Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate 6938035 Sama_2168 3-ketoacyl-CoA thiolase (RefSeq)
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__SB2B:6938035 Length = 436 Score = 171 bits (434), Expect = 3e-47 Identities = 138/425 (32%), Positives = 209/425 (49%), Gaps = 38/425 (8%) Query: 6 ICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDNR 65 I G+RTP + A V A D+ + + ELL R+ LD + ++ ++ G Q Sbjct: 17 IVSGLRTPFAKQATAFHGVSALDMGKMVVNELLSRS-ELDPKLVEQLVYGQVVQMPAAP- 74 Query: 66 NVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAPF 125 N+AR L G+ + ++ R C + + A +I G+ ++ IAGG +S S P Sbjct: 75 NIAREIVLGTGMNVATDAYSVTRACATSFQSTVNIAESIMTGNIEIGIAGGADSSSVLPI 134 Query: 126 VMGKA----------ASAFSRQAEMFDTTIGWRF---VNPLMAQQFGTDSMPETAENVAE 172 + K A F ++ +F +G + V P +A+ SM +TAE +A+ Sbjct: 135 GVSKKLAHALVDLTKARTFGQKLAIF-RRLGIKDLLPVPPAVAEYSTGLSMGQTAEQMAK 193 Query: 173 LLKISREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTL 232 ISR DQD+ A RS A+ +SG++ E V++ + I+ D ++R + L Sbjct: 194 THGISRADQDAMAHRSHTLAAQTWASGVMKNE---VMVAHVPPYNQFIEKDNNIRESSDL 250 Query: 233 EQLRGLKAPF-RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVE 291 L+ F R +G +TA N++ + DGA+AL++ SE A A G TP I + A A ++ Sbjct: 251 ASYAKLRPVFDRKHGSVTAANSTPLTDGASALLLMSEGRAKALGYTPIGYIKSYAFAAID 310 Query: 292 P-RLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQAL----------------GVL 334 M +GP AT L+RAG+ + D+ +IE++EAFAAQAL G Sbjct: 311 VWEDMLMGPSYATPMALKRAGMQLEDLTLIEMHEAFAAQALANMKMFASKKFAEEKLGQN 370 Query: 335 RELGLPDDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGI 394 R +G D N GG++A GHP +GARL +EL RR G L T C G G Sbjct: 371 RAIG-EIDMSKFNVLGGSLAYGHPFAATGARLITQMCNELKRRGGGVGLTTACAAGGLGA 429 Query: 395 AMILE 399 AMILE Sbjct: 430 AMILE 434 Lambda K H 0.319 0.135 0.384 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: 357 Number of extensions: 21 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: 436 Length adjustment: 32 Effective length of query: 369 Effective length of database: 404 Effective search space: 149076 Effective search space used: 149076 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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