Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate BPHYT_RS28510 BPHYT_RS28510 dioxygenase
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__BFirm:BPHYT_RS28510 Length = 492 Score = 352 bits (904), Expect = e-101 Identities = 198/494 (40%), Positives = 277/494 (56%), Gaps = 16/494 (3%) Query: 1 MKLNKQNLTQLAP----EVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGL 56 M+L+ L LA +V +PAY A GI H+G+G FHRAHQA YT+ + G+ Sbjct: 1 MRLSNAALASLAARAAGKVVVPAYDRASLAPGIVHLGLGAFHRAHQALYTEHALRAGDHR 60 Query: 57 DWSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALI 116 W I GV LR D + L QD+L+ + T D+ ++VIG++ L+A S A++ Sbjct: 61 -WGIVGVSLRRADTS--EALTAQDHLYAVDVRDGTADS-LQVIGALIASLVAPQSPAAVL 116 Query: 117 DKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQR 176 D + P IVSLTITE GYC + ++G P I HDL ++P++ GF+ AL R Sbjct: 117 DAMTDPRCHIVSLTITEKGYCRNPASGALQFDHPDIAHDLRAAAAPRSAIGFVVRALALR 176 Query: 177 RAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMT 236 RAAG+ FTV+SCDNLP NG R LAFA + L DWI+ +FPN MVDRI P+T Sbjct: 177 RAAGLGPFTVLSCDNLPSNGDTMRALTLAFARETDPALADWIELEAAFPNTMVDRIVPLT 236 Query: 237 STAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKI 296 + A RL++ + G DDAWPV+ EPF QWV+ED+F RPAWE+ G D PYE+ K+ Sbjct: 237 TDADRLRVAKQLGADDAWPVITEPFSQWVIEDRFAGPRPAWERAGATLVGDARPYEQAKL 296 Query: 297 GLLNGSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQ 356 +LNG+H AL YLG L GY V + + P + ++ + + +V P L+ L Y+ Sbjct: 297 RMLNGAHSALAYLGSLIGYDTVDQAIGAPAVLNFVESMLRDEVEPTLSRPA---LATYRA 353 Query: 357 TLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKG 416 L RF N A+ +L+++ +DGS K P+ + ++ + G TER A +A W YL G Sbjct: 354 ELFARFRNTALDHRLQQIATDGSQKLPQRWLESVRANLKSGAPTERLAFALAGWIAYLGG 413 Query: 417 VDENGVSYTIPDPRAEFCQGLV-----SDDALISQRLLAVEEIFGTAIPNSPEFVAAFER 471 DE G +Y I DP A+ V +D A + L +E IFG + P FVA R Sbjct: 414 HDETGRTYAIADPLADRLTEAVRATLHADAADAVRTLFEIEPIFGRDLCAHPRFVAQVAR 473 Query: 472 CYGSLRDNGVTTTL 485 ++R GV + Sbjct: 474 HLAAIRAQGVVKAM 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: 625 Number of extensions: 33 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: 493 Length of database: 492 Length adjustment: 34 Effective length of query: 459 Effective length of database: 458 Effective search space: 210222 Effective search space used: 210222 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