GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Shewanella loihica PV-4

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate 5210422 Shew_2863 short-chain dehydrogenase/reductase SDR (RefSeq)

Query= metacyc::MONOMER-20835
         (262 letters)



>FitnessBrowser__PV4:5210422
          Length = 248

 Score =  119 bits (298), Expect = 6e-32
 Identities = 78/252 (30%), Positives = 134/252 (53%), Gaps = 13/252 (5%)

Query: 10  YPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESAL-AVFRDKYPGTVATRADVSD 68
           + G  VLI+G A+G G++LA      GA++ + D++++AL A+  +     V  R DVS 
Sbjct: 5   FEGKVVLITGAASGFGKLLAQRLAPQGAKLVLGDINDTALDALCSELGECAVGLRCDVSI 64

Query: 69  AAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHA 128
            A+  A+ ++  E  G LD+ +NNAGI+ P   + A ++A+   +  IN    +      
Sbjct: 65  EAEQLALAQLAEESFGRLDIAINNAGISAPMKSLLATTEADMDLSFAINTKGVFFGMKAQ 124

Query: 129 VPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLP 188
           +P++++   G +L++AS+AG  G    TPY A K A+VG+ ++ A E     I+VNA+ P
Sbjct: 125 IPLMQKHKCGAILNVASMAGINGAPKLTPYVAAKHAVVGITRTAALEFAAQGIQVNAICP 184

Query: 189 GIVEGPRM-DGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARN 247
                P + +GV  A  EQ+              + ++R+    +V +  L + +P    
Sbjct: 185 FFTPTPMVTEGVDPALIEQL-----------TRAVPMRRLADPNEVVSAMLHMVNPDNGF 233

Query: 248 VTGQAISVDGNV 259
           +TGQAI++DG V
Sbjct: 234 MTGQAIAIDGGV 245


Lambda     K      H
   0.318    0.133    0.383 

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: 137
Number of extensions: 7
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: 262
Length of database: 248
Length adjustment: 24
Effective length of query: 238
Effective length of database: 224
Effective search space:    53312
Effective search space used:    53312
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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