GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Pedobacter sp. GW460-11-11-14-LB5

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate CA265_RS04230 CA265_RS04230 short-chain dehydrogenase

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



>FitnessBrowser__Pedo557:CA265_RS04230
          Length = 256

 Score =  119 bits (298), Expect = 6e-32
 Identities = 79/248 (31%), Positives = 128/248 (51%), Gaps = 9/248 (3%)

Query: 15  VLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRD-KYPGTVATRADVSDAAQIE 73
           ++++GGA GIG   A AY +AGA V + D +  A +   + +    +A   ++ +  ++ 
Sbjct: 9   IILTGGADGIGWECAKAYSKAGATVCILDKNPIAESKLNELETAQKIAITCNLVNENEVA 68

Query: 74  AVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVPMLK 133
           A F+   +  G +D + NNAGIA P+  +D  +DAEW   +N+NL +      + +  LK
Sbjct: 69  AAFETIIQKFGNIDAIHNNAGIAHPSKTLDQTTDAEWDLLMNVNLKSILYTTRYGIEQLK 128

Query: 134 ESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGIVEG 193
           ++  G +L+ +S+ G +G      Y ATK AI  L K++A +     IRVNA+ P  +  
Sbjct: 129 KTK-GCILNTSSMVGTIGQDNHAAYVATKGAINALTKAMALDYAPYQIRVNAVSPAAINT 187

Query: 194 PRMDGVIRARAEQVGVPEAEMRQEYLNKIS-LKRMVTAEDVAAMALFLCSPAARNVTGQA 252
           P +    + +      P  E  Q YL+K+  L  M   + +A   LFL S AAR +TG  
Sbjct: 188 PTLQLWSKEQ------PNKEEIQHYLDKLQPLGGMPAGDVIADACLFLLSDAARFITGTI 241

Query: 253 ISVDGNVE 260
           + V G  E
Sbjct: 242 LPVSGGAE 249


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: 143
Number of extensions: 8
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: 256
Length adjustment: 24
Effective length of query: 238
Effective length of database: 232
Effective search space:    55216
Effective search space used:    55216
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