Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate N515DRAFT_3403 N515DRAFT_3403 CDP-4-dehydro-6-deoxyglucose reductase
Query= reanno::WCS417:GFF4631 (335 letters) >FitnessBrowser__Dyella79:N515DRAFT_3403 Length = 352 Score = 130 bits (328), Expect = 4e-35 Identities = 98/324 (30%), Positives = 157/324 (48%), Gaps = 14/324 (4%) Query: 17 FPVGANEILLDAALRNGIKIPLDCREGVCGTCQGRCESGDYSQDYVDEEALSSLDLQQRK 76 FPV E +L+AA R GI +P CR GVCG+C+ G ALS Q Sbjct: 13 FPVEPGETVLEAAQRAGIALPYSCRAGVCGSCKAILLEGQCQYPRNPPVALSGTSPAQHA 72 Query: 77 MLSCQTRVKSDATFYFDFDSSLCNAPGPVQVKGTVSAVEQVSASTAILQVQLDQA----- 131 +L CQ D + + + + V E+ + + ++ ++L+ A Sbjct: 73 VLLCQAVPCGDLLI---AAREVTSVEDIARRRLEVVVTEKSALAPDVIGLRLEPAPGETR 129 Query: 132 LDFLPGQYARLSVPGTDSWRSYSFANLP--GNHLQFLVRLLPDGVMSNYLRERCQVGDEL 189 L++LPGQY + + R +S A P ++ VR + G ++++ + +VGD L Sbjct: 130 LNWLPGQYLDVLLE-DGRRRPFSIAGGPRADGSIEMHVRHVAGGGFTSWVADGLRVGDRL 188 Query: 190 LMEAPLGAFYLRHVTQ-PLVLVAGGTGLSALLGMLDQLAANGCEQPVHLYYGVRGAEDLC 248 +EAPLG F R ++ P+V +AGGTG + + +++ A G +P+ +Y+G R A DL Sbjct: 189 RLEAPLGTFVPREDSERPMVFMAGGTGFAPVKAIVEHFLALGTRRPIEVYWGARNAADLY 248 Query: 249 EAARIRAYAAKIPNLRYTEVLSAPSE-EWSGKRGYLTEHFDLAELRDGSA-DMYLCGPPP 306 R + LR+ VLS P + SG R L L +L D S D+Y+ GPP Sbjct: 249 LLELARGWERSAHALRFHPVLSDPEQAAASGLRMGLVHEAVLEDLPDLSGHDVYMSGPPA 308 Query: 307 MVESIQQWLADQALDGVQLYYEKF 330 M+++ ++ D L +LYY+ F Sbjct: 309 MIDAGRKLFLDAGLPEERLYYDSF 332 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: 314 Number of extensions: 20 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: 335 Length of database: 352 Length adjustment: 29 Effective length of query: 306 Effective length of database: 323 Effective search space: 98838 Effective search space used: 98838 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