GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Shewanella sp. ANA-3

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate 7025539 Shewana3_2690 short chain dehydrogenase (RefSeq)

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



>FitnessBrowser__ANA3:7025539
          Length = 255

 Score =  118 bits (296), Expect = 1e-31
 Identities = 89/265 (33%), Positives = 132/265 (49%), Gaps = 21/265 (7%)

Query: 1   MSVLQRLQPYPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKY---- 56
           M+VLQ      G   +I+G ++GIG   A  +   GA++ +     + LA   D+     
Sbjct: 1   MAVLQ------GKVAIITGASSGIGYATAKRFAREGAKLVLGARRGAILASLVDEIITQG 54

Query: 57  PGTVATRADVSDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTG-GIDAISDAEWQATIN 115
              +    DV+D      +  +  E  GGLD+  NN GI G  G   DA+S AEW+ T+ 
Sbjct: 55  GEAIYLAGDVTDEVYASDLVALAVEQYGGLDIAFNNVGINGELGVDSDALSRAEWENTLT 114

Query: 116 INLTAQYRFAHHAVPMLKESSHGHLLHIASVAG-RLGYAWRTPYAATKWAIVGLMKSLAS 174
            NLT+ +  A + +P + +   G ++  +S  G  +G+     YAA+K  ++GL +SLA 
Sbjct: 115 TNLTSAFLAAKYQLPQMLKRGAGSIIFTSSFVGYTIGFPQTAAYAASKAGMIGLTQSLAV 174

Query: 175 ELGESDIRVNALLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVA 234
           E G   IRVNALLPG  + P          E    PEA    + L+  +LKR+    ++A
Sbjct: 175 EYGARGIRVNALLPGGTDTP-------MGREFANTPEAMAFVKNLH--ALKRLADPAEIA 225

Query: 235 AMALFLCSPAARNVTGQAISVDGNV 259
             AL+L S AA   TG A+ VDG V
Sbjct: 226 QSALYLASDAASFTTGIALLVDGGV 250


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: 156
Number of extensions: 10
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: 262
Length of database: 255
Length adjustment: 24
Effective length of query: 238
Effective length of database: 231
Effective search space:    54978
Effective search space used:    54978
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