Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate BPHYT_RS10690 BPHYT_RS10690 Rieske (2Fe-2S) protein
Query= SwissProt::O85673 (471 letters) >FitnessBrowser__BFirm:BPHYT_RS10690 Length = 427 Score = 199 bits (505), Expect = 2e-55 Identities = 133/404 (32%), Positives = 195/404 (48%), Gaps = 45/404 (11%) Query: 27 RIARDMFTEPELFELEMELIFEKVWIYACHESEIPNNNDFVTVQIGRQPMIVSRDGKGEL 86 R+A ++ +P +FE E+E IF K WI+ HESE+PN DF T IGRQP+IV RD G + Sbjct: 22 RVAPSLYYDPAVFEAELERIFYKTWIWVAHESELPNPGDFRTTTIGRQPVIVVRDKSGAV 81 Query: 87 HAMVNACEHRGATLTRVAKGNQSVFTCPFHAWCYKSDGRLVKVKAPGEYCEDFDKSSRGL 146 + + N C HRGAT+ KGN FTCP+H+W Y DG L + Y DK+ L Sbjct: 82 NVLQNRCRHRGATVCEQHKGNAKGFTCPYHSWTYGLDGTLRALPYGDGYEGVVDKTELPL 141 Query: 147 KQGRIASYRGFVFVSLDTQATDSLEDFLGDAKVFLDLMVDQSPTGELEVLQGKSAYTFAG 206 R+ Y+G +F S + Q + LEDFLG AK ++DL + Q ++ G+ + F G Sbjct: 142 ASLRVGIYQGLIFASFN-QEIEPLEDFLGGAKPWIDLFMKQGAGYPIKA-NGEHRFRFNG 199 Query: 207 NWKLQNENGLDGYHVSTVHYNYVSTVQHRQQVNAAKGDELDTLDYSKLGAGDSETDDGWF 266 NWK+Q EN D YH VH +++ ++ D + T D F Sbjct: 200 NWKIQLENTTDLYHFPVVHKSWMKSID----------------DETAAAITSFMTSDQAF 243 Query: 267 --SFKNGHS--VLFSDMPNPTVRPGYNTVMPYLVEKFGEKRAEWAMHRLR---------- 312 S NGHS VL ++ + G + E+F E A A Sbjct: 244 CRSLGNGHSLAVLVPEIVDLDKDDG-----APIPERFEELAASLARDHTPEEVRRIVRSL 298 Query: 313 -----NLNLYPSLFFMDQISSQLRIIRPVAWNKTEVISQCIGVKGESSEARRNRIRQFED 367 NLNL+P+L + R++RP++ N+TE+ + + G EA R R+R E Sbjct: 299 MGVGFNLNLFPNLALS---MAFFRVLRPISANETEIRHVALAMDGGPEEANRVRLRIHEH 355 Query: 368 FFNVSGLGTPDDLVEFREQQKGFQGRIERWSDISRGYHQWTYGP 411 F G G+PDD + Q+G + ++RG ++ + P Sbjct: 356 FQGPFGFGSPDDAEAWERVQRGSHAGPDLPILVNRGLNRESTAP 399 Score = 24.6 bits (52), Expect = 0.007 Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 7/60 (11%) Query: 404 YHQWTYGPTQNSQDL----GIEPVITGREFTHEGLYVNQHGQWQRLILDGLNKKALKMHD 459 YH WTYG + L G E V+ E L V G +Q LI N++ + D Sbjct: 110 YHSWTYGLDGTLRALPYGDGYEGVVDKTELPLASLRV---GIYQGLIFASFNQEIEPLED 166 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: 547 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 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