Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate RR42_RS34965 RR42_RS34965 dioxygenase
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__Cup4G11:RR42_RS34965 Length = 511 Score = 346 bits (887), Expect = 1e-99 Identities = 193/499 (38%), Positives = 273/499 (54%), Gaps = 18/499 (3%) Query: 2 KLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNT----GEGLD 57 +L+ L QL +V P Y R GI H+G+G FHRAHQA T A ++ LD Sbjct: 5 RLHPDTLAQLPHDVLRPRYARERLRGGIVHLGIGAFHRAHQAAVTQAALHADAADAHSLD 64 Query: 58 WSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDD----TEVRVIGSISDMLLAEDSAQ 113 W I GV LR D RD LA Q L+TL G DD +++VIG++ +L+A D Sbjct: 65 WGIVGVSLRRPD--TRDALAPQQGLYTLALRGVRDDGSRFVQLQVIGAVMAVLVAADDPD 122 Query: 114 ALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAAL 173 A+++++A + RIVSLT+TE GYC D + G P I HDL H +P T G++ L Sbjct: 123 AVLERIAHEDARIVSLTVTEKGYCHDPATGTLNFSDPGIAHDLLHAGAPVTAIGYLARGL 182 Query: 174 TQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRIT 233 +R A G+P T++SCDN+ NG R LLAF A + LHDW+ FPNAMVDRI Sbjct: 183 QRRMARGLPPLTLLSCDNIAANGDTLRGLLLAFCARVDGALHDWVAERCGFPNAMVDRIV 242 Query: 234 PMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEE 293 P T+ ++ G++DAWPVV EPF+QWV+ED+FV GRP WE G QF + P+E Sbjct: 243 PKTTVDDAARISAALGVEDAWPVVGEPFLQWVMEDRFVAGRPRWEAGGAQFVEHAHPFET 302 Query: 294 MKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTD 353 +K L+NGSH + YLG + G+ + P A + M+ ++ P L +PG+D Sbjct: 303 LKHRLVNGSHSTMAYLGMVAGWATTDRAIAVPAMRALVAGMMEQEMQPTLPALPGLDTAA 362 Query: 354 YKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALY 413 Y++ L+ RF+N A+ + ++ DGS K P+ + I + G R AL VA W + Sbjct: 363 YRRDLLARFANPALQHKTSQIAMDGSQKIPQRLLAPIRERLRAGAPFPRLALGVAGWLHF 422 Query: 414 LKGVDENGVSYTIPDPRAEFCQGLVSD----DALISQRLLAVEE---IFGTAIPNSPEFV 466 L+G DE+G Y I DP A + L+++ A + R+ A+ +FG + S FV Sbjct: 423 LRGRDEHGAEYRIEDPLASSLRALLAEAEARHAREADRIAAIASFTPVFGD-LAASRVFV 481 Query: 467 AAFERCYGSLRDNGVTTTL 485 LR+ GV T+ Sbjct: 482 ETLATQTRMLRERGVLATI 500 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: 698 Number of extensions: 34 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: 511 Length adjustment: 34 Effective length of query: 459 Effective length of database: 477 Effective search space: 218943 Effective search space used: 218943 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