Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate Pf1N1B4_4846 Multiple polyol-specific dehydrogenase (EC 1.1.1.-)
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4846 Length = 491 Score = 358 bits (919), Expect = e-103 Identities = 187/429 (43%), Positives = 261/429 (60%), Gaps = 4/429 (0%) Query: 2 ITRETLKSLPANVQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILE--HAPDWAIVG 59 + ++ L L V P Y + + GI H GVG F RAH+A+Y + ++ A DWAI G Sbjct: 3 LNKQNLNRLAPEVALPAYTLSDTRQGIAHIGVGGFHRAHQAYYTDALMNTGEALDWAICG 62 Query: 60 VGLTGSDRSKKKAEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLV 119 VGL DR + ++ K QD L++L E + + VRV+GA+RD LLA PE ++ L Sbjct: 63 VGLRAEDRRAR--DDLKEQDYLFTLFELGDADDAEVRVIGAIRDMLLAEDSPEVLIDKLA 120 Query: 120 DPAIRIVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAG 179 DP IRIVS+TITEGGY I+++ G F ++ DL +P P TVFG++ AL +R AG Sbjct: 121 DPDIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPNAPKTVFGFLCAALAKRRAAG 180 Query: 180 GKAFTVMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEI 239 AFT+MSCDNL HNG V RKA L +A RD +L WIE + +FPN MVDRITP S E Sbjct: 181 TPAFTLMSCDNLPHNGAVTRKALLAFAALRDADLRDWIERHVSFPNAMVDRITPMTSTEH 240 Query: 240 AKKLNAASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLN 299 +L+ +DD P+V E F QWVLED+F +GRP EK GVQ DVT +E +KI++LN Sbjct: 241 RLQLHDKHSIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIKLLN 300 Query: 300 AGHVMLCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVIS 359 H+ L + G L GY V + + D + ++ Y++ DV P L G+ L Y++++++ Sbjct: 301 GSHLALTYLGFLKGYRFVHETMNDPLFVRYMRAYMDLDVTPQLAPVPGIDLTEYKNTLVA 360 Query: 360 RFSNKAMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEK 419 RFSN+A++DQ R+ SDG SK F T+ I D ++ R A +A++ L+G DE Sbjct: 361 RFSNQAIADQLERVCSDGSSKFPKFTVPTINCLIADGQETKRAALVVAAWALYLKGVDEN 420 Query: 420 GGTYESSEP 428 G TY +P Sbjct: 421 GQTYAIPDP 429 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: 595 Number of extensions: 23 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: 491 Length adjustment: 34 Effective length of query: 451 Effective length of database: 457 Effective search space: 206107 Effective search space used: 206107 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