Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_053546284.1 CDES_RS13820 S-(hydroxymethyl)mycothiol dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >NCBI__GCF_001277995.1:WP_053546284.1 Length = 368 Score = 132 bits (331), Expect = 2e-35 Identities = 91/293 (31%), Positives = 146/293 (49%), Gaps = 37/293 (12%) Query: 27 VPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFILGHECAGEIAAVGSSVDQF 86 +PD +V++K+ + G+C +DL Y R G+ E PF+LGHE AG + VG +V Sbjct: 24 IPDPGPHDVIVKIQSTGVCHTDLAY----RDGDISDEFPFLLGHESAGVVETVGDAVTHV 79 Query: 87 KVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLA-----------TPPVD-GAFVQYIK 134 +VGD V + CG C AC++G C + + TP + G+F + Sbjct: 80 EVGDFVVLNWRAVCGECRACRKGDLEYCFNTHNASKKMTLTDGTELTPALGIGSFAEKTL 139 Query: 135 MRQDFVFLI-PDSLSYEEAALIEPFSVGIHAAART-KLQPGSTIAIMGMGPVGLMAVAAA 192 + + + PD+ L G+ +A T +++ G ++A+ G+G VG+ AVA A Sbjct: 140 VHEGQCTKVNPDADPAAAGLLGCGIMAGLGSAVNTGEVKRGESVAVFGLGGVGMAAVAGA 199 Query: 193 KAFGAGTIIVTDLEPLRLEAAKKMGATHIINIRE-------QDALEEIKTITNDRGVDVA 245 K GA TII D++ +LE AK+ GATH+I+ + + ++++ IT+ G DVA Sbjct: 200 KIAGATTIIAVDIDAKKLEWAKEFGATHVIDSSQLSGEGENSEVAQKVREITDGFGTDVA 259 Query: 246 WETAGNPAALQSALASVRRGGKLAIVGLP---SQNEIPLNVPFIADNEIDIYG 295 + G Q A S G++ +VG+P S+ E+P ID YG Sbjct: 260 IDAVGIMPTWQQAFYSRDHAGRMVMVGVPNLTSRIEVP---------AIDFYG 303 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: 324 Number of extensions: 14 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: 368 Length adjustment: 29 Effective length of query: 324 Effective length of database: 339 Effective search space: 109836 Effective search space used: 109836 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