Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate HSERO_RS06720 HSERO_RS06720 Rieske (2Fe-2S) protein
Query= SwissProt::Q84BZ3 (423 letters) >FitnessBrowser__HerbieS:HSERO_RS06720 Length = 428 Score = 158 bits (400), Expect = 3e-43 Identities = 118/422 (27%), Positives = 198/422 (46%), Gaps = 57/422 (13%) Query: 33 VFSSRAVYDREQERIFRGPTWNFVALEAEIPNAGDFKSTFVGDTPVVVTRTEDGALSAWV 92 +++ A+++ E ++IF TW +VA E+EI N GDFK+ +G PV+V R + G ++ Sbjct: 29 LYTDPALFEAEMDKIFY-KTWIWVAHESEIKNPGDFKTAQIGRQPVIVVRDKTGKINVLE 87 Query: 93 NRCAHRGAQVCRKSRGNASSHTCVYHQWSFDNEGNLLGVPFRRGQKGMTGMPADFDPKQH 152 NRC HRGA VC K +GNA+ TC YH WS+ +G L G+P+ G + + + Sbjct: 88 NRCRHRGATVCEKHKGNATGFTCPYHSWSYGLDGKLRGLPYPEGYEDV------IEKADL 141 Query: 153 GLRKLRVDSYRGLVFATFSDDVAPLPDYLGAQMRPWIDRIFHK-----PIEYLGCTRQYS 207 L+ LR +SY G++FA+F+ ++ PL D+LG + WID +F K PI+ G + Sbjct: 142 PLQSLRCESYHGMIFASFNQEIEPLSDFLG-HAKKWID-LFMKQGAGFPIKVQGEHKFSF 199 Query: 208 KSNWKLYMENVKDPYHASMLH------LFHTTFNIFRVGMKARSIPDANHGLHSIITVTK 261 K NWK+ +EN D YH ++H + T + +SI + HS++ + Sbjct: 200 KGNWKIQLENTTDGYHFPVVHKTFLSSVDEETSEMLSFMTDDQSITRSLGNGHSVMIMVP 259 Query: 262 TGDDTSAAYKQQNIRSFDEGFHLEDESILDLVSEYDEDCTNHIQPIFPQLVIQQIHNTLV 321 D D+G E + + + E+ + + P + +++ +H Sbjct: 260 EHVDLDV----------DDG----SEQLQERFAHVTEELSKTMPPEQVRRIVRSLHGAGF 305 Query: 322 ARQILPKGPDNFEL-------------IFHFFGYADDTPEL---RALRIKQANLVGPAGY 365 + P + I H D PE+ LRI + + GP G+ Sbjct: 306 NLNLFPNVAMSMSFFRVLHPVSVGETQIRHVALGMDGGPEIANRERLRIHE-HFQGPFGF 364 Query: 366 ISMEDTEATELVQRGTVRDADATSVI------EMSRGNPEQQDTVITESLIRKFWVGYQK 419 S +D EA E VQ G+ DA ++ E N ++ E+ +R+ + ++K Sbjct: 365 GSPDDAEAWERVQAGSHAGRDAPILVNRGLNREWVDDNGDKVSHSTDETGMREAYAMWKK 424 Query: 420 LM 421 +M Sbjct: 425 MM 426 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: 526 Number of extensions: 27 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: 428 Length adjustment: 32 Effective length of query: 391 Effective length of database: 396 Effective search space: 154836 Effective search space used: 154836 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