Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate H281DRAFT_01519 H281DRAFT_01519 fructuronate reductase
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__Burk376:H281DRAFT_01519 Length = 498 Score = 342 bits (878), Expect = 1e-98 Identities = 188/465 (40%), Positives = 260/465 (55%), Gaps = 7/465 (1%) Query: 28 GIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYE 87 GI H+G+G FHRAHQA YT+ M EG DW ICGV L+ + K R+ L Q+ ++++ E Sbjct: 36 GIVHLGIGNFHRAHQALYTEEAM-LAEGGDWGICGVTLQGDVAK-RNALMEQEGVYSVVE 93 Query: 88 LGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMA 147 G + +V V+ ++ ++L AL +LA P +RIVSLT+TE GYC + G+ Sbjct: 94 RGP-EGAKVTVVRALREVLAMPHDHDALFARLADPSVRIVSLTVTEKGYCRNAKTGDVAL 152 Query: 148 HLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFA 207 P + HDL+HP +P++V G + AAL QRR A FTV+SCDNL HNGA R+ + +FA Sbjct: 153 DNPAVVHDLSHPHAPRSVPGILVAALRQRRDAAREPFTVLSCDNLAHNGAALRQVVCSFA 212 Query: 208 ALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLE 267 + L DWI V+FP+ MVDRI P T+ + G DA PV CEPF QWV+E Sbjct: 213 REFDPALADWIAVEVAFPSTMVDRIAPATTDFEHATVAAALGYRDAAPVPCEPFRQWVIE 272 Query: 268 DKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLF 327 D+F GRPAW VG Q DDVTP+E K+ +LNG+H L YL L G+ + E + DP Sbjct: 273 DRFPAGRPAWHAVGAQLVDDVTPFELAKLRMLNGTHSTLAYLSMLGGFTTIDEAIADPAM 332 Query: 328 VAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTV 387 + A M ++ P L D+ +Y+ L+ R++N A+ + ++ DGS K P + Sbjct: 333 RNLIHAMMTEEIAPTLNMPASFDVANYRDALLARYANPALKHRCAQIAMDGSQKIPPRLL 392 Query: 388 PTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVS----DDAL 443 TI I G+ R AL VA W +L+G ++G Y I DP AE + L + D Sbjct: 393 GTIAARIDAGQPFTRLALAVAGWMTFLRGYADDGSRYDISDPLAENLKALAASANGDPRA 452 Query: 444 ISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHL 488 + LL V EIF + P F AA L+DNG + L Sbjct: 453 LMDTLLGVREIFTAELAAQPAFRAALLHALQLLQDNGARAAVAAL 497 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: 621 Number of extensions: 22 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: 498 Length adjustment: 34 Effective length of query: 459 Effective length of database: 464 Effective search space: 212976 Effective search space used: 212976 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