Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate CCNA_03124 CCNA_03124 NAD/mycothiol-dependent formaldehyde dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Caulo:CCNA_03124 Length = 366 Score = 149 bits (377), Expect = 9e-41 Identities = 110/355 (30%), Positives = 167/355 (47%), Gaps = 32/355 (9%) Query: 9 MKAAVMHNT-REIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFI 67 MKAAV+ + ++IET+ + EVLI+ A G+C SDLH+ G+Y P + Sbjct: 1 MKAAVLREVGKPLQIETVAIGKPGPREVLIRTKAAGVCHSDLHFVE----GSYTHALPAV 56 Query: 68 LGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLC---------PDVQ 118 LGHE AG + AVGS V KVGD V CG CE C G NLC D Sbjct: 57 LGHESAGIVEAVGSEVRTVKVGDHVITCLNPYCGHCEVCLTGHMNLCISPETRRSKSDAP 116 Query: 119 FLATPPVDGA------------FVQYIKMRQDFVFLIPDSLSYEEAALIE-PFSVGIHAA 165 L ++GA F + + + + I + ++ AALI G+ A Sbjct: 117 RLFKEDLNGATGPMAQFLNLSSFAEMMLVHEHACVAIRKDMPFDRAALIGCSVMTGVGAV 176 Query: 166 ARTK-LQPGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINI 224 T ++PG T+A++G G VGL + A GAG II D +LE AK GAT +++ Sbjct: 177 MHTSNVRPGETVAVIGCGGVGLATINGAAIAGAGRIIAIDRLAGKLELAKTFGATDVVDA 236 Query: 225 REQDALEEIKTITNDRGVDVAWETAGNPAALQSALASVRRGGKLAIVG-LPSQNEIPLN- 282 + D + + GV ++E G A +++ +RRGG ++G +P +I L+ Sbjct: 237 SQVDDIAKAVVELTGGGVHHSFEAIGLKATAEASFKMLRRGGTANVIGMIPVGTKIELHG 296 Query: 283 VPFIADNEI--DIYGIFRYANTYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAME 335 V F+ + I G R+ P+ ++F SG + L++ + LE A + Sbjct: 297 VDFLGERRIQGSYMGSNRFPVDMPRLVDFYMSGKLKLDELISRRIKLEDVNSAFD 351 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: 293 Number of extensions: 17 Number of successful extensions: 3 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: 366 Length adjustment: 29 Effective length of query: 324 Effective length of database: 337 Effective search space: 109188 Effective search space used: 109188 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