Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate 6935813 Sama_0031 3-ketoacyl-CoA thiolase (RefSeq)
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__SB2B:6935813 Length = 387 Score = 311 bits (798), Expect = 2e-89 Identities = 189/404 (46%), Positives = 246/404 (60%), Gaps = 21/404 (5%) Query: 1 MNDAYICDAIRTPIGRY-GGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQ 59 M A I D IRTP+GR GG ++VRA+ L A +KAL+ RNPGVD ++DVI+GC Q Sbjct: 1 MKQAVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQ 60 Query: 60 AGEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVES 119 E N+AR ++LLAG+P A T+NRLCGS M+A+ A+RAI G I GGVE Sbjct: 61 TLEQGFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEH 120 Query: 120 MTRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRA 179 M P G + H + + + G+ M TAE + + GISR Sbjct: 121 MGHVPMNHG---------VDFHPG------LAANVAKASGM--MGLTAEMLGKLHGISRE 163 Query: 180 DQDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPR-ETSLESLARLK 238 QD FA+ S Q+A A +G A EI +E G I+V DE R ET+LESLA L+ Sbjct: 164 MQDQFAVRSHQRAHAASIEGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLR 223 Query: 239 GVVRP-DGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIG 297 V P +GTVTAG +S ++DGA A+L+ ++ A GL RARV MA AG + IMG G Sbjct: 224 PVFDPANGTVTAGTSSALSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYG 283 Query: 298 PAPATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRD-DDPRVNPNGGAIALGH 356 P PATQK L + G+++ +DVIELNEAFA+Q L ++ LGL D + +VN NGGAIALGH Sbjct: 284 PVPATQKALARAGLSIQDMDVIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGH 343 Query: 357 PLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 PLG SGAR+ TT ++ +E + L TMCIG+GQGIA V ER+ Sbjct: 344 PLGCSGARISTTLINLMEHKDATLGLATMCIGLGQGIATVFERV 387 Lambda K H 0.319 0.134 0.386 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: 20 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: 400 Length of database: 387 Length adjustment: 31 Effective length of query: 369 Effective length of database: 356 Effective search space: 131364 Effective search space used: 131364 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