Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_086510166.1 BZY95_RS12005 SDR family NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_002151265.1:WP_086510166.1 Length = 257 Score = 274 bits (700), Expect = 2e-78 Identities = 150/262 (57%), Positives = 186/262 (70%), Gaps = 5/262 (1%) Query: 1 MSVLQRLQPYPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTV 60 M V+ L P GLRVL++ GA GIG +A A+ EAGA+VHVCDV E+ALA + G Sbjct: 1 MKVVDSLIPRQGLRVLVTAGANGIGLAIAQAFHEAGARVHVCDVDEAALAALPE---GIA 57 Query: 61 ATRADVSDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTA 120 ATRADVS A++ +F + LGGLDV+VNNAGIAGPT GID I W+ TI+INL Sbjct: 58 ATRADVSREAEVARLFD-EAAGLGGLDVVVNNAGIAGPTAGIDEIESEAWRQTIDINLNG 116 Query: 121 QYRFAHHAVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESD 180 QY A A L+ES G LL++ASVAGRLG+A+RTPYAA+KW +VGL KSLA ELG + Sbjct: 117 QYYVAKRAAGALRES-RGVLLNMASVAGRLGFAYRTPYAASKWGVVGLTKSLACELGPAG 175 Query: 181 IRVNALLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFL 240 +RVNA+LPGIV GPR++ VI RA Q G+ EM QE L K+S+++MV D+AAMALFL Sbjct: 176 VRVNAILPGIVRGPRIERVIADRAAQRGIGRDEMEQENLAKVSMRKMVEPSDIAAMALFL 235 Query: 241 CSPAARNVTGQAISVDGNVEYL 262 SP N++GQA+SV NVE L Sbjct: 236 ASPGGANISGQALSVCANVESL 257 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: 209 Number of extensions: 8 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: 262 Length of database: 257 Length adjustment: 24 Effective length of query: 238 Effective length of database: 233 Effective search space: 55454 Effective search space used: 55454 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 24 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