Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate BPHYT_RS07855 BPHYT_RS07855 benzoate 1,2-dioxygenase subunit alpha
Query= SwissProt::Q84BZ3 (423 letters) >FitnessBrowser__BFirm:BPHYT_RS07855 Length = 452 Score = 145 bits (365), Expect = 3e-39 Identities = 114/377 (30%), Positives = 183/377 (48%), Gaps = 23/377 (6%) Query: 33 VFSSRAVYDREQERIFRGPTWNFVALEAEIPNAGDFKSTFVGDTPVVVTRTEDGALSAWV 92 +F++ +++ E + IF W ++A E++IPN D+ +T++G PVVVTR + G L A + Sbjct: 34 IFTNAELFELEMKHIFES-NWVYLAHESQIPNNNDYYTTWIGRQPVVVTRDKSGELHAVI 92 Query: 93 NRCAHRGAQVCRKSRGNASSHTCVYHQWSFDNEGNLLGVPFRRGQKGMTGMPADFDPK-Q 151 N CAH+GA +CRK GN + TC +H WSF N G LL V T P F+ Sbjct: 93 NACAHKGAMLCRKKHGNKGTFTCPFHGWSFANTGKLLKVK----DVKTTEYPIQFNTNGS 148 Query: 152 HGLRKL-RVDSYRGLVFATFSDDVAPLPDYLGAQMRPWIDRIFHKPIEYLGCTRQYSK-- 208 H L+K+ R SYRG +F T + D PL DYLG + R ID+I + + L R S Sbjct: 149 HDLKKVARFQSYRGFLFGTLNADAIPLEDYLG-ETRVIIDQIVDQAPDGLEVLRGNSSYI 207 Query: 209 --SNWKLYMENVKDPYHASMLHLFHTTFNIFRVGMKARSIPDANHGLHSIITVTKTGDDT 266 NWK+ MEN D YH S +H ++ + R ++ DAN S+ V Sbjct: 208 YDGNWKVQMENGCDGYHVSTVH-WNYAATMDRRKVEGTKAVDANSWSKSVAGVYGFEHGH 266 Query: 267 SAAYKQQNIRSFDEGFHLEDE---SILDLVSEYDEDCTNHIQPIFPQLVIQQIHNTLVAR 323 + + + DE + ++ +++ + T ++ ++P + + +T + R Sbjct: 267 ILLWTKTMNPEVRPVYQYRDEIKARVGEVKADFIVNQTRNL-CLYPNVFLMDQFSTQI-R 324 Query: 324 QILPKGPDNFELIFHFFGYADDTPELRALRIKQ-ANLVGPAGYISMEDTEATELVQRGTV 382 + P D E+ F ++ RA RI+Q + +G + +D E Q G Sbjct: 325 VVRPISVDKTEVSIFCFAPKGESASDRATRIRQYEDFFNVSGMGTADDLEEFRACQAGY- 383 Query: 383 RDADATSV-IEMSRGNP 398 A T++ ++SRG P Sbjct: 384 --AGTTAMWNDLSRGAP 398 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: 507 Number of extensions: 27 Number of successful extensions: 3 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: 452 Length adjustment: 32 Effective length of query: 391 Effective length of database: 420 Effective search space: 164220 Effective search space used: 164220 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