Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate SMc00680 SMc00680 zinc-type alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__Smeli:SMc00680 Length = 347 Score = 328 bits (841), Expect = 1e-94 Identities = 166/341 (48%), Positives = 225/341 (65%), Gaps = 2/341 (0%) Query: 13 AFGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGH 72 A G+AA D + L+PF F RR + DV + + +CGVCHSD H + WG +T+P+VPGH Sbjct: 4 ARGYAATDASKPLAPFTFERREPRDDDVVIDIKYCGVCHSDIHQARDEWGNSTFPMVPGH 63 Query: 73 EIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHCENTIDTYGSIYFDGT 132 EIVG+V VGS+V + K+GD VG+GC V SC +C + E + + TY + DGT Sbjct: 64 EIVGIVRAVGSQVTRFKIGDRVGVGCFVDSCTTCAKRDLDLEQYLPGLVVTYNGVEADGT 123 Query: 133 MTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGL 192 T GGYSD +V E ++L P+NLPLD+ APLLCAGIT YSPL+++ PG K+ +VGL Sbjct: 124 PTQGGYSDHIVVKEGYVLSIPENLPLDAAAPLLCAGITLYSPLRHWKAG-PGKKVAIVGL 182 Query: 193 GGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDGII 252 GGLGH+ VK+A A GA+VTV+ + SK+++ L KLGAD + D E S D II Sbjct: 183 GGLGHMGVKLAHAMGAEVTVLSQTLSKKEDGL-KLGADHYYATKDPETFTKLAGSFDLII 241 Query: 253 DTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEM 312 TV +LLK +G+LV+VG PE P + FSL+ R+ + G++ G IKETQEM Sbjct: 242 CTVAAEIDWNAYLNLLKVDGELVLVGIPENPVPVHAFSLVPARRSISGSMIGSIKETQEM 301 Query: 313 LDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDI 353 LDF +H I +++E I M+ +N A ER+V+SDVRYRFVID+ Sbjct: 302 LDFCGEHGIVSEIETIRMEQINEAYERVVRSDVRYRFVIDM 342 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: 325 Number of extensions: 10 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: 365 Length of database: 347 Length adjustment: 29 Effective length of query: 336 Effective length of database: 318 Effective search space: 106848 Effective search space used: 106848 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