GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Arenitalea lutea P7-3-5

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_143148066.1 P735_RS0114205 SDR family oxidoreductase

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



>NCBI__GCF_000283015.1:WP_143148066.1
          Length = 257

 Score =  111 bits (278), Expect = 1e-29
 Identities = 75/250 (30%), Positives = 125/250 (50%), Gaps = 14/250 (5%)

Query: 12  GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRD---KYPGTVATRADVSD 68
           G + ++ GGA  +G  +  A  EAGAQ  V D  +    + +D   K       +ADVS 
Sbjct: 13  GKKAIVVGGAGDLGIAMVEAISEAGAQTVVIDYDDRVFDMCKDLNKKGLDVSPLKADVSQ 72

Query: 69  AAQIEAVFKVQREHLGG-LDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHH 127
             QI+  +K   + LGG +D+L+N+AGI       +   + EW   I+INL A + +  +
Sbjct: 73  IEQIKESYKAALDILGGTVDILINSAGIQRRYPS-EEFPEEEWSKVISINLDATFYYCKY 131

Query: 128 AVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALL 187
           A   + ++  G +++IAS+   LG      YAA+K  +  L K+L+++     I VN + 
Sbjct: 132 AGNTMLKNGGGKIINIASLMSFLGGITIPAYAASKGGVAQLTKALSNDWAAKGICVNGIA 191

Query: 188 PGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARN 247
           PG ++      +I          + +  +E   ++ +KR  T ED+  + +FL SPA+  
Sbjct: 192 PGYMDTQLNTALIN---------DKKRTEEVFIRVPMKRWGTGEDLKGLTVFLASPASDY 242

Query: 248 VTGQAISVDG 257
           +TG  I VDG
Sbjct: 243 ITGTIIPVDG 252


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: 168
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: 257
Length adjustment: 24
Effective length of query: 238
Effective length of database: 233
Effective search space:    55454
Effective search space used:    55454
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