GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt1d in Escherichia coli BW25113

Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate 18294 b4269 putative oxidoreductase (VIMSS)

Query= BRENDA::Q38707
         (365 letters)



>FitnessBrowser__Keio:18294
          Length = 339

 Score =  222 bits (565), Expect = 1e-62
 Identities = 114/338 (33%), Positives = 191/338 (56%), Gaps = 11/338 (3%)

Query: 16  WAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGHEIV 75
           +AA++  G L  +++       +DV ++V +CG+CHSD  MI N WGF+ YP+V GHE++
Sbjct: 7   YAAKEAGGELEVYEYDPGELRPQDVEVQVDYCGICHSDLSMIDNEWGFSQYPLVAGHEVI 66

Query: 76  GVVTEVGSKVEK--VKVGDNVGIGCLVGSCRSCESCCDNRESHCENTIDTYGSIYFDGTM 133
           G V  +GS  +   ++VG  VGIG    SC  C++C    + +CE      G++     M
Sbjct: 67  GRVVALGSAAQDKGLQVGQRVGIGWTARSCGHCDACISGNQINCEQ-----GAV--PTIM 119

Query: 134 THGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGLG 193
             GG+++ + AD  +++  P+N+ ++S  PLLC GIT + PL  + +    +++GV+G+G
Sbjct: 120 NRGGFAEKLRADWQWVIPLPENIDIESAGPLLCGGITVFKPLLMHHITAT-SRVGVIGIG 178

Query: 194 GLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDGIID 253
           GLGH+A+K+  A G +VT    + +K +E L  +GAD  + + D + +K      D II+
Sbjct: 179 GLGHIAIKLLHAMGCEVTAFSSNPAKEQEVLA-MGADKVVNSRDPQALKALAGQFDLIIN 237

Query: 254 TVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEML 313
           TV V+    P F+ L   G    VGA   P  +P F+L+ G + + G+  G   E ++++
Sbjct: 238 TVNVSLDWQPYFEALTYGGNFHTVGAVLTPLSVPAFTLIAGDRSVSGSATGTPYELRKLM 297

Query: 314 DFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVI 351
            FAA+  +    E+ PM  +N A++ +     RYR V+
Sbjct: 298 RFAARSKVAPTTELFPMSKINDAIQHVRDGKARYRVVL 335


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: 283
Number of extensions: 15
Number of successful extensions: 5
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: 339
Length adjustment: 29
Effective length of query: 336
Effective length of database: 310
Effective search space:   104160
Effective search space used:   104160
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.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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