Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate WP_086510924.1 BZY95_RS16165 mannitol dehydrogenase family protein
Query= BRENDA::O08355 (493 letters) >NCBI__GCF_002151265.1:WP_086510924.1 Length = 491 Score = 285 bits (729), Expect = 3e-81 Identities = 176/474 (37%), Positives = 247/474 (52%), Gaps = 16/474 (3%) Query: 28 GIAHIGVGGFHRAHQAYYTDAL-MNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLY 86 GI H+G+G FHRAHQA Y + +G+G W +C LR D L + + Sbjct: 17 GIVHLGLGAFHRAHQAVYLERYRQRSGDGA-WGVCSANLRGGVALV-DALRDAGCRYHVA 74 Query: 87 ELGDTDDTEVRVIGSISDMLLA-EDSA-------QALIDKLASPEIRIVSLTITEGGYCI 138 E D+D +R IG I L D A +L+ ++ASPE RIV+LT+TE GY + Sbjct: 75 EYADSDTVTLREIGVIEQALFTGRDLAGEWGRDLASLLARMASPETRIVTLTVTEKGYFL 134 Query: 139 DDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAV 198 + G + P I HD+ P +P+T G + AL +RR+AG+P FTV+ CDN+P+NG Sbjct: 135 SPAEGNLLRDDPLIAHDIDQPQAPRTAPGILVEALARRRSAGVPPFTVLCCDNMPNNGQR 194 Query: 199 TRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVC 258 TR A++ AA +AEL WI+ V+FP +MVDRI P + A +L E G++D VV Sbjct: 195 TRAAVVQLAACRDAELAAWIEREVAFPCSMVDRIVPAMTAADFARL-AELGVEDLNAVVG 253 Query: 259 EPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFV 318 E F QWV+ED F GRP WE GV+ DV P+E MK+ +LNGSH L YLG L V Sbjct: 254 EAFSQWVVEDDFPLGRPDWEAEGVEMVTDVAPFETMKLRMLNGSHSLLAYLGALDDIETV 313 Query: 319 HETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDG 378 + ++ VA +R YM + P LA G DL Y +L+ RF N ++ +L+++ DG Sbjct: 314 FDAVSRDDLVALLRRYMLCEAEPTLAMPEGTDLVAYADSLLVRFGNDSLRHRLQQIAMDG 373 Query: 379 SSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLV 438 S K P+ + + G E AL +AAW Y G D +G + + DP A + L Sbjct: 374 SQKLPQRWLHGALARLEAGGEVPCTALGLAAWIRYTAGSDLHGNDHVVDDPMAGTFRLLH 433 Query: 439 SDDALISQRL----LAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHL 488 + L L ++ + A+ F AA Y L G+ L L Sbjct: 434 EAHGENVEELVPAFLELDAVVPPALAEHAGFTAAVVAAYRCLTTYGLAAALARL 487 Lambda K H 0.321 0.137 0.414 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: 648 Number of extensions: 38 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: 493 Length of database: 491 Length adjustment: 34 Effective length of query: 459 Effective length of database: 457 Effective search space: 209763 Effective search space used: 209763 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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