Align protocatechuate 3,4-dioxygenase, beta chain; EC 1.13.11.3 (characterized)
to candidate BWI76_RS13290 BWI76_RS13290 protocatechuate 3,4-dioxygenase subunit beta
Query= CharProtDB::CH_121290 (241 letters) >FitnessBrowser__Koxy:BWI76_RS13290 Length = 246 Score = 348 bits (894), Expect = e-101 Identities = 161/227 (70%), Positives = 183/227 (80%) Query: 12 RNTEDHPPAYAPGYKTSVLRSPKNALISIAETLSEVTAPHFSADKFGPKDNDLILNYAKD 71 R+ HPPAYAPGYKTSVLRSP+NALIS+ +LSE+T P FS+D G DNDLILNYAKD Sbjct: 13 RDYSSHPPAYAPGYKTSVLRSPRNALISLQNSLSEITGPVFSSDDLGALDNDLILNYAKD 72 Query: 72 GLPIGERVIVHGYVRDQFGRPVKNALVEVWQANASGRYRHPNDQYIGAMDPNFGGCGRML 131 GLPIGER+IVHGYVRD FGRP+KN LVEVWQANA GRYRH DQY+ +DPNFGGCGR+L Sbjct: 73 GLPIGERIIVHGYVRDGFGRPMKNTLVEVWQANAGGRYRHKKDQYLAPIDPNFGGCGRVL 132 Query: 132 TDDNGYYVFRTIKPGPYPWRNRINEWRPAHIHFSLIADGWAQRLISQFYFEGDTLIDSCP 191 TD+NGYY FRTIKPGPYPWRN++++WRPAHIHFSL D WAQRLI+Q YFEGD LI CP Sbjct: 133 TDENGYYCFRTIKPGPYPWRNQVSDWRPAHIHFSLCGDAWAQRLITQMYFEGDPLIKQCP 192 Query: 192 ILKTIPSEQQRRALIALEDKSNFIEADSRCYRFDITLRGRRATYFEN 238 I+KTI ++ R LIA D + DS YRFD+ LRG RAT FEN Sbjct: 193 IVKTINNDDAIRTLIAELDTHAAVPLDSLAYRFDLVLRGHRATLFEN 239 Lambda K H 0.321 0.139 0.439 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: 289 Number of extensions: 10 Number of successful extensions: 1 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: 241 Length of database: 246 Length adjustment: 23 Effective length of query: 218 Effective length of database: 223 Effective search space: 48614 Effective search space used: 48614 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: 46 (22.3 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