GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlD in Pseudomonas fluorescens FW300-N2E3

Align Mannitol-1-phosphate 5-dehydrogenase; EC 1.1.1.17 (uncharacterized)
to candidate AO353_25900 AO353_25900 mannitol dehydrogenase

Query= curated2:O65992
         (384 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25900
          Length = 491

 Score = 99.8 bits (247), Expect = 2e-25
 Identities = 69/225 (30%), Positives = 111/225 (49%), Gaps = 19/225 (8%)

Query: 91  NNLKSTGELLRGFLKKRSEINDKPLDIIACENALFASDVLKKAILDGA---DEELKKYLE 147
           N  K+    L   L KR         +++C+N      V +KA+L  A   D +L+ ++ 
Sbjct: 160 NAPKTVFGFLCAALAKRRAAGIPAFTLMSCDNLPHNGAVTRKALLAFAALRDADLRDWIG 219

Query: 148 KSVGFPNCTVDRIVP------NVDIEKELPID----VAVEDFYEWDIEKNKVKINN--KI 195
            +V FPN  VDRI P       + +  E  ID    V  E F +W +E N V      + 
Sbjct: 220 ANVSFPNAMVDRITPMTSSAHRLHLHDEHGIDDLWPVVCEPFVQWVLEDNFVNGRPAWEK 279

Query: 196 IGAEYVEKLDPYLERKLFLLNGAHATIAYLGYLKGYKYIHEAIKDKEINKIIVGFHS-EA 254
           +G ++ + + PY E K+ LLNG+H  + YLG+LKGY+++HE + D    + +  +   + 
Sbjct: 280 VGVQFTDDVTPYEEMKIKLLNGSHLALTYLGFLKGYRFVHETMNDPLFVRYMRAYMDLDV 339

Query: 255 VQALSEKHKIDIQILKEYSNKLLKRFENEYLKDDVSRVGRDPMRK 299
              L+    ID   L +Y N L++RF N+ + D ++RV  D   K
Sbjct: 340 TPQLAPVPGID---LTQYKNTLVERFSNQAIADQLARVCSDGSSK 381


Lambda     K      H
   0.316    0.137    0.381 

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: 369
Number of extensions: 15
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: 384
Length of database: 491
Length adjustment: 32
Effective length of query: 352
Effective length of database: 459
Effective search space:   161568
Effective search space used:   161568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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