Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate H281DRAFT_04458 H281DRAFT_04458 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
Query= BRENDA::Q9L3I0 (626 letters) >FitnessBrowser__Burk376:H281DRAFT_04458 Length = 661 Score = 681 bits (1757), Expect = 0.0 Identities = 361/620 (58%), Positives = 443/620 (71%), Gaps = 13/620 (2%) Query: 12 GKTIRLTMAQAVAHFLKVQMTIV-DGKKV-PIFGGVWAIFGHGNVAGIGEALYQVREELT 69 G TIRLT AQA+ +L Q DG P+FGGV+AIFGHGNVAG+GEALYQ R+EL Sbjct: 22 GTTIRLTTAQALVRYLAAQRVATEDGSGTEPLFGGVFAIFGHGNVAGMGEALYQHRDELP 81 Query: 70 TYRAHNEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAHVNRIPVLFLPGD 129 T RAHNEQ MAH+AIAYAKA+FR R MA T+SIGPGA N++TAA +AHVNR+PVL LPGD Sbjct: 82 TLRAHNEQAMAHSAIAYAKAHFRRRMMAVTTSIGPGATNLLTAAALAHVNRLPVLLLPGD 141 Query: 130 VFANRAPDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITALKRAMQVLTDPLD 189 +F +RAPDPVLQQ+ED VSANDAF+ VSRYFDRI P Q+++AL RA++VLTD Sbjct: 142 IFVSRAPDPVLQQVEDFHDGGVSANDAFKPVSRYFDRIMHPAQLLSALPRALRVLTDAAS 201 Query: 190 CGPVTLSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALIKASQKPVIVAGG 249 CGPVTL+L QDVQA+A+D+P FA ++ T P P DE+ A+A ++ +++P+IVAGG Sbjct: 202 CGPVTLALPQDVQAQAWDFPADFFAPRIVTFYAPAPRVDEIDAAVARLQRAKRPLIVAGG 261 Query: 250 GVLYSQATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGTSAANAIAEETDL 309 GVLY +AT L FA AHGIPV +QAGKS++ PL GS+GVTG+ AANA+A + D Sbjct: 262 GVLYGRATDALQRFAAAHGIPVAETQAGKSSLAWDDPLNAGSLGVTGSPAANALARDADC 321 Query: 310 VIAVGTRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADAREGLKALSAGLS 369 V+A+GTR QDFTTGS LF +IG+N A+DA+KH + + ADAR L AL+ L Sbjct: 322 VLALGTRLQDFTTGSNTLF--TQADVIGINANAFDALKHRAQVVEADARLALDALAERLQ 379 Query: 370 GWKAPAALAEKAAAEKKIWMEA--AARAMATTNAALPSDAQVIGAVAR--TIGGENTTVL 425 W+A A +A W + + LP + VIGAV R T N V+ Sbjct: 380 DWQADRAWTSRAHELAASWRDTVHTLTHAPQRESVLPYEGDVIGAVQRSSTDSPANDIVV 439 Query: 426 CAAGGLPGELHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMARPERDVVVMVGDGSYM 485 CAAG LPGELHKLW A PG+YH+EYG+SCMGYEIAGGLG K+ARPER+V+VMVGDGSY+ Sbjct: 440 CAAGTLPGELHKLWRAGTPGAYHVEYGYSCMGYEIAGGLGVKLARPEREVIVMVGDGSYL 499 Query: 486 MMNSELATSVMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSYHEVM--PEIDF 543 MMNSE+ATSVMLG KL ++VLDNRGYGCINRLQ GGA FNNLL+DS + P+IDF Sbjct: 500 MMNSEIATSVMLGAKLIVVVLDNRGYGCINRLQQACGGAPFNNLLEDSMQGPLGAPQIDF 559 Query: 544 RAHAESMGAIAVKVASIAELEQALADSRKNDRTSVFVIDTDPLITTEAGGHWWDVAVPEV 603 AHA ++GA A A++AELE AL +R DRT V IDTDP TT GG WW+VAVPEV Sbjct: 560 AAHARALGARAEHAANVAELEAALQRARSADRTYVISIDTDPARTTSDGGWWWEVAVPEV 619 Query: 604 SSRSEVNRA---HEAYVKAR 620 S R+ V A ++A + AR Sbjct: 620 SPRASVREARANYDAQISAR 639 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: 1053 Number of extensions: 37 Number of successful extensions: 5 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: 661 Length adjustment: 38 Effective length of query: 588 Effective length of database: 623 Effective search space: 366324 Effective search space used: 366324 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 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