Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate HSERO_RS18285 HSERO_RS18285 Rieske (2Fe-2S) protein
Query= SwissProt::Q84BZ3 (423 letters) >FitnessBrowser__HerbieS:HSERO_RS18285 Length = 426 Score = 693 bits (1788), Expect = 0.0 Identities = 326/405 (80%), Positives = 362/405 (89%) Query: 19 VHFPHDDGSRVPYKVFSSRAVYDREQERIFRGPTWNFVALEAEIPNAGDFKSTFVGDTPV 78 V FP DG+R PYKVFSSR VYD EQERI+RG TW+F+ALEAEIPN GD+KSTFVGDTPV Sbjct: 16 VQFPRTDGARTPYKVFSSREVYDLEQERIYRGETWSFLALEAEIPNNGDYKSTFVGDTPV 75 Query: 79 VVTRTEDGALSAWVNRCAHRGAQVCRKSRGNASSHTCVYHQWSFDNEGNLLGVPFRRGQK 138 VVTRTEDGAL+AWVN+C+HRGA VCR RGNASSH+C YHQWSFD+ GNLLGVPFRRGQK Sbjct: 76 VVTRTEDGALAAWVNKCSHRGAMVCRTPRGNASSHSCAYHQWSFDSRGNLLGVPFRRGQK 135 Query: 139 GMTGMPADFDPKQHGLRKLRVDSYRGLVFATFSDDVAPLPDYLGAQMRPWIDRIFHKPIE 198 G TGM DFDPK HGLR+LRVDSY+GLVFATFS+ V LPDY+GA+MRPWIDRIFHKPI Sbjct: 136 GATGMAKDFDPKCHGLRQLRVDSYKGLVFATFSETVEALPDYIGAEMRPWIDRIFHKPIV 195 Query: 199 YLGCTRQYSKSNWKLYMENVKDPYHASMLHLFHTTFNIFRVGMKARSIPDANHGLHSIIT 258 YLGCTRQYSKSNWKLY+ENVKDPYHAS+LHLFHTTFNIFRVGMKARS+ D +HGLHSIIT Sbjct: 196 YLGCTRQYSKSNWKLYLENVKDPYHASLLHLFHTTFNIFRVGMKARSLADKHHGLHSIIT 255 Query: 259 VTKTGDDTSAAYKQQNIRSFDEGFHLEDESILDLVSEYDEDCTNHIQPIFPQLVIQQIHN 318 TK +T+ AYKQQ IRSFDEGF L+D S+L + E++E TNHIQPIFPQLV+QQIHN Sbjct: 256 ATKNEVETADAYKQQEIRSFDEGFSLQDPSVLGQIKEFEELTTNHIQPIFPQLVVQQIHN 315 Query: 319 TLVARQILPKGPDNFELIFHFFGYADDTPELRALRIKQANLVGPAGYISMEDTEATELVQ 378 TLVARQ+LPKGP NFEL+FHFFGY DDTPELRALRIKQANLVGPAGYISMEDTEATELVQ Sbjct: 316 TLVARQLLPKGPSNFELVFHFFGYEDDTPELRALRIKQANLVGPAGYISMEDTEATELVQ 375 Query: 379 RGTVRDADATSVIEMSRGNPEQQDTVITESLIRKFWVGYQKLMGY 423 RGT RD D SVI+M+R NP+Q+DT+ITESLIRKFW+GYQKLMG+ Sbjct: 376 RGTARDPDQCSVIDMARDNPDQEDTLITESLIRKFWMGYQKLMGF 420 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: 731 Number of extensions: 17 Number of successful extensions: 1 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: 426 Length adjustment: 32 Effective length of query: 391 Effective length of database: 394 Effective search space: 154054 Effective search space used: 154054 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