Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate BPHYT_RS13915 BPHYT_RS13915 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
Query= BRENDA::Q9L3I0 (626 letters) >FitnessBrowser__BFirm:BPHYT_RS13915 Length = 657 Score = 660 bits (1702), Expect = 0.0 Identities = 351/618 (56%), Positives = 433/618 (70%), Gaps = 10/618 (1%) Query: 14 TIRLTMAQAVAHFLKVQMTIV-DGKKV-PIFGGVWAIFGHGNVAGIGEALYQVREELTTY 71 T+RLT AQA+ +L Q DG+ P+FGGV+AIFGHGNVAGIGEALYQ REEL T Sbjct: 26 TVRLTTAQALVRYLAAQRVATEDGEGTEPLFGGVFAIFGHGNVAGIGEALYQHREELPTL 85 Query: 72 RAHNEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAHVNRIPVLFLPGDVF 131 RAHNEQ MAH+AIAYAKA+FR R MA T+SIGPGA N+VTAA +AHVNR+PVL LPGD+F Sbjct: 86 RAHNEQAMAHSAIAYAKAHFRRRMMAVTTSIGPGATNLVTAAALAHVNRLPVLLLPGDIF 145 Query: 132 ANRAPDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITALKRAMQVLTDPLDCG 191 +RAPDPVLQQ+ED VSANDA + VSRYFDRI P Q++ AL RA++VLTD CG Sbjct: 146 VSRAPDPVLQQVEDFHDGGVSANDALKPVSRYFDRIVHPAQLLNALPRAVRVLTDAALCG 205 Query: 192 PVTLSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALIKASQKPVIVAGGGV 251 PVTL+L QDVQA+A+D+P F +V T P P ADE+ AIA ++ +++P+IVAGGG+ Sbjct: 206 PVTLALPQDVQAQAWDFPVDFFKPRVVTFYSPAPRADEIEAAIARLRHAKRPLIVAGGGL 265 Query: 252 LYSQATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGTSAANAIAEETDLVI 311 LY +AT L FA HGIPV +QAGK A+ PL G++GVTG+ AANA+A + D V+ Sbjct: 266 LYGRATDALHRFATTHGIPVAETQAGKGALAWNDPLNAGALGVTGSPAANALAHDADCVL 325 Query: 312 AVGTRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADAREGLKALSAGLSGW 371 A+GTR QDFTTGS LF +I +N A+D +K + + ADAR L+AL+ L GW Sbjct: 326 AIGTRLQDFTTGSNTLF--TQADVIAVNANAFDGLKQRAQVVEADARLALEALAEPLQGW 383 Query: 372 KAPAALAEKAAAEKKIWMEAAARA--MATTNAALPSDAQVIGAVARTIGGE--NTTVLCA 427 A A +A W + + + LP + VIGAV R+ N V+CA Sbjct: 384 HADRAWTARAHKLAASWRDTVSTLTHAPQRDTVLPYEGDVIGAVQRSSASSPTNDIVVCA 443 Query: 428 AGGLPGELHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMARPERDVVVMVGDGSYMMM 487 AG LP ELHKLW A PG+YH+EYG+SCMGYEIAGGLG K+ARP R+V+VMVGDGSY+MM Sbjct: 444 AGTLPAELHKLWRAGKPGAYHVEYGYSCMGYEIAGGLGVKLARPAREVIVMVGDGSYLMM 503 Query: 488 NSELATSVMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSYHEVM--PEIDFRA 545 NSE+ATSVM+G KL ++VLDNRGYGCINRLQ GGA FNNLL++ + P+IDF A Sbjct: 504 NSEIATSVMIGAKLIVVVLDNRGYGCINRLQQACGGAPFNNLLENCMQGPLGAPKIDFAA 563 Query: 546 HAESMGAIAVKVASIAELEQALADSRKNDRTSVFVIDTDPLITTEAGGHWWDVAVPEVSS 605 HA ++GA A A++AEL AL +R DRT V IDTDP TT+ GG WW+VAVPEVS+ Sbjct: 564 HARALGAQAEHAANVAELAAALQRARAADRTYVISIDTDPAHTTDEGGWWWEVAVPEVST 623 Query: 606 RSEVNRAHEAYVKARAAQ 623 R V A Y AA+ Sbjct: 624 RPAVRDARAKYETQLAAR 641 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: 1057 Number of extensions: 39 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: 657 Length adjustment: 38 Effective length of query: 588 Effective length of database: 619 Effective search space: 363972 Effective search space used: 363972 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