Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_057507224.1 ABB28_RS03140 NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_001431535.1:WP_057507224.1 Length = 267 Score = 134 bits (336), Expect = 3e-36 Identities = 80/252 (31%), Positives = 128/252 (50%), Gaps = 7/252 (2%) Query: 12 GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESAL-AVFRDKYP--GTVATRADVSD 68 G L+SG +G+G+ A L+AG +V + DV++ L ++ P +A DV+D Sbjct: 7 GRIALVSGADSGMGKQSARELLQAGVRVAITDVADGTLDEALQELTPLGEVMAVAGDVTD 66 Query: 69 AAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHA 128 A +E ++ R LG D+ VN AG+ G TG + DA W T++INL R A Sbjct: 67 ANDVERIWATVRSRLGDPDIYVNAAGVTGATGDFLDVDDAGWLRTLDINLMGAVRMCRQA 126 Query: 129 VPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLP 188 +P ++ G ++ AS Y PY A+K ++ L K L+ + G+ ++ +N + P Sbjct: 127 IPAMRAKGWGRIVLFASEDAVQPYTDELPYCASKAGVLSLAKGLSKQYGKDNVMINTVSP 186 Query: 189 GIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNK----ISLKRMVTAEDVAAMALFLCSPA 244 + P D ++ RA++ GV E + +L++ + LKR E+VAA L LCS Sbjct: 187 AFIHTPMTDAMMHKRAKEKGVSFDEAVRSFLDEERPGMVLKRRGRPEEVAAAVLLLCSER 246 Query: 245 ARNVTGQAISVD 256 A + G I VD Sbjct: 247 ASFINGANIRVD 258 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: 140 Number of extensions: 4 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: 267 Length adjustment: 25 Effective length of query: 237 Effective length of database: 242 Effective search space: 57354 Effective search space used: 57354 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