Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate H281DRAFT_01517 H281DRAFT_01517 L-idonate 5-dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Burk376:H281DRAFT_01517 Length = 348 Score = 209 bits (533), Expect = 7e-59 Identities = 117/347 (33%), Positives = 191/347 (55%), Gaps = 12/347 (3%) Query: 9 MKAAVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFIL 68 M AAV+H + I+I+ + P+ +V ++V A GICGSDL YY G+ G++ V +PF+L Sbjct: 1 MLAAVLHEPKLIRIDEVAPPEPGPGQVRVRVRAGGICGSDLSYYFKGKSGDFAVREPFVL 60 Query: 69 GHECAGEIAAVGSSVD---QFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLAT--- 122 GHE AGEI ++G V + G RVAV PG+ CG C+ C G N C +++F+ + Sbjct: 61 GHEVAGEIDSLGEGVSADARLVPGQRVAVNPGLACGTCKYCTIGMPNHCLNMRFMGSAST 120 Query: 123 -PPVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGM 181 P G F QYI + + DS+ + +A++ EP +V +HA R G+++ ++G Sbjct: 121 FPHTQGMFRQYIVVAARQCIPVADSVDFAQASMAEPLAVALHAVKRAGSLVGASVLLIGC 180 Query: 182 GPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRG 241 GP+G + ++ A+ GA ++ DL L+ A ++GA +N + +E+ RG Sbjct: 181 GPIGCILLSVARRAGAHRVVAVDLSSRALQVAAQLGADQTVNAADSATIEQWSA---QRG 237 Query: 242 V-DVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIFRYA 300 DV E +G+PA L++AL S R GG + VG + P+ + E+ G FR+ Sbjct: 238 TFDVVIEASGSPAGLETALRSARAGGTVIQVGNLPAGQSPVAANLVMSKELRYQGSFRFT 297 Query: 301 NTYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQFKNECLKV 347 + Y + +ASG VD + L+T +++ A E AL +++ +KV Sbjct: 298 DEYAIAADEIASGKVDLRPLMTHAFAMSDANQAFEVALD-RSQSMKV 343 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: 272 Number of extensions: 17 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: 348 Length adjustment: 29 Effective length of query: 324 Effective length of database: 319 Effective search space: 103356 Effective search space used: 103356 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