Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_086510924.1 BZY95_RS16165 mannitol dehydrogenase family protein
Query= BRENDA::Q9KWR5 (485 letters) >NCBI__GCF_002151265.1:WP_086510924.1 Length = 491 Score = 245 bits (626), Expect = 2e-69 Identities = 146/415 (35%), Positives = 212/415 (51%), Gaps = 14/415 (3%) Query: 27 GIVHFGVGNFFRAHEAFYVEQILEHAPD--WAIVGVGLTGSDRSKKKAEEFKAQDCLYSL 84 GIVH G+G F RAH+A Y+E+ + + D W + L G + + C Y + Sbjct: 17 GIVHLGLGAFHRAHQAVYLERYRQRSGDGAWGVCSANLRGG---VALVDALRDAGCRYHV 73 Query: 85 TETAPSGKSTVRVMGALRDYLLAPADPE--------AVLKHLVDPAIRIVSMTITEGGYN 136 E A S T+R +G + L D ++L + P RIV++T+TE GY Sbjct: 74 AEYADSDTVTLREIGVIEQALFTGRDLAGEWGRDLASLLARMASPETRIVTLTVTEKGYF 133 Query: 137 INETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAGGKAFTVMSCDNLRHNGN 196 ++ G ++ + D+ P+ P T G +VEAL RR AG FTV+ CDN+ +NG Sbjct: 134 LSPAEGNLLRDDPLIAHDIDQPQAPRTAPGILVEALARRRSAGVPPFTVLCCDNMPNNGQ 193 Query: 197 VARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEIAKKLNAASGLDDDLPLV 256 R A + A RD ELA WIE FP MVDRI P ++A +L A G++D +V Sbjct: 194 RTRAAVVQLAACRDAELAAWIEREVAFPCSMVDRIVPAMTAADFARL-AELGVEDLNAVV 252 Query: 257 AEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLNAGHVMLCFPGILVGYEN 316 E F QWV+ED F GRP E GV+MV DV +E +K+RMLN H +L + G L E Sbjct: 253 GEAFSQWVVEDDFPLGRPDWEAEGVEMVTDVAPFETMKLRMLNGSHSLLAYLGALDDIET 312 Query: 317 VDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVISRFSNKAMSDQTLRIASD 376 V DA+ +L+ L+ Y+ + PTL P G L Y DS++ RF N ++ + +IA D Sbjct: 313 VFDAVSRDDLVALLRRYMLCEAEPTLAMPEGTDLVAYADSLLVRFGNDSLRHRLQQIAMD 372 Query: 377 GCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEKGGTYESSEPTYG 431 G K+ W +E ++ A G+A+++ G D G + +P G Sbjct: 373 GSQKLPQRWLHGALARLEAGGEVPCTALGLAAWIRYTAGSDLHGNDHVVDDPMAG 427 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: 38 Number of successful extensions: 4 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