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::Q84BZ3 (423 letters) >FitnessBrowser__BFirm:BPHYT_RS10690 Length = 427 Score = 161 bits (407), Expect = 4e-44 Identities = 136/436 (31%), Positives = 208/436 (47%), Gaps = 75/436 (17%) Query: 28 RVPYKVFSSRAVYDREQERIFRGPTWNFVALEAEIPNAGDFKSTFVGDTPVVVTRTEDGA 87 RV ++ AV++ E ERIF TW +VA E+E+PN GDF++T +G PV+V R + GA Sbjct: 22 RVAPSLYYDPAVFEAELERIFY-KTWIWVAHESELPNPGDFRTTTIGRQPVIVVRDKSGA 80 Query: 88 LSAWVNRCAHRGAQVCRKSRGNASSHTCVYHQWSFDNEGNLLGVPFRRGQKGMTGMPADF 147 ++ NRC HRGA VC + +GNA TC YH W++ +G L +P+ G +G+ Sbjct: 81 VNVLQNRCRHRGATVCEQHKGNAKGFTCPYHSWTYGLDGTLRALPYGDGYEGVV------ 134 Query: 148 DPKQHGLRKLRVDSYRGLVFATFSDDVAPLPDYLGAQMRPWIDRIFHK-----PIEYLGC 202 D + L LRV Y+GL+FA+F+ ++ PL D+LG +PWID +F K PI+ G Sbjct: 135 DKTELPLASLRVGIYQGLIFASFNQEIEPLEDFLGG-AKPWID-LFMKQGAGYPIKANGE 192 Query: 203 TRQYSKSNWKLYMENVKDPYHASMLHLFHTTFNIFRVGMKARSIPDANHGLHSIITVTKT 262 R NWK+ +EN D YH ++H + MK SI D + IT T Sbjct: 193 HRFRFNGNWKIQLENTTDLYHFPVVH---------KSWMK--SIDDET---AAAITSFMT 238 Query: 263 GDDTSAAYKQQNIRSFDEGFHLEDESILDLVSEYDEDCTNHIQPIFPQLVIQQIHN---- 318 D Q RS G L ++ + + D+D I F +L + Sbjct: 239 SD-------QAFCRSLGNGHSL--AVLVPEIVDLDKDDGAPIPERFEELAASLARDHTPE 289 Query: 319 --TLVARQILPKGPD-----NFELIFHFFGY-----ADDTPELRALRI------KQANLV 360 + R ++ G + N L FF A++T E+R + + ++AN V Sbjct: 290 EVRRIVRSLMGVGFNLNLFPNLALSMAFFRVLRPISANET-EIRHVALAMDGGPEEANRV 348 Query: 361 ---------GPAGYISMEDTEATELVQRGTVRDADATSVI------EMSRGNPEQQDTVI 405 GP G+ S +D EA E VQRG+ D ++ E + N E+ Sbjct: 349 RLRIHEHFQGPFGFGSPDDAEAWERVQRGSHAGPDLPILVNRGLNRESTAPNGEKTAHAT 408 Query: 406 TESLIRKFWVGYQKLM 421 E+ +R+ + ++ +M Sbjct: 409 DETGMREAYAQWRTMM 424 Lambda K H 0.321 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: 546 Number of extensions: 31 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 423 Length of database: 427 Length adjustment: 32 Effective length of query: 391 Effective length of database: 395 Effective search space: 154445 Effective search space used: 154445 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