Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate PfGW456L13_3754 Ring hydroxylating dioxygenase, alpha subunit/Rieske (2Fe-2S) protein (EC 1.14.12.18)
Query= SwissProt::O85673 (471 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3754 Length = 427 Score = 207 bits (527), Expect = 6e-58 Identities = 130/395 (32%), Positives = 203/395 (51%), Gaps = 37/395 (9%) Query: 27 RIARDMFTEPELFELEMELIFEKVWIYACHESEIPNNNDFVTVQIGRQPMIVSRDGKGEL 86 R+ ++ +P LFE E++ IF + W++ HESE+ N+ DF T IGR+P+IV RD K + Sbjct: 23 RVDVSLYNDPALFEAELDKIFYRTWVWVAHESEVRNSGDFKTATIGRRPVIVVRDKKNNI 82 Query: 87 HAMVNACEHRGATLTRVAKGNQSVFTCPFHAWCYKSDGRLVKVKAPGEYCEDFDKSSRGL 146 + + N C HRGAT+ KGN + FTCP+H+W Y DG+L + P Y +KS L Sbjct: 83 NVLENRCRHRGATVCEKHKGNATGFTCPYHSWSYGLDGKLRALPYPDGYEGILEKSELPL 142 Query: 147 KQGRIASYRGFVFVSLDTQATDSLEDFLGDAKVFLDLMVDQSPTGELEVLQGKSAYTFAG 206 R+ SY G VF S + + + LEDFLG AK ++DL + Q ++ QG+ ++F G Sbjct: 143 TSLRVESYAGMVFASYNDE-IEPLEDFLGGAKHWMDLFMKQGAGYPIKT-QGEHKFSFKG 200 Query: 207 NWKLQNENGLDGYHVSTVHYNYVSTVQHRQQVNAAKGDELDTLDYSKLGAGDSETDDGWF 266 NWK+Q EN DGYH VH +++S+V + S++ + ++ Sbjct: 201 NWKIQLENTTDGYHFPIVHKSFMSSVDE---------------ETSEMLSFMTDEQAVTH 245 Query: 267 SFKNGHSVLFSDMPNPTVRPGYNTVMPYLVEKFGE--------------KRAEWAMHRLR 312 S NGHSV+ M V ++ L E+F +R ++H Sbjct: 246 SLGNGHSVMV--MVPEHVDLDHDDGTEQLQERFAHVTEELSKTLPADQVRRIVRSLHGAG 303 Query: 313 -NLNLYPSLFFMDQISSQLRIIRPVAWNKTEVISQCIGVKGESSEARRNRIRQFEDFFNV 371 NLNL+P++ S R++RPV+ +TE+ +G+ G A R R+R E F Sbjct: 304 FNLNLFPNVAMS---MSFFRVLRPVSVTETEIRHVALGMDGGPEIANRERMRIHEHFQGP 360 Query: 372 SGLGTPDDLVEFREQQKGFQGRIERWSDISRGYHQ 406 G G+PDD + Q+G ++ ++RG ++ Sbjct: 361 FGFGSPDDAEAWDRVQRGSYAGVDAPILVNRGLNR 395 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: 540 Number of extensions: 24 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