Align protocatechuate 4,5-dioxygenase beta chain (EC 1.13.11.8) (characterized)
to candidate AZOBR_RS26885 AZOBR_RS26885 protocatechuate 3 4-dioxygenase subunit beta
Query= metacyc::MONOMER-15117 (302 letters) >FitnessBrowser__azobra:AZOBR_RS26885 Length = 280 Score = 281 bits (718), Expect = 2e-80 Identities = 131/279 (46%), Positives = 190/279 (68%), Gaps = 2/279 (0%) Query: 1 MARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYND 60 MA++ G+T+SHIPA+G AI ++ YW P F GY R+W+ + PDV I+VYND Sbjct: 1 MAKIVGGVTTSHIPAIGNAIANELFEDPYWKPFFDGYPKAREWLAEV--KPDVAIVVYND 58 Query: 61 HASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIM 120 H F ++ +PTF+IG A ++ DEGWG +P+P G P+L+WHI +SL+ DEFD+ Sbjct: 59 HGLNFFLDKMPTFSIGAAPEYQNKDEGWGLKPLPPYPGDPELSWHIIESLVNDEFDICSC 118 Query: 121 NQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFP 180 +M VDHG TVP+++++ + + P + IP VN V +P P+ RC LG++I AV S+P Sbjct: 119 QEMAVDHGFTVPMALLWPDQTQRPVRTIPVAVNTVQHPLPTPARCLKLGEAIGRAVASYP 178 Query: 181 EDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEG 240 +DL V V GTGG+SHQL G RAG INK+FDL ++K++ +PE L+K +R +G++G Sbjct: 179 KDLKVVVLGTGGLSHQLDGERAGFINKDFDLMCLEKIVDEPEALAKYSIHDLVRLAGAQG 238 Query: 241 VELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQ 279 EL++WLIMRGAL KV +++ YHIP SNT G ++L+ Sbjct: 239 AELILWLIMRGALGRKVSKVHSNYHIPISNTGAGLLVLE 277 Lambda K H 0.319 0.138 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: 323 Number of extensions: 13 Number of successful extensions: 2 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: 302 Length of database: 280 Length adjustment: 26 Effective length of query: 276 Effective length of database: 254 Effective search space: 70104 Effective search space used: 70104 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: 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