Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate Ga0059261_2655 Ga0059261_2655 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__Korea:Ga0059261_2655 Length = 259 Score = 125 bits (314), Expect = 9e-34 Identities = 88/262 (33%), Positives = 136/262 (51%), Gaps = 15/262 (5%) Query: 7 LQPYPGLRVLISGGAAGIGEVLAAAYLEAGAQVHV----CDVS--ESALAVFRDKYPGTV 60 ++ + G +ISGG GIG +A + GA + + D+S E ALA + G V Sbjct: 1 MRRFEGKCAVISGGNKGIGLAIAERFASEGANIVIGAIEADLSPAEQALAGYGT---GVV 57 Query: 61 ATRADVSDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTA 120 A R DV+ A + A+F+ E GG+D+ V NAG+ ++ +++ EW + +N Sbjct: 58 AQRCDVTKADDVRALFEAA-EAFGGVDIAVQNAGVI-TIAKVEDLTEGEWDLNLAVNTKG 115 Query: 121 QYRFAHHAVPMLK-ESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGES 179 + A+ L+ G L++ AS R G+ + YAA+K+ +VG+ +SLA E+ Sbjct: 116 AFLCCQEAIRRLRARGKPGRLINTASGQARDGFIFTPHYAASKFGVVGMTQSLAKEVATQ 175 Query: 180 DIRVNALLPGIVEGPRMDGVIRARAEQVG--VPEAEMRQEYLNKISLKRMVTAEDVAAMA 237 I VNA+ PGI+ D R +G P A M +E++ I +KR T DVAA+ Sbjct: 176 GITVNAICPGIIHTDMWDYNDREWGRLMGDYAPGALM-EEWVQGIPMKRAGTGADVAALV 234 Query: 238 LFLCSPAARNVTGQAISVDGNV 259 FL S A +TGQ I+VDG + Sbjct: 235 AFLASADASYITGQTINVDGGL 256 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: 173 Number of extensions: 10 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: 262 Length of database: 259 Length adjustment: 25 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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