Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate N515DRAFT_0334 N515DRAFT_0334 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Dyella79:N515DRAFT_0334 Length = 249 Score = 128 bits (321), Expect = 1e-34 Identities = 94/261 (36%), Positives = 138/261 (52%), Gaps = 34/261 (13%) Query: 4 RLAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKPVEARKLD-------V 56 +L GK A+IT G+GLATA LF REGA VI T G +EA K D V Sbjct: 3 KLDGKVAVITGGSAGMGLATARLFLREGATVIVT-----GRDEAALEAAKRDLGGGAEIV 57 Query: 57 RDD----AAIKALAAEI----GAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYR 108 R D A I++L+A + G VD++F AG SE+D+DF D N K Y Sbjct: 58 RCDNSKVADIESLSAYVETKHGRVDIVFANAGGGRPALFEHTSEDDFDFMIDTNFKGAYF 117 Query: 109 MIRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVR 168 ++ LP L K G S+I ++++ S +G P YSA+KAA+ L +S++ + RG+R Sbjct: 118 TVQKLLP--LVKAGASVI-LNTSTLSTQGRPYVSVYSAAKAAIRSLARSLSVELSERGIR 174 Query: 169 CNAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFV---ARQPMGRIGKPEEIAALALY 225 NA+ PG + + QA+ G + + ++ + A+ PM R G +EIA L+ Sbjct: 175 VNALAPGYIDTD--------QARKVGMSEEMIEQTKIQVHAQVPMHRSGTVDEIANAVLF 226 Query: 226 LGSDESSFTTGHAHVIDGGWS 246 L S +S++ TG +DGGW+ Sbjct: 227 LASHDSAYVTGIELCVDGGWA 247 Lambda K H 0.320 0.133 0.381 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: 139 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: 247 Length of database: 249 Length adjustment: 24 Effective length of query: 223 Effective length of database: 225 Effective search space: 50175 Effective search space used: 50175 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 (21.8 bits) S2: 46 (22.3 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