Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate SMc00372 SMc00372 short chain dehydrogenase
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__Smeli:SMc00372 Length = 256 Score = 133 bits (335), Expect = 3e-36 Identities = 91/251 (36%), Positives = 130/251 (51%), Gaps = 12/251 (4%) Query: 12 GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPG----TVATRADVS 67 G +++G ++GIG A + GA+V V + +ALA D+ G A DV Sbjct: 6 GKIAIVTGASSGIGRAAALLFAREGAKVVVTARNGNALAELTDEIAGGGGEAAALAGDVG 65 Query: 68 DAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHH 127 D A EA+ ++ GGLD NNAG G G I ++S W+ T++ NLT+ + A + Sbjct: 66 DEALHEALVELAVRRFGGLDTAFNNAGALGAMGEISSLSVEGWRETLDTNLTSAFLAAKY 125 Query: 128 AVPMLKESSHGHLLHIASVAGR-LGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNAL 186 VP + G L +S G G+A PYAA+K ++GL+++LA ELG IRVNAL Sbjct: 126 QVPAIAALGGGSLTFTSSFVGHTAGFAGVAPYAASKAGLIGLVQALAVELGARGIRVNAL 185 Query: 187 LPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAAR 246 LPG + P + A PE E L+ +LKR+ E++A AL+L S A Sbjct: 186 LPGGTDTPANFANLPGAA-----PETRGFVEGLH--ALKRIARPEEIAEAALYLASDGAS 238 Query: 247 NVTGQAISVDG 257 VTG A+ DG Sbjct: 239 FVTGAALLADG 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: 169 Number of extensions: 10 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: 256 Length adjustment: 24 Effective length of query: 238 Effective length of database: 232 Effective search space: 55216 Effective search space used: 55216 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