GapMind for catabolism of small carbon sources

 

Alignments for a candidate for KDF-hydrolase in Cupriavidus basilensis 4G11

Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate RR42_RS24170 RR42_RS24170 hypothetical protein

Query= metacyc::MONOMER-16233
         (285 letters)



>FitnessBrowser__Cup4G11:RR42_RS24170
          Length = 285

 Score =  140 bits (354), Expect = 2e-38
 Identities = 92/269 (34%), Positives = 140/269 (52%), Gaps = 39/269 (14%)

Query: 20  DGKIRDLSGVVPELTIEALAAAKGADVASLPLVEGEPRYGVPVKGIGKIVAIGLNYEDHA 79
           D  I +   V P +  EA+ + +   +AS+       R   PV   GKI+A  +NY+DH 
Sbjct: 40  DWIINNFESVRPHID-EAIESGRRVPLASV-------RLRAPVANPGKIIAAPINYKDHI 91

Query: 80  IESNLPIPTEPMM--------------FMKALSSLNGPNDEVVLPKNSTHGDWEVELGVV 125
            E+N     +P +              F+KA SS+ G ++++ +P      D EVEL VV
Sbjct: 92  AEAN----NDPQINHGKTFTDLSTLGVFLKANSSVIGCHEDIRIPFPDRRTDHEVELAVV 147

Query: 126 IGETCRFVSEDEALSKVAGYVLVNDVSERFNQKQRGTQWSKGKGHDTFCPVGPWLVTPDE 185
           IG   + VS + AL+ V GY +  D++ R  +          K  DTF  +GPW+VT DE
Sbjct: 148 IGREAKKVSRENALAFVFGYCIGLDMTVRGPELP-----DFRKSADTFSVLGPWIVTADE 202

Query: 186 VGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPPGVGEG 245
           + +P  LD+ ++VNG   Q  NTK +I++V +LI Y S   TLYPGD+++TGTP GV   
Sbjct: 203 IPEPNSLDLSIHVNGELRQQSNTKYLIYDVQRLIEYASAMYTLYPGDVIMTGTPAGVSP- 261

Query: 246 KKPQAIYLKAGDVMELGIEKLGTQRQQVS 274
                  +  GD++E  +  +GT   +V+
Sbjct: 262 -------VTYGDILEASVSGIGTMTARVA 283


Lambda     K      H
   0.316    0.137    0.411 

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: 205
Number of extensions: 7
Number of successful extensions: 3
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: 285
Length of database: 285
Length adjustment: 26
Effective length of query: 259
Effective length of database: 259
Effective search space:    67081
Effective search space used:    67081
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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