GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Psychromonas ossibalaenae JAMM 0738

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_019615251.1 G327_RS0113160 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD

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



>NCBI__GCF_000381745.1:WP_019615251.1
          Length = 251

 Score = 93.6 bits (231), Expect = 4e-24
 Identities = 74/252 (29%), Positives = 118/252 (46%), Gaps = 19/252 (7%)

Query: 12  GLRVLISGGAAGIGEVLAAAYLEAGAQV----HVCDVSESALAVFRDKYPGTVATRADVS 67
           G   +++G   G+G+  A    +AGA +    H+      A      +    +     V 
Sbjct: 8   GKVAIVTGCNTGLGQGSAIGLAKAGADIVGIGHIPAPETQAQIEALGRKFHYITANLMVQ 67

Query: 68  DAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHH 127
           D  Q+E +     E +G +D+LVNNAGI      +D  S++ W   ININ    + F   
Sbjct: 68  D--QLENIVAETVEVMGRVDILVNNAGIIRREDFLD-FSESNWDDVININQKTVF-FLSQ 123

Query: 128 AVP--MLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNA 185
           AV    +K+   G +++IAS+    G      Y A+K A++GL ++LA+EL + ++ VNA
Sbjct: 124 AVAKQFVKQGKGGKIINIASMLSFQGGIRVPSYTASKSAVMGLTRALANELAQYEVNVNA 183

Query: 186 LLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAA 245
           + PG +     + +    A    +         L +I   R  T ED+A   +FL SPA+
Sbjct: 184 IAPGYMATDNTEALRADEARNAAI---------LERIPANRWGTPEDLAGPIVFLASPAS 234

Query: 246 RNVTGQAISVDG 257
             V G  I+VDG
Sbjct: 235 DYVNGYTIAVDG 246


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: 9
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: 251
Length adjustment: 24
Effective length of query: 238
Effective length of database: 227
Effective search space:    54026
Effective search space used:    54026
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 24 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