Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_047094432.1 AAV99_RS12695 NAD(P)-dependent alcohol dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >NCBI__GCF_001013305.1:WP_047094432.1 Length = 354 Score = 158 bits (400), Expect = 2e-43 Identities = 122/358 (34%), Positives = 179/358 (50%), Gaps = 23/358 (6%) Query: 9 MKAAVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFIL 68 MKAA+ I + PVPD+ + L+K+ ICG+D+H G Y VEK + Sbjct: 1 MKAAIFVEPGRIVLGEKPVPDVGPLDALMKITTTTICGTDVHILK----GEYPVEKGLTV 56 Query: 69 GHECAGEIAAVGSSVDQFKVGDRV---AVEPGVT-----CGRCEAC--KEGR-YNLCPDV 117 GHE G I +GS+V F G RV A+ P T CG C +EG + Sbjct: 57 GHEPVGRIEKLGSAVYGFTEGQRVIAGAITPSGTSTASLCGFHAQCGGQEGHGWKAIGGW 116 Query: 118 QFLATPPVDGAFVQYIKMRQDFVFL--IPDSLSYEEAALI-EPFSVGIHAAARTKLQPGS 174 +F T +DGA +Y+ + L IPD LS E+ + + S G A K++ G Sbjct: 117 RFGNT--IDGAQAEYLLVPDAMANLAPIPDGLSDEQVLMCPDIMSTGFGGAESGKIRIGD 174 Query: 175 TIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIK 234 T+A+ GP+GL A A A GA TII + P R+ +++MGATH+++ + D ++EI Sbjct: 175 TVAVFAQGPIGLFATAGAYMMGATTIIGVESIPARMAMSRQMGATHVVDFSKVDPVDEIM 234 Query: 235 TITNDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQN-EIPLNV--PFIADNEI 291 IT+ RGVDVA E G + + AL +R GG L+ +G+ S + IP + + DN I Sbjct: 235 KITDGRGVDVAIEALGLQSTFEGALRVLRPGGTLSSLGVYSGDLTIPCDAFSAGLGDNHI 294 Query: 292 DIYGIFRYANTYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQFKNECLKVMV 349 + + +ASG +DTK LVT ++ L+ DA E + LKV + Sbjct: 295 VTTLCPGGKERMRRLMATVASGRIDTKALVTHRFPLDSIVDAYELFANQRGGVLKVAI 352 Lambda K H 0.320 0.137 0.401 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: 323 Number of extensions: 20 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: 353 Length of database: 354 Length adjustment: 29 Effective length of query: 324 Effective length of database: 325 Effective search space: 105300 Effective search space used: 105300 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: 49 (23.5 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