Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate H281DRAFT_01653 H281DRAFT_01653 Phenylpropionate dioxygenase, large terminal subunit
Query= SwissProt::O85673 (471 letters) >FitnessBrowser__Burk376:H281DRAFT_01653 Length = 427 Score = 202 bits (515), Expect = 1e-56 Identities = 130/397 (32%), Positives = 200/397 (50%), Gaps = 31/397 (7%) Query: 27 RIARDMFTEPELFELEMELIFEKVWIYACHESEIPNNNDFVTVQIGRQPMIVSRDGKGEL 86 RIA ++ +P+LFE E++ IF + W++ H+SE+P DFVT IGRQP+IV RD G + Sbjct: 22 RIAPSLYYDPQLFEEELQRIFYRTWVWVAHDSELPKPGDFVTTTIGRQPVIVVRDKTGAV 81 Query: 87 HAMVNACEHRGATLTRVAKGNQSVFTCPFHAWCYKSDGRLVKVKAPGEYCEDFDKSSRGL 146 + + N C HRGAT+ KGN FTCP+H+W Y DG L + Y +K L Sbjct: 82 NVLQNRCRHRGATVCEEHKGNAKGFTCPYHSWSYALDGTLRALPYGDGYEGVCEKGDLPL 141 Query: 147 KQGRIASYRGFVFVSLDTQATDSLEDFLGDAKVFLDLMVDQSPTGELEVLQGKSAYTFAG 206 K+ R+ Y+G +F S + Q +SLEDFLG AK ++DL + Q ++ G+ + F G Sbjct: 142 KKLRVGVYQGLIFASFNEQ-IESLEDFLGGAKPWIDLFMKQGAGYPIKA-NGEHKFKFKG 199 Query: 207 NWKLQNENGLDGYHVSTVHYNYVSTVQHRQQVNAAKGDELDTLDYSKLGAGDSETDDGWF 266 NWK+Q EN D YH VH +++ ++ DE + S + + D+ Sbjct: 200 NWKIQLENTTDLYHFPVVHKSWMKSID----------DETAAVITSFMTSEDAFCR---- 245 Query: 267 SFKNGHSVL-----FSDMPNPTVRP---GYNTVMPYLVEKFGEKRAEWAMHRLR----NL 314 S NGHS+ D+ P +N + L +K + + L NL Sbjct: 246 SLGNGHSLAVLVPEIVDLDRDDGAPLPDRFNELAAQLSQKHTPEEVRRIVRSLMGVGFNL 305 Query: 315 NLYPSLFFMDQISSQLRIIRPVAWNKTEVISQCIGVKGESSEARRNRIRQFEDFFNVSGL 374 NL+P+L + R++RP++ +TE+ + + G EA R R+R E F G Sbjct: 306 NLFPNLALS---MAFFRVLRPISAEETEIRHVALAMDGGPDEANRVRLRIHEHFQGPFGF 362 Query: 375 GTPDDLVEFREQQKGFQGRIERWSDISRGYHQWTYGP 411 G+PDD + Q+G + ++RG ++ T P Sbjct: 363 GSPDDAEAWERVQRGSYAGPDVPILVNRGLNRETAAP 399 Lambda K H 0.319 0.136 0.420 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: 558 Number of extensions: 33 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: 471 Length of database: 427 Length adjustment: 33 Effective length of query: 438 Effective length of database: 394 Effective search space: 172572 Effective search space used: 172572 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: 51 (24.3 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