Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate RR42_RS23490 RR42_RS23490 NADH oxidase
Query= reanno::WCS417:GFF4631 (335 letters) >FitnessBrowser__Cup4G11:RR42_RS23490 Length = 339 Score = 246 bits (629), Expect = 5e-70 Identities = 138/341 (40%), Positives = 196/341 (57%), Gaps = 11/341 (3%) Query: 1 MNHKVAFSFADGKTLFFPVGANEILLDAALRNGIKIPLDCREGVCGTCQGRCESGDY--- 57 M + +A F DG T F ANE L DAA R I IPLDCR+G CGTC+G CESG+Y Sbjct: 1 MEYNIALQFEDGVTRFITCTANETLSDAAYRQQINIPLDCRDGACGTCRGLCESGEYDLP 60 Query: 58 SQDYVDEEALSSLDLQQRKMLSCQTRVKSDATFYFDFDSSLCNAPGPVQVKGTVSAVEQV 117 + Y+ E+AL+ + + +L+CQTR +SD S+ C G + +G ++AV+++ Sbjct: 61 ASSYI-EDALTPEEAAKGYVLACQTRPRSDCVIKVPASSAACKT-GVTRYQGKLAAVDKL 118 Query: 118 SASTAILQVQLDQAL--DFLPGQYARLSVPGTDSWRSYSFANLPGN-HLQFLVRLLPDGV 174 S ST + L +A FL GQY + +PGT RSYSF++ PG F+VR +P+G Sbjct: 119 SDSTIGFSIDLGEAAAPTFLAGQYVNVDIPGTGLTRSYSFSSAPGAARTSFVVRNVPNGR 178 Query: 175 MSNYLRERCQVGDELLMEAPLGAFYLRHVTQPLVLVAGGTGLSALLGMLDQLAANGCEQP 234 MS +L G + P G+FYLR V +P++ +AGGTG++ L MLD LAANG P Sbjct: 179 MSEFLSNEALPGQPISFAGPYGSFYLREVARPVLFLAGGTGIAPFLSMLDVLAANGSPHP 238 Query: 235 VHLYYGVRGAEDLCEAARIRAYAAKIPNLRY-TEVLSAPSEEWSGKRGYLTEHFDLAELR 293 + L YGV DL A++ ++ Y T VL S E ++GY+T+H + L Sbjct: 239 IRLVYGVTHEIDLVALAQLDRAKDQLAGFEYRTCVLDPVSNE--TRKGYVTQHVERDWLN 296 Query: 294 DGSADMYLCGPPPMVESIQQWLADQALDGVQLYYEKFTQSN 334 G D+YLCGP MV++++ WL D + +YEKF+ SN Sbjct: 297 GGDVDIYLCGPVAMVDAVRAWLQDAGVTPASFHYEKFSASN 337 Lambda K H 0.320 0.136 0.412 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: 333 Number of extensions: 17 Number of successful extensions: 5 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: 335 Length of database: 339 Length adjustment: 28 Effective length of query: 307 Effective length of database: 311 Effective search space: 95477 Effective search space used: 95477 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: 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