Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate PfGW456L13_3038 Multiple polyol-specific dehydrogenase (EC 1.1.1.-)
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3038 Length = 490 Score = 357 bits (917), Expect = e-103 Identities = 191/424 (45%), Positives = 260/424 (61%), Gaps = 4/424 (0%) Query: 7 LKSLPANVQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEHAP--DWAIVGVGLTG 64 L L V P Y + + GI H GVG F RAH+A+Y + ++ DWAI GVGL Sbjct: 8 LNRLAPEVVLPAYALGETRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWAICGVGLRA 67 Query: 65 SDRSKKKAEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLVDPAIR 124 DR + ++ K QD L++L E SG + VRV+GALRD LLA +A++ L P IR Sbjct: 68 EDRRAR--DDLKDQDYLFTLFELGDSGDTEVRVIGALRDMLLAEDSAQALIDKLASPEIR 125 Query: 125 IVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAGGKAFT 184 IVS+TITEGGY I+++TG F ++ DL +P P TVFG++ AL +R AG AFT Sbjct: 126 IVSLTITEGGYCIDDSTGEFMAHLPQIQHDLAHPGAPKTVFGFLCAALAKRRAAGTAAFT 185 Query: 185 VMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEIAKKLN 244 +MSCDNL HNG V RKA L +A D +L WI+ N +FPN MVDRITP S +L Sbjct: 186 LMSCDNLPHNGAVTRKALLAFAALHDSQLRDWIDTNVSFPNAMVDRITPMTSTLHRLQLA 245 Query: 245 AASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLNAGHVM 304 G+DD P+V E F QWVLED+F +GRP EK GVQ DVT +E +KI++LN H+ Sbjct: 246 DRHGVDDAWPVVCEPFAQWVLEDRFVNGRPAWEKVGVQFTDDVTPYEEMKIKLLNGSHLA 305 Query: 305 LCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVISRFSNK 364 L + G L GY V +A+ D + ++ Y++ DV P L A G+ L Y++++++RFSN+ Sbjct: 306 LTYLGFLKGYRFVHEAMNDPLFVRYMRAYMDLDVTPQLPAVPGIDLAEYKNTLVARFSNQ 365 Query: 365 AMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEKGGTYE 424 A++DQ R+ SDG SK F T+ R I D D R A +A++ L+G DE+G TY Sbjct: 366 AIADQLERVCSDGSSKFPKFTVPTINRLIADGCDTRRAALVVAAWALYLKGVDEQGETYT 425 Query: 425 SSEP 428 ++P Sbjct: 426 IADP 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: 558 Number of extensions: 21 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: 490 Length adjustment: 34 Effective length of query: 451 Effective length of database: 456 Effective search space: 205656 Effective search space used: 205656 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