Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_039104414.1 FPB0191_RS04895 NAD(P)-dependent alcohol dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >NCBI__GCF_000807275.1:WP_039104414.1 Length = 348 Score = 96.7 bits (239), Expect = 8e-25 Identities = 67/215 (31%), Positives = 110/215 (51%), Gaps = 18/215 (8%) Query: 30 INHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFILGHECAGEIAAVGSSVDQFKVG 89 + ++V I+++ GIC SDLH G G P + GHE G++ +VG +V ++KVG Sbjct: 25 LRDNDVAIEILYSGICHSDLHT-VKGDWGQQPY--PLVPGHEIIGQVISVGKNVQKYKVG 81 Query: 90 DRVAVEPGV-TCGRCEACKEGRYNLCPDVQFLATPPVD--------GAFVQYIKMRQDFV 140 D+VAV V +C C+ CK+G C + L D G + ++I +R++FV Sbjct: 82 DKVAVGCMVDSCQCCDQCKQGEEQYCRNGLTLTYGAPDRITGEITQGGYAKHIVVREEFV 141 Query: 141 FLIPDSLSYEEAALIEPFSVGIHAAARTK---LQPGSTIAIMGMGPVGLMAVAAAKAFGA 197 +P L AA I GI + K ++ G+ + ++G G +G MAV A A A Sbjct: 142 LKVPSQLDLSRAAPI--LCAGITTFSPLKKWNVKKGTKVGVIGFGGLGHMAVKLAVAMEA 199 Query: 198 GTIIVTDLEPLRLEAAKKMGATHIINIREQDALEE 232 ++T + + AKK+GA ++ + DA+E+ Sbjct: 200 EVTVITRSNS-KQDVAKKLGAKDVLVTADMDAMEK 233 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: 288 Number of extensions: 18 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: 348 Length adjustment: 29 Effective length of query: 324 Effective length of database: 319 Effective search space: 103356 Effective search space used: 103356 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