Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate BWI76_RS13705 BWI76_RS13705 Rieske (2Fe-2S) domain-containing protein
Query= SwissProt::Q84BZ3 (423 letters) >FitnessBrowser__Koxy:BWI76_RS13705 Length = 460 Score = 143 bits (361), Expect = 9e-39 Identities = 114/384 (29%), Positives = 181/384 (47%), Gaps = 39/384 (10%) Query: 33 VFSSRAVYDREQERIFRGPTWNFVALEAEIPNAGDFKSTFVGDTPVVVTRTEDGALSAWV 92 +F+ ++D E + IF G W F+A E++I GD+ + +G PV++TR + L A + Sbjct: 31 IFTDPQLFDFEMKHIFEG-NWLFLAHESQIAQPGDYYTLTLGRQPVIITRDKKNELHALI 89 Query: 93 NRCAHRGAQVCRKSRGNASSHTCVYHQWSFDNEGNLLGVPFRRGQKGMTGMPADFDPK-Q 151 N CAHRGA +CR+ GN +S TC +H W+F N G LL + + G P F + Sbjct: 90 NSCAHRGAMLCRRKTGNKNSLTCPFHGWTFSNNGKLL----KAKDESTGGYPDSFKQEGS 145 Query: 152 HGLRKL-RVDSYRGLVFATFSDDVAPLPDYLGAQMRPWIDRIFHKPIEYL----GCTRQY 206 H L KL + SYRG +F + + DV PL +YLG + R ID I + + L G + Sbjct: 146 HDLTKLPKFQSYRGFLFGSLNADVQPLEEYLG-ETRKIIDLIVDQAPQGLEVLKGSSSYV 204 Query: 207 SKSNWKLYMENVKDPYHASMLHL-FHTTFNIFRVGMKARSIPDAN---------HGL--- 253 + NWKL EN D YH S++H + +T + + DAN +G Sbjct: 205 YEGNWKLGAENGADGYHVSVVHWNYASTMSRRNYEAEGTHAVDANGWSKSVGGGYGFENG 264 Query: 254 HSIITVTKTGDDTSAAYKQQNIRSFDEGFHLEDESILDLVSEYDEDCTNHIQPIFPQLVI 313 H ++ + Y+ + + G D +V+E C ++P + + Sbjct: 265 HMLLWTRALNPEVRPVYEHRERLRAEFGESRADR----MVNETRNLC------LYPNVYL 314 Query: 314 QQIHNTLVARQILPKGPDNFELIFHFFGYADDTPELRALRIKQ-ANLVGPAGYISMEDTE 372 +T + R I P D E+ F ++ + RALRI+Q + +G + +D E Sbjct: 315 MDQFSTQI-RVIRPIAVDKTEVTIWCFAPRGESDQARALRIRQYEDFFNVSGMGTPDDLE 373 Query: 373 ATELVQRGTVRDADATSVIEMSRG 396 QRG + + A S ++SRG Sbjct: 374 EFSACQRGYLGENLAWS--DLSRG 395 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: 506 Number of extensions: 29 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: 460 Length adjustment: 32 Effective length of query: 391 Effective length of database: 428 Effective search space: 167348 Effective search space used: 167348 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