GapMind for catabolism of small carbon sources

 

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

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate CA265_RS08355 CA265_RS08355 short-chain dehydrogenase

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



>lcl|FitnessBrowser__Pedo557:CA265_RS08355 CA265_RS08355 short-chain
           dehydrogenase
          Length = 254

 Score =  119 bits (297), Expect = 8e-32
 Identities = 77/248 (31%), Positives = 130/248 (52%), Gaps = 12/248 (4%)

Query: 14  RVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRD--KYPGTVATR--ADVSDA 69
           + +++GG +GIG+ +A    + GA+VH+ ++         D  K  G VA     DVSD 
Sbjct: 8   KAVVTGGGSGIGKAIATILAKQGAEVHIIELGTEHAQDTLDEIKTNGGVAFSYGCDVSDH 67

Query: 70  AQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAV 129
             + AVF      +G +++L+NNAGIA   G  D   +A++   + +N+   Y   H A+
Sbjct: 68  QAVAAVFN----EIGNINILINNAGIAH-IGKADTTDEADFDRVMRVNVKGVYNCLHAAI 122

Query: 130 PMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPG 189
           P ++ S  G ++++AS+A  +G   R  Y+A K A+  +  S+A +    +IR N++ P 
Sbjct: 123 PQIRLSGGGVIINMASIAALIGLPDRFVYSAAKGAVKAITMSVAKDYIGENIRCNSISPA 182

Query: 190 IVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVT 249
            V  P +DG ++       +P  EM ++      + RM   E+V A+AL+LCS  A  +T
Sbjct: 183 RVHTPFVDGFLQKNYPD-NIP--EMFEKLSKTQPIGRMAKPEEVGALALYLCSDEASFIT 239

Query: 250 GQAISVDG 257
           G    +DG
Sbjct: 240 GCDYPIDG 247


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: 175
Number of extensions: 11
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: 254
Length adjustment: 24
Effective length of query: 238
Effective length of database: 230
Effective search space:    54740
Effective search space used:    54740
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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