Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_058857811.1 AS188_RS04280 thiolase family protein
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_001482365.1:WP_058857811.1 Length = 390 Score = 216 bits (549), Expect = 1e-60 Identities = 159/396 (40%), Positives = 204/396 (51%), Gaps = 28/396 (7%) Query: 10 RTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGEDNRNVARM 69 RTP R G AL V L A + +L+E G+ +V D++ G A AG N AR+ Sbjct: 18 RTPLARAGTALAGVPVHRLLAPVLDALLEET-GLAPEQVADVVVGNAVGAGG---NPARL 73 Query: 70 AGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRAPFVMGKA 129 A L AGLP +VPG TV+R CGS LDAV +A ++G + +AGG ES++ AP + Sbjct: 74 AALEAGLPQSVPGLTVDRQCGSGLDAVVLACHLARAGAGRAFLAGGAESISTAPLRGRRQ 133 Query: 130 ES---AFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDAFALR 186 E AF R A +G +P M E AE VA + I R QDAFALR Sbjct: 134 EDGGVAFYRRAQFAPEHLG----DP---------DMGEAAETVAREHGIGRERQDAFALR 180 Query: 187 SQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVVRPDGT 246 S +R AA AAG FAGE+ P+ P+ VT D PRP A LA+ V GT Sbjct: 181 SHRRALAAAAAGAFAGELVPVRTPRG-----AVTADNGPRPRLDAALLARFPPVFAAGGT 235 Query: 247 VTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPAVRKVL 306 VTAGN+ G DGA A+L+A P AA G AT GV P +G G A A R++L Sbjct: 236 VTAGNSCGDADGAAAVLVADPAAARELGTATALAFRGAATVGVDPARLGLGAAVAARRLL 295 Query: 307 AQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGASGA-RL 365 A+ + + + E NEAFA Q LA LGL ++ +N GGA+A+GH GASGA + Sbjct: 296 AEQAVPVRALAAAEFNEAFAGQVLACTDLLGLDEEV--LNAEGGALALGHAYGASGAVSV 353 Query: 366 VTTAINQLERSGGRYALCTMCIGVGQGIALVIERVA 401 V E G L + G G A + E+VA Sbjct: 354 VRLLARARELPEGSLLLAMISSAGGIGTAALFEKVA 389 Lambda K H 0.320 0.135 0.394 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: 438 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: 390 Length adjustment: 31 Effective length of query: 370 Effective length of database: 359 Effective search space: 132830 Effective search space used: 132830 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 24 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