Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate N515DRAFT_0381 N515DRAFT_0381 uncharacterized zinc-type alcohol dehydrogenase-like protein
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__Dyella79:N515DRAFT_0381 Length = 353 Score = 299 bits (765), Expect = 9e-86 Identities = 159/345 (46%), Positives = 225/345 (65%), Gaps = 7/345 (2%) Query: 15 GWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGHEI 74 G+AA+ T L+P +F RR DV + +L+CGVCHSD H N W + YP+VPGHEI Sbjct: 7 GYAAQSATTPLAPHRFERRDPRPDDVVIDILYCGVCHSDIHQARNEWHNSIYPMVPGHEI 66 Query: 75 VGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHC-ENTIDTY-GSIYFDGT 132 +G V+ VG++V K KVGD VG+GC+V SC+ C +C E +C E TY G DG Sbjct: 67 IGRVSAVGAQVSKFKVGDMVGVGCMVDSCQHCGACHAGLEQYCVEGATWTYNGMDRRDGL 126 Query: 133 MTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGL 192 T GGYS+ +V+ + F++ L + APLLCAGITT+SPL+++ + + G+++ +VGL Sbjct: 127 PTFGGYSERIVSSDKFVVSISDKLDPKAAAPLLCAGITTWSPLRHWKIGQ-GSRVAIVGL 185 Query: 193 GGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDGII 252 GGLGH+ +K AKA GA VT+ + K EA +LGAD +L++D QMK + D I+ Sbjct: 186 GGLGHMGLKFAKAMGADVTLFTRTPDKEAEA-RRLGADHVVLSTDPAQMKAVSRAFDFIL 244 Query: 253 DTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFE--LPVFSLLKGRKLLGGTINGGIKETQ 310 DTVP H L P + L +G L +VG E P E + +++ GR+ + G+ GGI ETQ Sbjct: 245 DTVPSPHDLNPYLETLDIDGTLCLVGLLE-PIEPAVAAHNVVLGRRSIAGSGIGGIAETQ 303 Query: 311 EMLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDIAN 355 EMLD+ A+H I +D+E+I + +N A ER++KSDVRYRFVID+A+ Sbjct: 304 EMLDYCAEHGIVSDIEMIDIQDINKAYERMLKSDVRYRFVIDLAS 348 Lambda K H 0.319 0.137 0.415 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: 349 Number of extensions: 17 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: 365 Length of database: 353 Length adjustment: 29 Effective length of query: 336 Effective length of database: 324 Effective search space: 108864 Effective search space used: 108864 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 (21.7 bits) S2: 49 (23.5 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