Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_086511126.1 BZY95_RS17225 mannitol dehydrogenase family protein
Query= BRENDA::Q9KWR5 (485 letters) >NCBI__GCF_002151265.1:WP_086511126.1 Length = 491 Score = 358 bits (918), Expect = e-103 Identities = 188/421 (44%), Positives = 254/421 (60%), Gaps = 4/421 (0%) Query: 2 ITRETLKSLPANVQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEH--APDWAIVG 59 ++ TL L + V P YD + PGIVH GVG F RAH+A Y++ ++ A DW IVG Sbjct: 4 LSNATLSHLDSRVAVPRYDRREVTPGIVHIGVGGFHRAHQAMYLDALMNRGEALDWGIVG 63 Query: 60 VGLTGSDRSKKKAEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLV 119 VG+ DR + E AQD LY+L P+G+ RV+GA+ DYL AP DPEAV++ + Sbjct: 64 VGVMPGDR--RMQEVLAAQDHLYTLVVKHPNGEREPRVIGAMLDYLYAPDDPEAVVERMA 121 Query: 120 DPAIRIVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAG 179 DPAIRIVS+T+TEGGYN + TG FDL N V+ DL +P P T FG VVEAL RR G Sbjct: 122 DPAIRIVSLTVTEGGYNFHPVTGEFDLANPDVRHDLDSPAAPRTTFGLVVEALARRRARG 181 Query: 180 GKAFTVMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEI 239 FT+MSCDN++ NG VAR+ F+ +A+ARDP LA+WIE FPN MVDRITP A Sbjct: 182 LAPFTLMSCDNIQGNGEVARRMFVAFARARDPALAEWIEAEVPFPNAMVDRITPVTQAVD 241 Query: 240 AKKLNAASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLN 299 ++L G++D P+V E F QWVLED F GRP E+ GVQ+V DV +E +K+R+LN Sbjct: 242 IEELAGEFGVEDAWPVVCEPFTQWVLEDHFICGRPAFERVGVQVVEDVEPYELMKLRLLN 301 Query: 300 AGHVMLCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVIS 359 A H LC+ G L GY + D + L Y+ + PTL G+ LE YR ++I Sbjct: 302 ASHQALCYFGTLAGYRYAHEVCRDPLFVDFLLGYMRHEGSPTLAPVPGVDLEQYRLTLIE 361 Query: 360 RFSNKAMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEK 419 RF+N + D R+ ++ ++ + +R + ++ R A +AS+ G DE+ Sbjct: 362 RFANPEIKDTLARLCAESSDRIPKWLVPVIREQLAKGGEIHRSAAVVASWARYAEGLDEQ 421 Query: 420 G 420 G Sbjct: 422 G 422 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: 600 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: 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 24 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