GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Caulobacter crescentus NA1000

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate CCNA_01110 CCNA_01110 2-dehydro-3-deoxygluconokinase

Query= reanno::Dyella79:N515DRAFT_1919
         (326 letters)



>FitnessBrowser__Caulo:CCNA_01110
          Length = 308

 Score = 99.4 bits (246), Expect = 1e-25
 Identities = 82/265 (30%), Positives = 120/265 (45%), Gaps = 15/265 (5%)

Query: 5   ILCFGEALIDFHAEGRDAQGFPRSFIPFAGGAPANVSVAVARLGGPAAFAGMLGQ-DMFG 63
           I   GE +++   E  D  G P   + FAG    N ++ +ARLG   A+   LGQ D F 
Sbjct: 4   ITVLGECMVELSPEAGDG-GAPLYRMGFAGDT-FNTAIYMARLGDQVAYCTALGQGDPFS 61

Query: 64  DFLLDSLRRAGVDTAGVARTGEANTALAFVALDSHGERSFSFYRP--PSADLLFRPEHFR 121
           + +L ++RR G+DT  V +       L  + LD HGER F ++R   P  DL     H  
Sbjct: 62  EGVLAAMRREGMDTQLVRQVENRLPGLYAIVLDEHGERKFHYWRERAPIRDLF--SAHTA 119

Query: 122 AESFRGAAVFH-VCSNSMTEPALAEATREGMRR----AHTAGAWVSFDLNLRPALWPNQS 176
            +    A     V  + +T   + +  R  +R      H+ G  V+ D N RPALWP+  
Sbjct: 120 DQLIEAAKASDLVYLSGVTLAVIGDIGRARLRDILAYVHSHGVAVALDFNYRPALWPSAE 179

Query: 177 ASHDELWPALHLADVVKLSAEEFHWLAGDEGEEATLDRLWAGRARLLVVTDGSRTLRWFH 236
           A+   L   +     + LS+E+   L G E E+   +  WA     +V  D S  +    
Sbjct: 180 AARAALDGVVPACRYISLSSEDSRPLYGREAEDLAAE--WAAAGAEVVARDESHAVNVHT 237

Query: 237 PDASGEMPVYA-VPTVDSTAAGDAF 260
           P+     P  A V  VD+T AGD+F
Sbjct: 238 PEGRTATPAPARVKAVDTTGAGDSF 262


Lambda     K      H
   0.322    0.135    0.418 

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: 298
Number of extensions: 24
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: 326
Length of database: 308
Length adjustment: 27
Effective length of query: 299
Effective length of database: 281
Effective search space:    84019
Effective search space used:    84019
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 (22.0 bits)
S2: 48 (23.1 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