Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate CCNA_01357 CCNA_01357 myo-inositol catabolism protein IolD
Query= BRENDA::Q9L3I0 (626 letters) >FitnessBrowser__Caulo:CCNA_01357 Length = 614 Score = 726 bits (1873), Expect = 0.0 Identities = 368/612 (60%), Positives = 449/612 (73%), Gaps = 2/612 (0%) Query: 15 IRLTMAQAVAHFLKVQMTIVDGKKVPIFGGVWAIFGHGNVAGIGEALYQVREELTTYRAH 74 +RLT AQA +L Q +VP F GVWAIFGHGNVAG+GEAL+ VR+ L TYRAH Sbjct: 4 VRLTAAQATVRWLAAQHVETSDGEVPYFAGVWAIFGHGNVAGLGEALHGVRDVLLTYRAH 63 Query: 75 NEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAHVNRIPVLFLPGDVFANR 134 NEQGMAHAAIA+AK + R R M CT+SIGPGA NMVTAA +AHVNR+PVLFLPGDV+A+R Sbjct: 64 NEQGMAHAAIAFAKQSRRERAMVCTTSIGPGATNMVTAAALAHVNRLPVLFLPGDVYASR 123 Query: 135 APDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITALKRAMQVLTDPLDCGPVT 194 PDPVLQQIED ++SAN+ F+ VSRYFDRITRPEQI+ AL RA+ V+ DP CGP T Sbjct: 124 RPDPVLQQIEDFGDGTISANECFKPVSRYFDRITRPEQILDALPRALAVMLDPATCGPAT 183 Query: 195 LSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALIKASQKPVIVAGGGVLYS 254 L+ CQDVQAEA+DYP++ FA++VW R PQPD EL + + LIKA+++P+IVAGGGVLY+ Sbjct: 184 LAFCQDVQAEAFDYPQAFFAKRVWRIRAPQPDPRELDDLVGLIKAAERPLIVAGGGVLYA 243 Query: 255 QATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGTSAANAIAEETDLVIAVG 314 +A LA A G+PVV +Q GK ++ HPL LG+VGVTGT+A+ A AE DLVI +G Sbjct: 244 RAEAALADLANDAGLPVVETQGGKGSLAWDHPLNLGAVGVTGTTASVAAAEAADLVIGLG 303 Query: 315 TRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADAREGLKALSAGLSGWKAP 374 TR QDFTTGS ALF + K++ +N+A +DA KH + +V DA L+AL+ L GW+AP Sbjct: 304 TRLQDFTTGSRALFGAEGRKLVQVNVAPHDAHKHGATSVVGDALAVLEALAERLDGWRAP 363 Query: 375 AALAEKAAAEKKIWMEAAARAMATTNAALPSDAQVIGAVARTIGGENTTVLCAAGGLPGE 434 A ++A + W + LP+DAQV+GAV R +++ V+CAAGGLPGE Sbjct: 364 VAWTDQATSGVPAWNAIFDASTRADTRPLPTDAQVLGAVWRA-SSDDSVVVCAAGGLPGE 422 Query: 435 LHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMARPERDVVVMVGDGSYMMMNSELATS 494 LHKLW PG YH+EYGFSCMGYEIAG +G KMA P+R+V VMVGDGSY+M+NSELATS Sbjct: 423 LHKLWRTRMPGGYHVEYGFSCMGYEIAGAVGVKMAEPDREVHVMVGDGSYLMLNSELATS 482 Query: 495 VMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSYHEVMPEIDFRAHAESMGAIA 554 VMLG KL + VLDNRGYGCINRLQ TGGA FNNLL D+ HE +P+IDF AHA S+GA + Sbjct: 483 VMLGTKLIVTVLDNRGYGCINRLQAATGGAAFNNLLADTLHETLPDIDFAAHAASLGARS 542 Query: 555 VKVASIAELEQALADSRKNDRTSVFVIDTDPLITTEAGGHWWDVAVPEVSSRSEVNRAHE 614 KV ++ LE AL ++ +DRT V VIDTDP+ TTE GG WWDVAVPEVS R VN A Sbjct: 543 EKVGDLSSLEAALQRAKASDRTYVVVIDTDPMPTTE-GGAWWDVAVPEVSVRPSVNAARA 601 Query: 615 AYVKARAAQRVG 626 Y QR G Sbjct: 602 DYDLKIKQQRTG 613 Lambda K H 0.318 0.131 0.382 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: 1052 Number of extensions: 35 Number of successful extensions: 3 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: 626 Length of database: 614 Length adjustment: 37 Effective length of query: 589 Effective length of database: 577 Effective search space: 339853 Effective search space used: 339853 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 (21.7 bits) S2: 53 (25.0 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