Align Catechol 1,2-dioxygenase; EC 1.13.11.1 (characterized)
to candidate HSERO_RS18575 HSERO_RS18575 hydroxyquinol 1,2-dioxygenase
Query= SwissProt::P86029 (303 letters) >FitnessBrowser__HerbieS:HSERO_RS18575 Length = 288 Score = 197 bits (500), Expect = 3e-55 Identities = 106/265 (40%), Positives = 152/265 (57%), Gaps = 9/265 (3%) Query: 20 RAKKLIASLVQHVHDFARENHLTTEDWLWGVDFINRIGQMSDSRRNEGILVCDIIGLETL 79 R ++++ SLVQH+H FARE LT ++W G+DF+ GQ+ +R E IL+ D +GL TL Sbjct: 24 RLREIMTSLVQHLHAFAREVKLTEKEWFAGIDFLTETGQICSDQRQEFILLSDTLGLSTL 83 Query: 80 VDALTNESEQSNHTSSAILGPFYLPDSPVYPNGGSIVQKAIPTDVKCFVRGKVTDTEGKP 139 V A N + + T + + GPF++ D+P YP G I A CFV G V G+P Sbjct: 84 VMAQQNH-KPAGCTEATVFGPFHVEDAPQYPLGADIANGA--KGEPCFVSGSVRGRNGRP 140 Query: 140 LGGAQLEVWQCNSAGFYS-QQADHDGPEFNLRGTFITDDEGNYSFECLRPTSYPIPYDGP 198 L A++EVWQ + GFY Q AD D ++ RGT TD EG Y F + YPIP+DGP Sbjct: 141 LAHARMEVWQADENGFYDVQYADLD--QYRARGTLFTDAEGRYHFRSILANPYPIPHDGP 198 Query: 199 AGDLLKIMDRHPNRPSHIHWRVSHPGYHTLITQIYDAECPYTNNDSVYAVKDDIIVHF-- 256 G +L+ + RHP RP+H+H+R+ GY TLIT ++ + Y ++D+V+ V+ +I + Sbjct: 199 VGRMLEKLGRHPWRPAHLHFRIQAEGYETLITHVFRRDDVYLDSDAVFGVRSTLIADWPC 258 Query: 257 -EKVDNKDKDLVGKVEYKLDYDISL 280 D + Y LDYD L Sbjct: 259 HPAGTAPDGTQCEQPFYTLDYDFVL 283 Lambda K H 0.316 0.134 0.407 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: 278 Number of extensions: 13 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: 303 Length of database: 288 Length adjustment: 26 Effective length of query: 277 Effective length of database: 262 Effective search space: 72574 Effective search space used: 72574 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 (21.6 bits) S2: 48 (23.1 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