Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 18347 b4323 D-mannonate oxidoreductase, NAD-binding (NCBI)
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__Keio:18347 Length = 486 Score = 296 bits (758), Expect = 1e-84 Identities = 164/418 (39%), Positives = 234/418 (55%), Gaps = 6/418 (1%) Query: 14 VQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEHAP-DWAIVGVGLT-GSDRSKKK 71 V P +D ++ IVH G G F RAH+A Y +LE DW I V L G+DR Sbjct: 11 VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVL-- 68 Query: 72 AEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADP-EAVLKHLVDPAIRIVSMTI 130 E K Q LY++ E + ++++G++++ L D E +L + P IVS+T+ Sbjct: 69 IENLKKQQLLYTVAEKGAES-TELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTV 127 Query: 131 TEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAGGKAFTVMSCDN 190 TE GY + +G DL N +K DL+NP P + GY+VEALR R + G KAFTVMSCDN Sbjct: 128 TEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDN 187 Query: 191 LRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEIAKKLNAASGLD 250 +R NG+VA+ A LG A+ARDP+LA WIEEN TFP MVDRI P + E +++ G+ Sbjct: 188 VRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVY 247 Query: 251 DDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLNAGHVMLCFPGI 310 D + E F QWV+ED F +GRP +K G Q V DV +E +K+RMLN H L + G Sbjct: 248 DPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGY 307 Query: 311 LVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVISRFSNKAMSDQT 370 L GYE + D + + + ++ PTL P G L Y +I RFSN ++ +T Sbjct: 308 LGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRT 367 Query: 371 LRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEKGGTYESSEP 428 +IA DG K+ + VR +++ +A G+A ++ +G DE+G + +P Sbjct: 368 WQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDP 425 Lambda K H 0.317 0.135 0.398 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: 573 Number of extensions: 26 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: 485 Length of database: 486 Length adjustment: 34 Effective length of query: 451 Effective length of database: 452 Effective search space: 203852 Effective search space used: 203852 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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