Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate Echvi_1105 Echvi_1105 Homogentisate 1,2-dioxygenase
Query= reanno::MR1:201124 (386 letters) >FitnessBrowser__Cola:Echvi_1105 Length = 386 Score = 327 bits (837), Expect = 5e-94 Identities = 168/387 (43%), Positives = 233/387 (60%), Gaps = 3/387 (0%) Query: 1 MPFYVKQGQVPHKRHIAFEKENGELYREELFSTHGFSNIYSNKYHHNMPTKALEVA-PYR 59 M FY + G++P KRH F + +G LY+EEL S+ GFS IY+ YH + P + + P+ Sbjct: 1 MAFYHRLGEIPPKRHTQFRQPDGSLYKEELVSSKGFSGIYATLYHIHNPNRVTAMGQPFP 60 Query: 60 LGHGAHWEDSLVQNYKLDSRSADREGNFFSARNKIFYNNDVAIYTAKVTQDTAEFY-RNA 118 + L Q + S A ++ SAR + N+DV + + Y +NA Sbjct: 61 FSWEIASDYGLQQTHLDTSAVAVTGADYLSARKILLRNHDVMMGICIPEHPQMDHYFKNA 120 Query: 119 YADEVVFVHEGEGTLYSEYGTLEIKKWDYLVIPRGTTHQLKFNNYSNVRLFVIEAFSMVE 178 DEV+F+HEG G L+S++G L +K DY+VIPR T ++ ++ VRL +IEA + +E Sbjct: 121 DGDEVIFIHEGSGVLFSQFGRLAVKAGDYVVIPRTTIYRFEWEK-GKVRLLIIEASNPIE 179 Query: 179 VPKHCRNEYGQLLESAPYCERDLRTPILQAAVVERGAFPLVCKFGDKYQLTTLEWHPFDL 238 + RN+ GQLLE +PYCERD+R P E+G + + K E P D+ Sbjct: 180 TVRRYRNDVGQLLEHSPYCERDIRVPDRLVVEEEKGDYLIQIKKNGHLYPYHYEHSPLDV 239 Query: 239 VGWDGCVYPWAFNITEYAPKVGKIHLPPSDHLVFTAHNFVVCNFVPRPYDFHERAIPAPY 298 VGWDG +YP+A +I ++ P G+IH PP H F + FV+C+FVPR +D+H ++IPAPY Sbjct: 240 VGWDGYLYPYALSIHDFEPITGRIHQPPPVHQTFQSAGFVICSFVPRLFDYHPQSIPAPY 299 Query: 299 YHNNIDSDEVLYYVDGDFMSRTGIEAGYITLHQKGVAHGPQPGRTEASIGKKETYEYAVM 358 H+NIDSDEVLYYVDG+FMSR GI+ G TLH G+ HGP PG E SIG +T E AVM Sbjct: 300 NHSNIDSDEVLYYVDGEFMSRKGIQKGSFTLHMGGLPHGPHPGMVEKSIGATKTEETAVM 359 Query: 359 VDTFAPLKLTEHVQHCMSKDYNRSWLE 385 +DTF PL+LT+ + K Y SW E Sbjct: 360 LDTFRPLQLTQEALQYVDKRYPMSWTE 386 Lambda K H 0.321 0.137 0.435 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: 557 Number of extensions: 30 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: 386 Length of database: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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