GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Cupriavidus basilensis 4G11

Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate RR42_RS35005 RR42_RS35005 L-idonate 5-dehydrogenase

Query= BRENDA::Q6ECH5
         (336 letters)



>FitnessBrowser__Cup4G11:RR42_RS35005
          Length = 342

 Score =  144 bits (362), Expect = 4e-39
 Identities = 101/316 (31%), Positives = 153/316 (48%), Gaps = 15/316 (4%)

Query: 15  EDIKEPEIKPD-----EVLIHTAYAGICGTDKALYA-GLPGSASAVPPIVLGHENSGVVT 68
           ED++  +++P      EV +    AGICG+D   Y  G  G+     P+  GHE +G+V+
Sbjct: 11  EDLRFTQVEPAAPGPFEVEVRLGAAGICGSDLHYYFHGKVGAFVIREPLTPGHEAAGIVS 70

Query: 69  KVGSEVTNVKPGDRVTVDPNIYCGQCKYCRTQRPELCEHLDAVGVTR-----NGGFEEYF 123
           +VGS VT V PG++V ++P+  CGQC YCR  R  LC  +  +G         G F E+F
Sbjct: 71  RVGSAVTRVAPGNKVAINPSHACGQCDYCRAGRDNLCRSMRFLGSASIYPHVQGMFREHF 130

Query: 124 TAPAKVVYPIPDDVSLKAAAVVEPISCAMHGVDLLETHPYQKALVLGDGFEGQLFAQILK 183
               + + P+  D+SL   A  EP+S A+HGV+       +  LV G G  G L     +
Sbjct: 131 LMHERQLTPVDSDISLGELAFAEPLSVALHGVNRAGELLGKTVLVTGGGTIGSLAVMAAR 190

Query: 184 ARGIHEVTLAGRSDEKLENNRKHFGVKTIDTTKEEIPA--DAYDIVVEAVGLPATQEQAL 241
             G   +     +D  LE   +    + I T +E   A  D  D+ +EA G  A  +  L
Sbjct: 191 LAGAAHIIACDIADRPLEVALRVGADQVIRTDREPPRALQDLADVCLEAAGSGAALDTCL 250

Query: 242 AAAARGAQVLMFGVGNPDDKFSVNTYDVFQKQLTIQGAFVNPYTFEDSIALLSSGVVDPL 301
            AA RGA+++  G   P +       ++  ++L   GAF     F+ ++  L+ G +D  
Sbjct: 251 LAARRGARIVQIGT-LPAEGLHFPANNIMARELEYVGAFRFGREFDWAVRYLTQGRLDVR 309

Query: 302 PLFSHELDL-DGVEDF 316
           PL S +L L   VE F
Sbjct: 310 PLLSAQLPLAQAVEAF 325


Lambda     K      H
   0.316    0.136    0.393 

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: 226
Number of extensions: 13
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: 336
Length of database: 342
Length adjustment: 28
Effective length of query: 308
Effective length of database: 314
Effective search space:    96712
Effective search space used:    96712
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: 41 (21.6 bits)
S2: 49 (23.5 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