Align protocatechuate 3,4-dioxygenase, alpha chain; EC 1.13.11.3 (characterized)
to candidate BPHYT_RS33455 BPHYT_RS33455 protocatechuate 3,4-dioxygenase subunit beta
Query= CharProtDB::CH_121294 (209 letters) >FitnessBrowser__BFirm:BPHYT_RS33455 Length = 234 Score = 84.7 bits (208), Expect = 1e-21 Identities = 62/180 (34%), Positives = 89/180 (49%), Gaps = 8/180 (4%) Query: 31 NIEVFEHNLDNNLVQDNTQ-GQRIRLEGQVFDGLGLPLRDVLIEIWQADTNGVYPSQADT 89 ++ +H+L N V++ G+RI + G+V D P+R+ L+EIWQA+ G Y +AD Sbjct: 53 DLGALDHDLTRNAVRNGEPLGERIIVTGRVLDEGNRPVRNTLVEIWQANAAGRYVHKADQ 112 Query: 90 QGKQVDPNFLGWGRTGADFGTGFWSFNTIKPGAVP-GRKGSTQAP-HISLIIFARGINIG 147 +DPNFLG GR D G + F TIKPGA P G + P HI +F Sbjct: 113 HDAPLDPNFLGAGRCITD-NEGRYRFLTIKPGAYPWGNHPNAWRPNHIHFSLFGDHFGSR 171 Query: 148 LHTRVYFDDEAEANAKDPVLNSIEWATRRQTLVAKREERDGEVV---YRFDIRIQGENET 204 L T++YF + A DP+ R + + + E Y FDI ++G NET Sbjct: 172 LVTQMYFPGD-PLLAFDPIFQGTPEHARDRLIADFSLDTTQEAYALGYDFDIVLRGRNET 230 Lambda K H 0.318 0.139 0.426 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: 169 Number of extensions: 12 Number of successful extensions: 3 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: 209 Length of database: 234 Length adjustment: 22 Effective length of query: 187 Effective length of database: 212 Effective search space: 39644 Effective search space used: 39644 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: 45 (21.9 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