Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate BWI76_RS19755 BWI76_RS19755 fructuronate reductase
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__Koxy:BWI76_RS19755 Length = 488 Score = 369 bits (948), Expect = e-106 Identities = 202/463 (43%), Positives = 279/463 (60%), Gaps = 8/463 (1%) Query: 9 TQLAPE-VKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRS 67 T PE V+LP Y + R I H G G FHRAHQA TD ++N G G DW IC + L S Sbjct: 6 TATLPEGVQLPQYDRSQLRSRIVHFGFGAFHRAHQALLTDRVLNAGGG-DWGICEISLFS 64 Query: 68 EDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAE-DSAQALIDKLASPEIRI 126 DR L QD+LFT+ E G + + V+G++ + L A+ DS A+I+K P++ I Sbjct: 65 GDR-LMSQLRQQDHLFTVLEKGAEGNQPI-VVGAVHECLNAKLDSLAAIIEKFCEPQVAI 122 Query: 127 VSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTV 186 VSLTITE GYCID ++G P+I HDL +P+ P++V G + AL++RR +P FTV Sbjct: 123 VSLTITEKGYCIDPASGLLDMTQPRIIHDLQNPTLPQSVPGILVEALSRRRQRELPPFTV 182 Query: 187 MSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHD 246 +SCDN+P+NG V + A+L A + EL WI VSFP MVDRI P + ++ Sbjct: 183 LSCDNIPNNGHVVKNAVLGMAEKRSPELAQWIAERVSFPGTMVDRIVPAATDESLAEISA 242 Query: 247 EHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLAL 306 G++D + CEPF+QWV+ED FV GRPAWE GVQ TDDV P+E+MK+ +LNGSH L Sbjct: 243 ALGVEDPCAISCEPFIQWVIEDNFVAGRPAWETAGVQMTDDVLPWEQMKLRMLNGSHSFL 302 Query: 307 TYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQA 366 +LG+L G+ + + M DP+F + M + P L+ + G+DLT Y +L++RFSN A Sbjct: 303 AWLGYLAGHAHISDCMQDPIFRSAAYRLMLDEQAPTLS-IQGVDLTAYADSLIERFSNPA 361 Query: 367 IADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTI 426 + + ++ DGS K P+ + I +A G AL VA W Y+ G+D+ G + I Sbjct: 362 LKHRTWQIAMDGSQKLPQRMLDGIRVHLAQGSHWPLLALGVAGWMRYVSGIDDGGNAIDI 421 Query: 427 PDPRAEFCQGLV--SDDALISQRLLAVEEIFGTAIPNSPEFVA 467 DP A+ Q LV SD+ LL +EEIFG +P P+FVA Sbjct: 422 RDPLADKIQKLVSASDEHQRVAALLTLEEIFGRDLPQDPQFVA 464 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: 656 Number of extensions: 33 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: 488 Length adjustment: 34 Effective length of query: 459 Effective length of database: 454 Effective search space: 208386 Effective search space used: 208386 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