Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate CCNA_01554 CCNA_01554 D-mannonate oxidoreductase
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__Caulo:CCNA_01554 Length = 482 Score = 279 bits (713), Expect = 2e-79 Identities = 152/407 (37%), Positives = 224/407 (55%), Gaps = 7/407 (1%) Query: 14 VQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEHAPDWAIVGVGLTGSDRSKKKAE 73 V P YD D ++ G+VHFG G F RAH+A Y +Q+L H P W + V L +S + Sbjct: 25 VAIPTYDRDKLQIGVVHFGPGAFHRAHQAHYFDQLLAHDPRWGVCAVSL----KSPGVRD 80 Query: 74 EFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLVDPAIRIVSMTITEG 133 K QD LY+L + ++T R++G++ + L+AP DP +V L P R+V++T+TE Sbjct: 81 ALKPQDGLYTLAQL--DAETTFRIVGSILEVLVAPEDPPSVFARLAAPTTRLVTLTVTEK 138 Query: 134 GYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAGGKAFTVMSCDNLRH 193 GY ++ G D + + DL NP +P + GY+VE LRRR+ AG + V++CDNL Sbjct: 139 GYTLS-ANGGLDESHPDIVHDLANPREPRSAVGYLVEGLRRRFAAGLAPYAVVACDNLAD 197 Query: 194 NGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEIAKKLNAASGLDDDL 253 NG + A + YA D LA WI+ FP MVD ITP + + AA+GL+D Sbjct: 198 NGWRLKAAVVAYAAKLDESLAAWIDREGRFPRTMVDSITPATDDALRARTLAATGLEDAW 257 Query: 254 PLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLNAGHVMLCFPGILVG 313 P+ E F QWV+ED P L GV M DV +E K+R+LN H L + GIL G Sbjct: 258 PIQREAFAQWVVEDVLPADGPDLASVGVIMTDDVRGFERAKLRLLNGVHSTLAYVGILRG 317 Query: 314 YENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVISRFSNKAMSDQTLRI 373 +E V +A+ D L + + KD+IPTL P G+ L+ Y D+++ RF N + +I Sbjct: 318 HETVFEAVSDPTLAALASDMMAKDIIPTLTPPRGLDLQAYADAILGRFRNPEIRHLLAQI 377 Query: 374 ASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEKG 420 A DG K+ T+ +E R + R+A +A+++ + R + G Sbjct: 378 AWDGSQKLPFRILGTLTETLEAGRSIERLAVPLAAWMRFVALRAKAG 424 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: 590 Number of extensions: 30 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: 482 Length adjustment: 34 Effective length of query: 451 Effective length of database: 448 Effective search space: 202048 Effective search space used: 202048 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