Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate WP_045585170.1 AL072_RS30310 Rieske 2Fe-2S domain-containing protein
Query= SwissProt::Q84BZ3 (423 letters) >NCBI__GCF_001305595.1:WP_045585170.1 Length = 429 Score = 144 bits (363), Expect = 5e-39 Identities = 76/205 (37%), Positives = 113/205 (55%), Gaps = 12/205 (5%) Query: 28 RVPYKVFSSRAVYDREQERIFRGPTWNFVALEAEIPNAGDFKSTFVGDTPVVVTRTEDGA 87 R +++ A++++E +RIF W +VA +E+ AGD+KST+VG PVVV R Sbjct: 27 RAHTSLYTDPAIFEQEMDRIFAN-CWVWVAHVSEVKEAGDYKSTYVGRQPVVVVRDRKQK 85 Query: 88 LSAWVNRCAHRGAQVCRKSRGNASSHTCVYHQWSFDNEGNLLGVPFRRGQKGMTGMPADF 147 + +NRC HR A VC + +G +S C YH WS+ +G+L GVP Sbjct: 86 IHVLLNRCRHRAATVCEEKKGKTNSFVCPYHGWSYGLDGSLRGVPHPESYGQC------L 139 Query: 148 DPKQHGLRKLRVDSYRGLVFATFSDDVAPLPDYLGAQMRPWIDRIFHK----PIEYLGCT 203 D ++ L+ LRV+ Y G+VFATF +D+ PL D+LG + W+D + PI+ G Sbjct: 140 DKGEYPLKSLRVEEYAGMVFATFREDIEPLADWLG-PAKKWMDLFMRQGGGYPIKVAGEH 198 Query: 204 RQYSKSNWKLYMENVKDPYHASMLH 228 R NWK+ +EN D YH ++H Sbjct: 199 RFRFPGNWKIQLENTTDGYHFPVVH 223 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: 482 Number of extensions: 25 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: 429 Length adjustment: 32 Effective length of query: 391 Effective length of database: 397 Effective search space: 155227 Effective search space used: 155227 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 24 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