Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate PP_1946 PP_1946 Oxidoreductase, short chain dehydrogenase/reductase family
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__Putida:PP_1946 Length = 262 Score = 125 bits (313), Expect = 1e-33 Identities = 80/254 (31%), Positives = 129/254 (50%), Gaps = 15/254 (5%) Query: 10 YPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVS--ESALAVFRDKYPGTVAT--RAD 65 + G VL++G +GIG A A+ ++GA V V D+S V K G AT D Sbjct: 7 FSGKVVLVTGAGSGIGRATALAFAQSGASVAVADISTDHGLKTVELVKAEGGEATFFHVD 66 Query: 66 VSDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFA 125 V ++++ H GGLD+ NNAGI + + W+ I++NL++ + Sbjct: 67 VGSEPSVQSMLAGVVAHYGGLDIAHNNAGIEANIVPLAELDSDNWRRVIDVNLSSVFYCL 126 Query: 126 HHAVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNA 185 +P++ + G +++ AS +G +G + Y ATK +VGL K+ A + +IR+NA Sbjct: 127 KGEIPLMLKRGGGAIVNTASASGLIGGYRLSGYTATKHGVVGLTKAAAIDYANQNIRINA 186 Query: 186 LLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAA 245 + PG V+ P + +P+ MR L + R+ TAE++A L+LCS A Sbjct: 187 VCPGPVDSPFL----------ADMPQ-PMRDRLLFGTPIGRLATAEEIARSVLWLCSDDA 235 Query: 246 RNVTGQAISVDGNV 259 + V G ++SVDG V Sbjct: 236 KYVVGHSMSVDGGV 249 Lambda K H 0.318 0.133 0.383 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: 184 Number of extensions: 14 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: 262 Length of database: 262 Length adjustment: 25 Effective length of query: 237 Effective length of database: 237 Effective search space: 56169 Effective search space used: 56169 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 (21.7 bits) S2: 47 (22.7 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