GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Methylocystis bryophila S285

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase

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



>NCBI__GCF_002117405.1:WP_085770280.1
          Length = 246

 Score =  123 bits (309), Expect = 3e-33
 Identities = 74/253 (29%), Positives = 129/253 (50%), Gaps = 21/253 (8%)

Query: 12  GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADV----- 66
           G   L++G ++G+G  +A    +AGA V +      AL    +   G +  RA +     
Sbjct: 6   GKTALVTGASSGLGLAIARTLHQAGATVGLSGTRREAL----ETLAGELKERAHILPCNL 61

Query: 67  SDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAH 126
           SD A+ + +       +GG+D+LVNNAGI      +  + D +W A + +NLTA +R + 
Sbjct: 62  SDRAETDKLIPAAEGAMGGVDILVNNAGITRDMLFM-RMKDEDWDAVLAVNLTAAFRLSR 120

Query: 127 HAVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNAL 186
             +  +    HG +++I SVAG +G   +  Y+A K  + G+ KSLA+E+    + VN +
Sbjct: 121 AVLRGMMRKRHGRIINITSVAGAVGNPGQANYSAAKAGLTGMTKSLANEVASRGVTVNCV 180

Query: 187 LPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAAR 246
            PG++E P    +  A+           R+  L  I ++R  +A+++ A  L+L S  A 
Sbjct: 181 APGVIESPMTQVLNEAQ-----------RERLLKLIPMERFGSADEIGAAVLYLASDEAA 229

Query: 247 NVTGQAISVDGNV 259
            +TGQ + ++G +
Sbjct: 230 FITGQTLHINGGM 242


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: 149
Number of extensions: 6
Number of successful extensions: 4
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: 246
Length adjustment: 24
Effective length of query: 238
Effective length of database: 222
Effective search space:    52836
Effective search space used:    52836
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 Apr 09 2024. 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