GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Salinicoccus carnicancri Crm

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_017547482.1 C792_RS0100525 SDR family oxidoreductase

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



>NCBI__GCF_000330705.1:WP_017547482.1
          Length = 257

 Score =  139 bits (351), Expect = 5e-38
 Identities = 85/254 (33%), Positives = 141/254 (55%), Gaps = 7/254 (2%)

Query: 10  YPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPG---TVATRADV 66
           + G  V+I+GG+ GIG+  A  +L+ GA+V + D++E +L   R++       +A +ADV
Sbjct: 5   FEGQVVIITGGSGGIGKQTALQFLQEGAKVTIVDINEESLTSAREELSRQGEVLAVQADV 64

Query: 67  SDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAH 126
           SD A +E   +   E  G +DVL NNAGI G  G +       ++A   +N+   +    
Sbjct: 65  SDEADVENYIRATVEKFGKVDVLFNNAGIIGKVGSLVDQEYDNFKAVTGVNMNGVFLGLK 124

Query: 127 HAVP-MLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNA 185
           HA+  M+K+ + G +++  SV    G   ++ Y+ATK A+VGL K+ A E    +IRVN+
Sbjct: 125 HAIKQMIKQGTPGSIINTGSVDSFRGSPEQSAYSATKHAVVGLTKTAAVEAAGHNIRVNS 184

Query: 186 LLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAA 245
           + P  V+ P M  V  +R ++     A +R+++ + I L R   + D+A + LFL S  +
Sbjct: 185 IHPAPVDTPMMAHVEESRDKK---NSASVREKFTSGIPLNRYADSSDIADLVLFLASDDS 241

Query: 246 RNVTGQAISVDGNV 259
           + VTG   S+DG +
Sbjct: 242 KFVTGSQYSIDGGM 255


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: 141
Number of extensions: 7
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: 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