Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate GFF1300 PGA1_c13160 mannitol 2-dehydrogenase MtlK
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__Phaeo:GFF1300 Length = 488 Score = 294 bits (752), Expect = 5e-84 Identities = 168/442 (38%), Positives = 248/442 (56%), Gaps = 13/442 (2%) Query: 2 ITRETLKSLPANVQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEH--APDWAIVG 59 ++ +TL LP + P YD I PGIVH G+GNF RAH+A+Y+ +++ A DW I+G Sbjct: 3 LSNDTLSQLPQTIGRPSYDRAEISPGIVHIGLGNFHRAHQAWYLHALMQSGLAMDWGIIG 62 Query: 60 VGLTGSDRSKKKAEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLV 119 G+ +D + + AQDCL +L E P+G+S V+G L D+L AD ++++ + Sbjct: 63 AGVRAADAGMR--DRLLAQDCLTTLIELDPTGRSA-EVIGPLIDFLPVEADNASLIRCMA 119 Query: 120 DPAIRIVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAG 179 IRIVS+T+TEGGY + DL + ++ D+ P++P TVFG +VEALR R G Sbjct: 120 GSPIRIVSLTVTEGGYYQDAQHKGLDLNHEDIRHDIARPDRPRTVFGAIVEALRLRRGRG 179 Query: 180 GKAFTVMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITP-TVSAE 238 AFTV SCDNL+ NG + R A + A+ DPELA WI++ FPN MVD I P T AE Sbjct: 180 LPAFTVQSCDNLQGNGQITRTAVVTLAQQTDPELAAWIDQTGAFPNSMVDCIVPATGPAE 239 Query: 239 IAKKLNAASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRML 298 IA L G++D P+ E++ WV+ED+F GRPP + AG DV +E +KIR+L Sbjct: 240 IA--LARGYGIEDTAPVTHENYRHWVIEDEFCAGRPPWDLAGAIFTDDVHGYESMKIRVL 297 Query: 299 NAGHVMLCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVI 358 NAGH +L G L+ + D ++D L + +++P + A M + Y + Sbjct: 298 NAGHQVLANAGELLSIATIADCMKDPLLAAFFRTVQTAEILPHVIAVPEMAPKDYLTLIE 357 Query: 359 SRFSNKAMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDE 418 +RFSN + D T R+A DG S+ F +R A+ K + + A + +M G E Sbjct: 358 ARFSNPEIRDTTRRVAYDGSSRHPGFVMPILRDAVRSKGAIDGLCLVEALWAQMCTGLRE 417 Query: 419 KGGTYESSEPTYGDAEWKLAKA 440 ++SE D +W+ K+ Sbjct: 418 -----DASEIAPNDPDWETRKS 434 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: 608 Number of extensions: 23 Number of successful extensions: 5 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: 488 Length adjustment: 34 Effective length of query: 451 Effective length of database: 454 Effective search space: 204754 Effective search space used: 204754 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