Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_023430324.1 N177_RS00865 zinc-binding dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >NCBI__GCF_000496075.1:WP_023430324.1 Length = 388 Score = 187 bits (476), Expect = 3e-52 Identities = 111/361 (30%), Positives = 180/361 (49%), Gaps = 17/361 (4%) Query: 5 VPQNMKAAVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRI----GNY 60 +P+ MKA V+ + ++ + PVP EVL+++ AV IC +DL NG G Sbjct: 15 IPETMKAWVLGDPDQLTLTEKPVPSPKRAEVLVRIDAVAICATDLEIIHNGPPAMIQGGA 74 Query: 61 VVEKPFILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFL 120 K F GHE G + A+G VD++ +GDRV VE CG+C+ C++G Y C + Sbjct: 75 PFNKNFTPGHEYMGTVVALGEGVDEYTIGDRVTVEIHAGCGQCKRCRQGMYTSCHNYGLN 134 Query: 121 ATP----------PVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTK- 169 DG F +Y + + +PD +S EEA L+ ++ Sbjct: 135 YGDRNKGHRANGFTTDGGFAEYAVNNINTLVHVPDDMSDEEATLVVTAGTAMYGLTELGG 194 Query: 170 LQPGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDA 229 L G ++ + G GP+GL+ VA AKA GA +I+T RLE KK+GA H IN+R ++A Sbjct: 195 LVAGESVVVTGPGPIGLLGVAVAKALGAQPVILTGTRDNRLEMGKKLGADHTINVRNENA 254 Query: 230 LEEIKTITNDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADN 289 +E ++ I +GVD E +G A+ A V RGG++ + P + +P++V ++ N Sbjct: 255 VERVREIMGGKGVDYVVECSGASNAVNEAAQMVNRGGRICLAAFPHE-AVPVDVAYLVRN 313 Query: 290 EIDIYGIFRYANTYP-KGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQFKNECLKVM 348 I +YGI + + F+ D + T + + + A++ A + + +KV+ Sbjct: 314 NIYVYGIRGEGKSATHRAAAFMEQKRFDATLIHTHTFPMGDLETALKYARERIEDAIKVV 373 Query: 349 V 349 V Sbjct: 374 V 374 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: 315 Number of extensions: 17 Number of successful extensions: 5 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: 388 Length adjustment: 30 Effective length of query: 323 Effective length of database: 358 Effective search space: 115634 Effective search space used: 115634 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