Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate Ga0059261_0846 Ga0059261_0846 Zn-dependent alcohol dehydrogenases, class III
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Korea:Ga0059261_0846 Length = 361 Score = 157 bits (397), Expect = 4e-43 Identities = 114/355 (32%), Positives = 171/355 (48%), Gaps = 37/355 (10%) Query: 9 MKAAVMHNT-REIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFI 67 +KAAV+ R ++I + + EVLI+ A G+C SDLH+ G Y P I Sbjct: 1 VKAAVLFEAKRPLEIHDITIDKPGPREVLIRTAACGVCRSDLHFVD----GAYPHVMPTI 56 Query: 68 LGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPD----------- 116 GHE +G + AVGS V + + GD V V CG CE C GR +LC D Sbjct: 57 PGHEASGVVEAVGSEVTRLRPGDHVITFFTVFCGSCEFCVSGRPSLCVDGSTKRPKEGEP 116 Query: 117 ----------VQFLATPPVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSV-GIHAA 165 QFL AF + + + ++ I + + AAL+ + G A Sbjct: 117 KLRLPDGTPIAQFLNL----SAFAEQMLVHENACVAISKDMPLDRAALLGCAVITGAGAI 172 Query: 166 AR-TKLQPGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINI 224 R +K+ PG T+A++G G +GL AV AAK GAG II D P + E A+KMGATH+ + Sbjct: 173 FRDSKVTPGETVAVIGCGGIGLSAVNAAKIAGAGKIIAIDPVPEKREIARKMGATHVFDA 232 Query: 225 REQDALEEIKTITNDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGL--PSQNEIPLN 282 D ++++ +T D GVD A E G P + A +RRGG I+G+ P Q+ Sbjct: 233 MADDLVKQVAKLT-DGGVDYAIEAVGRPNTAELAWNLLRRGGTATILGMIAPGQSVSIPG 291 Query: 283 VPFIADNEI--DIYGIFRYANTYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAME 335 F+ ++ + G R+ P+ ++ G++D +V ++ LE A + Sbjct: 292 PTFLTGKKLQGSLLGSMRFPVDLPRLVQMYLDGLLDLDTMVAERIRLEDINHAFD 346 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: 281 Number of extensions: 12 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: 361 Length adjustment: 29 Effective length of query: 324 Effective length of database: 332 Effective search space: 107568 Effective search space used: 107568 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