Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate WP_110806484.1 C8J30_RS14065 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing)
Query= BRENDA::Q9L3I0 (626 letters) >NCBI__GCF_003217355.1:WP_110806484.1 Length = 613 Score = 686 bits (1771), Expect = 0.0 Identities = 364/615 (59%), Positives = 438/615 (71%), Gaps = 7/615 (1%) Query: 12 GKTIRLTMAQAVAHFLKVQMTIVDGKKVPIFGGVWAIFGHGNVAGIGEALYQVREELTTY 71 G+TIRLT AQA+ +L VQMT +G++ GVWAIFGHGNVAGIGEAL+ + + L T+ Sbjct: 3 GETIRLTAAQAMMRWLSVQMT-EEGER--FLEGVWAIFGHGNVAGIGEALHGIGDALPTW 59 Query: 72 RAHNEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAHVNRIPVLFLPGDVF 131 R NEQ MAHAAIAYAK R R MA TSSIGPGA NMVTAA +AHVNR+PVLF+PGDVF Sbjct: 60 RGQNEQTMAHAAIAYAKTMKRKRAMAVTSSIGPGATNMVTAAALAHVNRLPVLFIPGDVF 119 Query: 132 ANRAPDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITALKRAMQVLTDPLDCG 191 ANR PDPVLQQIED ++SAND FR V RYFDRI+RPE ++TAL RA V+TDP +CG Sbjct: 120 ANRRPDPVLQQIEDFDDGTISANDCFRPVVRYFDRISRPEHLLTALPRAFAVMTDPANCG 179 Query: 192 PVTLSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALIKASQKPVIVAGGGV 251 PV L+ CQDVQAEA+DYP FA KVW RRP+PD ELA +ALIKA++ PVIVAGGGV Sbjct: 180 PVCLAFCQDVQAEAFDYPVEFFAPKVWRIRRPEPDLQELAEVVALIKAAEAPVIVAGGGV 239 Query: 252 LYSQATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGTSAANAIAEETDLVI 311 +YS A +LAAFA AH IP V +QAGK A GS GVTG++ AN + + DLV+ Sbjct: 240 IYSGAEADLAAFAAAHNIPFVETQAGKGANGWDDAFNFGSPGVTGSACANELCAKADLVL 299 Query: 312 AVGTRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADAREGLKALSAGLSGW 371 VGTR QDFTTGSW +F + K++ +N+A YDA+KH + LV DA+ L+ +SA L Sbjct: 300 GVGTRFQDFTTGSWTVFGAEGRKLVSINLAGYDALKHGAVGLVGDAKVCLQKISAALGDH 359 Query: 372 KAPA-ALAEKAAAEKKIWMEAAARAMATTNAALPSDAQVIGAVARTIGGENTTVLCAAGG 430 KAPA A + A + + + A A N LPSDAQVIGAV R + +++ V+CAAG Sbjct: 360 KAPAFDAASRLAWQAAVKVVTAPPARGDAN-NLPSDAQVIGAVQRVV-TKDSIVMCAAGT 417 Query: 431 LPGELHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMARPERDVVVMVGDGSYMMMNSE 490 +PG L LW A APG YHMEYG+SCMGYE+AG LG +ARP ++V+ VGDGSYMM NSE Sbjct: 418 MPGALQVLWQA-APGGYHMEYGYSCMGYEVAGALGIALARPGKEVICFVGDGSYMMANSE 476 Query: 491 LATSVMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSYHEVMPEIDFRAHAESM 550 LAT+VM + I++ DNRGYGCINRLQ GGA FNNL KD E P+IDF AHA SM Sbjct: 477 LATAVMRHVPFTIVLTDNRGYGCINRLQQECGGAEFNNLYKDCRIEEGPQIDFVAHAASM 536 Query: 551 GAIAVKVASIAELEQALADSRKNDRTSVFVIDTDPLITTEAGGHWWDVAVPEVSSRSEVN 610 GA A KV SIA+LE A+ +R SV +IDTDP+ T AGGHWWDVAVP+V + + Sbjct: 537 GAHAEKVGSIADLEAAIVAARGRKIPSVILIDTDPVPGTGAGGHWWDVAVPQVGGPARLE 596 Query: 611 RAHEAYVKARAAQRV 625 A E YVKA A Q V Sbjct: 597 AARERYVKAAARQNV 611 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: 1021 Number of extensions: 45 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: 626 Length of database: 613 Length adjustment: 37 Effective length of query: 589 Effective length of database: 576 Effective search space: 339264 Effective search space used: 339264 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 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