVRSHQRVMAGRAKQA---FGEIVPLV--GNDG-TVYAEDDG 240 Query: 226 LRPDTTLEALAKLKPVNGPDKT---VTAGNASGVNDGSVALILASAEAVKKHGLKARAKV 282 +R D +++ + KLKP DK VT N+S + DG L+LAS AVK+ L+ ++ Sbjct: 241 VRVDASMDGMKKLKPFF--DKKYGRVTPANSSQITDGGAWLLLASESAVKRWKLEPLGRI 298 Query: 283 LGMASAGVAPRVMGIGPVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTR------- 335 + AG+ P MG+GPV AV +L+R L + D D++E+NEAFAAQ L + Sbjct: 299 VDAQWAGLDPSQMGLGPVHAVTPILQRHGLGLNDVDLMEINEAFAAQVLGCLKAWEDDAY 358 Query: 336 ---ELGIAD-----DDARVNPNGGAIALGHPLGASGARLVLTAVHQLEKSGGQRGLCTMC 387 ELG+ D ++N +GGA+A GHP+GASGAR+VL +H L+ GG+RG+ ++C Sbjct: 359 CREELGLPGALGSLDQDKLNVDGGAVAQGHPVGASGARIVLHLLHALKARGGKRGVASIC 418 Query: 388 VGVGQGVALAVE 399 +G GQG A+ VE Sbjct: 419 IGGGQGGAMLVE 430 Lambda K H 0.317 0.134 0.379 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: 494 Number of extensions: 32 Number of successful extensions: 6 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: 401 Length of database: 432 Length adjustment: 31 Effective length of query: 370 Effective length of database: 401 Effective search space: 148370 Effective search space used: 148370 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