Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate Dsui_0609 Dsui_0609 2-polyprenylphenol hydroxylase-like oxidoreductase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2738 (343 letters) >FitnessBrowser__PS:Dsui_0609 Length = 337 Score = 138 bits (347), Expect = 2e-37 Identities = 94/309 (30%), Positives = 158/309 (51%), Gaps = 7/309 (2%) Query: 17 FEVKPNELLLDAALRNGVNIPLDCREGVCGTCQGRCESGRYTQDYVDDEALSEQDLAQRK 76 F + +E +L+AALR G+ +P CR+G CG C+G+ G ALSE D A Sbjct: 14 FAAESDETILEAALRQGLTMPYGCRDGACGACKGKVLCGEVDHGKSQPHALSEADKAAGL 73 Query: 77 MLSCQTRVQSDASFYFDFDSSLCNAGATQLLQAVITGVEQVSATTAILHLDACSHPRQLD 136 L C + ++D + S + + L + I +E+V+A +LHL + R Sbjct: 74 TLFCCAKAKTDLTLECREVRSASDI-PVKTLPSRIEKMEKVAADVMVLHLRLPATER-FQ 131 Query: 137 FLPGQYARLHVPGTDEWRSYSFANRPNPDNQLQFLIRLLPDGVMSNFIREHCRPGEVLEF 196 FL GQY + + + RS+S AN P+ D LQ IRL+P G+ + + + ++L Sbjct: 132 FLTGQYVDILLK-DGKRRSFSLANAPHDDAFLQLHIRLVPGGLFTEHVFNGMKERDILRL 190 Query: 197 EAPLGSFYLRQVS-KPLVLVAGGTGLSAFLGMLDTIAEQGGCGHPIQLFYGVTQDNDLCE 255 P GSF+LR+ S KP++L+AGGTG + +++ A P+ +++G L Sbjct: 191 NGPHGSFFLREDSDKPMILLAGGTGFAPIKAIVEH-ALYTQSKRPMVIYWGNRNKAGLYM 249 Query: 256 TQRLADYRDKIANFDYHLVVSKP--SEHWKGKTGWIPDHFDRQSFEANPFDIYLCGPPPM 313 + A + + ++ Y V+S+P ++ W G+TG + + + + + +Y+CG P M Sbjct: 250 DELPARWAAEHSHITYVPVLSEPAATDGWNGRTGLVHEAVMQDFPDLSGHQVYVCGAPVM 309 Query: 314 VEAVKTWFS 322 VEA K F+ Sbjct: 310 VEAAKRDFT 318 Lambda K H 0.322 0.138 0.431 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: 312 Number of extensions: 14 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: 343 Length of database: 337 Length adjustment: 28 Effective length of query: 315 Effective length of database: 309 Effective search space: 97335 Effective search space used: 97335 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 (21.9 bits) S2: 49 (23.5 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