Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate WP_050654910.1 C1M55_RS10190 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing)
Query= BRENDA::Q9L3I0 (626 letters) >NCBI__GCF_002893965.1:WP_050654910.1 Length = 651 Score = 520 bits (1340), Expect = e-152 Identities = 279/636 (43%), Positives = 393/636 (61%), Gaps = 23/636 (3%) Query: 7 REDPMGKTIRLTMAQAVAHFLKVQMTIVDGKKVPIFGGVWAIFGHGNVAGIGEALYQV-- 64 R++P T+ LT++QAV FL Q T DG++ +F G + IFGHGNVAG+G+AL Q Sbjct: 14 RDEP---TVYLTVSQAVVRFLANQYTERDGQRTKLFAGCFGIFGHGNVAGLGQALLQAEI 70 Query: 65 ------REELTTY-RAHNEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAH 117 RE Y NEQ M H+A+A+A+ R + A +SS+GPGA NM+T A +A Sbjct: 71 QDLDAGREPTLPYVLGRNEQAMVHSAVAHARMKDRLQTWAVSSSVGPGATNMITGAALAT 130 Query: 118 VNRIPVLFLPGDVFANRAPDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITAL 177 +NR+PVL LP D FA RA PVLQ++E ++ V+ NDAF+ VSRYFDR+ RPEQ+ +AL Sbjct: 131 INRLPVLLLPADTFATRASAPVLQELELPSSGDVTVNDAFKPVSRYFDRVWRPEQLPSAL 190 Query: 178 KRAMQVLTDPLDCGPVTLSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALI 237 M+VLTDP++ G VT+++ QDVQAEA+D+PES FAE+VW RP P+ + A A+I Sbjct: 191 LAGMRVLTDPVETGAVTIAIPQDVQAEAFDWPESFFAERVWHVARPLPERSVIERAAAII 250 Query: 238 KASQKPVIVAGGGVLYSQATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGT 297 ++++KP+IVAGGGV+YSQAT LAAF GIPV SQAGK ++ HP ++G+VG TGT Sbjct: 251 RSARKPLIVAGGGVIYSQATDSLAAFCAQTGIPVGQSQAGKGSLVYDHPQSVGAVGSTGT 310 Query: 298 SAANAIAEETDLVIAVGTRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADA 357 +AANA+A E D+VI +GTR DFT+ S F N ++ + +N+A+ D+VK +VADA Sbjct: 311 TAANALATEADVVIGIGTRYSDFTSASRTAFTNPDVRFVNINVASLDSVKQGGVSVVADA 370 Query: 358 REGLKALSAGLSGWKAPAALAEKAAAEKKIW---MEAAARAMATTNAALPSDAQVIGAVA 414 RE L AL+ L+ ++ A + + W +E+ + QVIG V Sbjct: 371 REALDALALALNDYRVDEEYASRIGDLARDWDAIVESVYNPAEPAADGSLNQNQVIGLV- 429 Query: 415 RTIGGENTTVLCAAGGLPGELHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMARPERD 474 T+ V+CAAG +PG+LHKLW YH+EYG+SCMGYE+AGGLG +MA P+RD Sbjct: 430 NTLSDPRDVVVCAAGSMPGDLHKLWRTRDSKGYHVEYGYSCMGYEVAGGLGVRMACPDRD 489 Query: 475 VVVMVGDGSYMMMNSELATSVMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSY 534 V VMVGDGSY+MM +EL T+V LK+ ++++ N G+ I L G F + Sbjct: 490 VFVMVGDGSYLMMATELVTAVQERLKVIVVLVQNHGFASIGSLSESLGSQRFGTQYRYRS 549 Query: 535 HE------VMPEIDFRAHAESMGAIAVKVASIAELEQALADSRKNDRTSVFVIDTDPLIT 588 ++ V+P +D A+A S+G ++ + AE A+ ++ +D ++V ++TDPLI Sbjct: 550 NDGRLDGGVLP-VDLAANAASLGVDVIRANTAAEFADAIKVAKASDTSTVIHVETDPLIG 608 Query: 589 TEAGGHWWDVAVPEVSSRSEVNRAHEAYVKARAAQR 624 WWDV V S +A Y + QR Sbjct: 609 APDSESWWDVPVSATSELESTKKARTTYESWKKIQR 644 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: 940 Number of extensions: 35 Number of successful extensions: 4 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: 651 Length adjustment: 38 Effective length of query: 588 Effective length of database: 613 Effective search space: 360444 Effective search space used: 360444 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: 54 (25.4 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