Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate RR42_RS33930 RR42_RS33930 salicylate hydroxylase
Query= SwissProt::Q84BZ3 (423 letters) >FitnessBrowser__Cup4G11:RR42_RS33930 Length = 418 Score = 295 bits (756), Expect = 1e-84 Identities = 164/409 (40%), Positives = 235/409 (57%), Gaps = 18/409 (4%) Query: 24 DDGS-RVPYKVFSSRAVYDREQERIFRGPTWNFVALEAEIPNAGDFKSTFVGDTPVVVTR 82 D+GS R+P+ ++ VY +E ER F W ++ LEAEIPNAGDFK T +G+ V+ +R Sbjct: 15 DEGSSRIPFWAYTDDDVYRQELERFFYAGHWCYIGLEAEIPNAGDFKRTAIGERSVIASR 74 Query: 83 TEDGALSAWVNRCAHRGAQVCRKSRGNASSHTCVYHQWSFDNEGNLLGVPFRRGQK--GM 140 DG + N CAHRG Q CR+ GN TC YHQW++D +GNL+GVPFRRG K G Sbjct: 75 AADGEIYVVENVCAHRGVQFCRERSGNRKDFTCPYHQWNYDLKGNLVGVPFRRGVKLDGK 134 Query: 141 T--GMPADFDPKQHGLRKLRVDSYRGLVFATFSDDVAPLPDYLGAQMRPWIDRIFH-KPI 197 GMPADFDPK HGL KL+V G++FA+F +V L DYLG + + DR+F + + Sbjct: 135 VNGGMPADFDPKAHGLTKLKVARRNGVIFASFDHEVPTLEDYLGPTILAYFDRVFDGRKL 194 Query: 198 EYLGCTRQYSKSNWKLYMENVKDPYHASMLHLFHTTFNIFRVGMKARSIPDANHGLHSII 257 LG RQ NWKL EN+KDPYH +LH + TF ++R K+ D H H+ + Sbjct: 195 TILGYNRQQIPGNWKLMQENIKDPYHPGLLHTWFVTFGLWRADNKSALKMD-EHFRHAAM 253 Query: 258 TVTK----TGDDTSAAYKQQNIRSFDEGFHLEDESILDLVSE-YDEDCTNHIQPIFPQLV 312 T+ GD TS + SF E L D+ LD+ E + + T + +FP ++ Sbjct: 254 ISTRGQGGKGDVTS------GVSSFKEQMRLHDDRFLDVAQEPWWGEPTAVMMTLFPSVI 307 Query: 313 IQQIHNTLVARQILPKGPDNFELIFHFFGYADDTPELRALRIKQANLVGPAGYISMEDTE 372 IQQ N++ R I P G +F ++ FG+ D ++ R++QANL GPAG++S +D E Sbjct: 308 IQQQVNSVSTRHIQPTGHGSFNFVWTHFGFEGDDADMTRRRLRQANLFGPAGFVSADDGE 367 Query: 373 ATELVQRGTVRDADATSVIEMSRGNPEQQDTVITESLIRKFWVGYQKLM 421 E Q+G + +V E+ D ++TE+LIR + ++++M Sbjct: 368 VIEFSQQGFEQKPFHRTVAELGGREIGDTDHMVTETLIRGMYNYWRRVM 416 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: 540 Number of extensions: 34 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: 423 Length of database: 418 Length adjustment: 32 Effective length of query: 391 Effective length of database: 386 Effective search space: 150926 Effective search space used: 150926 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: 50 (23.9 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