Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate Echvi_3219 Echvi_3219 Zn-dependent alcohol dehydrogenases
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Cola:Echvi_3219 Length = 343 Score = 135 bits (341), Expect = 1e-36 Identities = 97/276 (35%), Positives = 150/276 (54%), Gaps = 15/276 (5%) Query: 5 VPQNMKAAVMHNTRE-IKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVE 63 +P+ MKAAV+ + +KIE +PV N +++L++VMA G+C +DLH G++ V+ Sbjct: 2 LPKTMKAAVVTEFGQPLKIEEIPVKAPNENQILVQVMASGVCHTDLH----AADGDWPVK 57 Query: 64 K--PFILGHECAGEIAAVGSSVDQFKVGDRVAVEPGV--TCGRCEACKEGRYNLCPDVQF 119 P I GHE G +AAVGS+V K GD V V P + CG CE C G LC + Q Sbjct: 58 PRLPLIPGHEGIGYVAAVGSNVKNTKEGDIVGV-PWLYSACGHCEHCITGWETLC-ESQV 115 Query: 120 LATPPVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAAR-TKLQPGSTIAI 178 VDG + +Y+ ++V ++ + + A I V ++ + T+++PG +AI Sbjct: 116 NGGYSVDGGYAEYVLADPNYVGRFSGAIDFVQMAPILCAGVTVYKGLKETEVRPGQWVAI 175 Query: 179 MGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITN 238 G+G +G +AV AKA G ++ D+ +L AKK+GA ++N + D + + T Sbjct: 176 SGIGGLGHVAVQYAKAMGL-HVLAVDVSDDKLNLAKKLGADRVVNGKNPDEVMNARKETG 234 Query: 239 DRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLP 274 GV TA +P A + AL +RR G L + GLP Sbjct: 235 --GVHGVLVTAVSPVAFRQALDLLRRKGTLVMNGLP 268 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: 284 Number of extensions: 14 Number of successful extensions: 6 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: 343 Length adjustment: 29 Effective length of query: 324 Effective length of database: 314 Effective search space: 101736 Effective search space used: 101736 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 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