Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate CA265_RS03135 CA265_RS03135 homogentisate 1,2-dioxygenase
Query= reanno::MR1:201124 (386 letters) >FitnessBrowser__Pedo557:CA265_RS03135 Length = 388 Score = 356 bits (914), Expect = e-103 Identities = 184/388 (47%), Positives = 242/388 (62%), Gaps = 4/388 (1%) Query: 1 MPFYVKQGQVPHKRHIAFEKENGELYREELFSTHGFSNIYSNKYHHNMPTKALEVA-PYR 59 MP Y K GQ+P KRH F K +G LY EEL ST GFS++YS YH + PT + PY Sbjct: 1 MPIYHKLGQIPAKRHTVFRKPDGNLYAEELVSTEGFSSLYSLVYHCHPPTIVKHLGEPYS 60 Query: 60 LGHGAHWEDSLVQNYKLDSRSADREGNFFSARNKIFYNNDVAIYTAKVTQDTAE-FYRNA 118 + E L ++ L + E +F +R + NND+ I A + + FY+N+ Sbjct: 61 VEPKIAREKHL-KHTSLIGFNITPEDDFLKSRKAVLVNNDLHIVLAAPRKSMTDYFYKNS 119 Query: 119 YADEVVFVHEGEGTLYSEYGTLEIKKWDYLVIPRGTTHQLKFNNYSNVRLFVIEAFSMVE 178 ADE++FVHEG G L + +G ++ DYL+IPRGT +QL+F+ N RLF++E+FS + Sbjct: 120 QADEMIFVHEGSGKLKTGFGEIKFAYGDYLIIPRGTIYQLEFDTEQN-RLFIVESFSPLR 178 Query: 179 VPKHCRNEYGQLLESAPYCERDLRTPILQAAVVERGAFPLVCKFGDKYQLTTLEWHPFDL 238 PK N++GQL+E APYCERDLR P E G F ++ K T HPFD Sbjct: 179 PPKRYLNQFGQLMEHAPYCERDLRLPENLQTHDEYGDFKVLIKKQGLIYPYTYGTHPFDY 238 Query: 239 VGWDGCVYPWAFNITEYAPKVGKIHLPPSDHLVFTAHNFVVCNFVPRPYDFHERAIPAPY 298 VGWDG YP+AF+I ++ P G++H PP H F HNFVVC+FVPR YD+H +IPAPY Sbjct: 239 VGWDGYHYPYAFSIHDFEPITGRLHQPPPVHQTFEGHNFVVCSFVPRKYDYHPDSIPAPY 298 Query: 299 YHNNIDSDEVLYYVDGDFMSRTGIEAGYITLHQKGVAHGPQPGRTEASIGKKETYEYAVM 358 H+N+DSDEVLYYVDGDFMSR + G ITLH G+ HGP PG E SIGK++T E AVM Sbjct: 299 NHSNVDSDEVLYYVDGDFMSRKSVFKGQITLHPGGIPHGPHPGTVEKSIGKEKTDELAVM 358 Query: 359 VDTFAPLKLTEHVQHCMSKDYNRSWLEN 386 +D F PL LT+ ++Y++SW N Sbjct: 359 IDPFKPLMLTQDALDIEDENYHKSWQVN 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: 630 Number of extensions: 34 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: 388 Length adjustment: 30 Effective length of query: 356 Effective length of database: 358 Effective search space: 127448 Effective search space used: 127448 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