Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate GFF710 PGA1_c07250 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase IolD
Query= BRENDA::Q9L3I0 (626 letters) >FitnessBrowser__Phaeo:GFF710 Length = 624 Score = 556 bits (1434), Expect = e-163 Identities = 295/622 (47%), Positives = 399/622 (64%), Gaps = 12/622 (1%) Query: 13 KTIRLTMAQAVAHFLKVQMTIVDGKKVPIFGGVWAIFGHGNVAGIGEALYQVREELTTYR 72 KT++LT AQA+ +L Q VDG+++ + GG + IFGHGNV +GEALY+ R+ L YR Sbjct: 6 KTVKLTTAQAIIRWLSNQFIEVDGEELRLCGGGFGIFGHGNVTCLGEALYEARDALPLYR 65 Query: 73 AHNEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAHVNRIPVLFLPGDVFA 132 NEQ M AA YAK R RFM CT+S GPG N++T+A +AH NR+P+L L GD F Sbjct: 66 GQNEQSMGFAAAGYAKQWLRQRFMFCTASAGPGTSNLLTSAALAHANRLPMLMLCGDTFL 125 Query: 133 NRAPDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITALKRAMQVLTDPLDCGP 192 R PDPVLQQ+E+ + NDAF+ VSRY+DRIT P QII +L A+ + DP DCGP Sbjct: 126 TRLPDPVLQQMENFNDPTFGVNDAFKPVSRYWDRITHPAQIIQSLPAAIATMLDPGDCGP 185 Query: 193 VTLSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALIKASQKPVIVAGGGVL 252 L L QDVQ YDYPE F +K+ RR PDA E+A A A ++ +++P+I+AGGGV Sbjct: 186 AFLGLPQDVQGWTYDYPEVFFEKKIHRIRRVTPDASEIAEAAAALRGAKRPMIIAGGGVQ 245 Query: 253 YSQATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGTSAANAIAEETDLVIA 312 YS+A EL AFAE H IPVV + AG++ + +THPL +G +GVTG+ +ANAIA E D+++A Sbjct: 246 YSRAVAELTAFAETHQIPVVETIAGRANLRDTHPLNIGPIGVTGSDSANAIAAEADVILA 305 Query: 313 VGTRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADAREGLKALSAGLSGWK 372 VGTR QDFTTGSW F D+ + I +N A +DA KH S P+V DA+ L+ L A G+ Sbjct: 306 VGTRLQDFTTGSWTAFAQDA-QFISINAARHDAGKHRSLPVVGDAQRALRDLGAACEGYS 364 Query: 373 APAALAEKAAAEKKIWMEAAARAMATTNAALPSDAQVIGAVARTIGGENTTVLCAAGGLP 432 P +A E+ W+ A ++ + S AQ IG V + V+ AAGGLP Sbjct: 365 TPQDWVARAQEERHSWVAYVADNVSYGDNRPNSYAQAIG-VVNALCNPKDRVVAAAGGLP 423 Query: 433 GELHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMAR----PERDVVVMVGDGSYMMMN 488 E+ W PG+ +E+GFSCMGYEIAG GA++A+ P+RD +V VGDGSYMM+N Sbjct: 424 AEVTANWRTLEPGTVDVEFGFSCMGYEIAGAWGARIAQAEREPDRDTIVFVGDGSYMMLN 483 Query: 489 SELATSVMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSYHEVMPE---IDFRA 545 S++ +SV+ KL I+VLDN G+ IN+LQ TG +FNNLL+D +PE +DF + Sbjct: 484 SDIYSSVLSQKKLIILVLDNGGFAVINKLQNNTGNTSFNNLLEDC--PTIPEAFGVDFAS 541 Query: 546 HAESMGAIAVKVASIAELEQALADSRKNDRTSVFVIDTDPLITTEAGGH-WWDVAVPEVS 604 HA SMGA+ VA+ AEL +A ++ +DRT+V V+ D GH WW+V P ++ Sbjct: 542 HAASMGALTETVANPAELGEAFKRAQASDRTTVIVMKVDAYEGWTTEGHAWWEVGTPHIT 601 Query: 605 SRSEVNRAHEAYVKARAAQRVG 626 + +V AH + +R+ QR G Sbjct: 602 NDPKVQEAHVDWESSRSRQRRG 623 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: 959 Number of extensions: 35 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: 624 Length adjustment: 38 Effective length of query: 588 Effective length of database: 586 Effective search space: 344568 Effective search space used: 344568 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