Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate BPHYT_RS23425 BPHYT_RS23425 mannitol dehydrogenase
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__BFirm:BPHYT_RS23425 Length = 496 Score = 340 bits (873), Expect = 5e-98 Identities = 197/485 (40%), Positives = 268/485 (55%), Gaps = 12/485 (2%) Query: 2 KLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSIC 61 +L +Q L L + P + + R GI H+G+G FHRAHQA YT+ M G DW IC Sbjct: 9 RLVRQALPTLQTHLLSPLWQ--EPRIGIVHLGIGNFHRAHQALYTEEAMLAAGG-DWGIC 65 Query: 62 GVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLAS 121 GV L+ + K RD L Q L+++ E G +V V+ ++ ++L AL +LA Sbjct: 66 GVTLQGDVGK-RDALMEQQGLYSVVERGP-HGAKVTVVRALREVLAMPHDQAALFARLAD 123 Query: 122 PEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRR--AA 179 P +RIVSLT+TE GYC D GE P + HDLA P P+TV G + AAL QR A Sbjct: 124 PAVRIVSLTVTEKGYCRDPRTGEVALDNPAVAHDLASPFEPRTVPGILVAALRQRHDDAR 183 Query: 180 GIPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTA 239 G P FTV+SCDNL HNGA R+ + +FA + L DWI AHV+FP+ MVDRI P T+ A Sbjct: 184 GQP-FTVLSCDNLSHNGAALRQVVCSFARQLDPALADWIAAHVAFPSTMVDRIVPATTHA 242 Query: 240 HRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLL 299 + + DA PV CEPF QWV+ED+F GRPAW+ VG Q DDVTP+E K+ +L Sbjct: 243 ESVTVAHAIVYQDAAPVPCEPFRQWVIEDRFPAGRPAWDAVGAQLVDDVTPFELAKLRML 302 Query: 300 NGSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLV 359 NG+H L YL L G+ + ++ P + A M ++ P L DL+ Y+ L+ Sbjct: 303 NGTHSTLAYLSMLGGFETIDAAISYPPMRNLIHAMMTEEIAPTLTMPASFDLSAYRDALL 362 Query: 360 DRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDE 419 +R++N A+ + ++ DGS K P + TI I G+ R L VAAW ++L+G + Sbjct: 363 ERYANPALKHRCSQIAMDGSQKIPPRLLDTIAARIDAGQSFTRLVLAVAAWMMFLRGHAD 422 Query: 420 NGVSYTIPDPRAEFCQGLV----SDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGS 475 +G Y I DP A L D + LL+V E+F + PEF A R Sbjct: 423 DGTRYEISDPLASRLHALAVSAHDDPQALMDALLSVREVFPADLTAFPEFREALLRALRL 482 Query: 476 LRDNG 480 LR+ G Sbjct: 483 LREEG 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: 643 Number of extensions: 27 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: 493 Length of database: 496 Length adjustment: 34 Effective length of query: 459 Effective length of database: 462 Effective search space: 212058 Effective search space used: 212058 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 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