GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Caulobacter crescentus NA1000

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate CCNA_02549 CCNA_02549 glucokinase

Query= SwissProt::P23917
         (302 letters)



>FitnessBrowser__Caulo:CCNA_02549
          Length = 296

 Score =  311 bits (797), Expect = 1e-89
 Identities = 165/303 (54%), Positives = 206/303 (67%), Gaps = 10/303 (3%)

Query: 1   MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQ-ATGQRGT 59
           +R G+D GGTK EV AL  AG+ + R R P P  +Y + +E +A LV  AE  A G    
Sbjct: 2   IRFGVDFGGTKIEVAALNAAGDFVARVRKPNP-GNYDEALEVVAALVADAESMAGGSCAR 60

Query: 60  VGMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAA 119
           +G+GIPGSISP TG+++NANST+LNG+PF ++L  RL R VR+ANDANCLA+SEA DGA 
Sbjct: 61  LGLGIPGSISPRTGLIRNANSTYLNGRPFGENLETRLARPVRIANDANCLALSEAADGAG 120

Query: 120 AGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCG 179
           AGA  VFA I+GTGCG GV  +G+   G NG  GEWGH PLPW   +E    +   C+CG
Sbjct: 121 AGASVVFAAIVGTGCGGGVVVDGKIINGHNGIGGEWGHAPLPWPKPEEYPGPD---CWCG 177

Query: 180 KQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHV 239
           ++GC+ET+I+G  FA D    +G A  G   ++ + E D  A  AL RY  RLA+SLA V
Sbjct: 178 RKGCLETWIAGPAFARD----AGFA-NGQAAMQAIGEGDVKASAALDRYVDRLARSLAVV 232

Query: 240 VNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWLW 299
            +++DPD+IVLGGGMSNVD LY+ +   I   VF    ETPVRKA HGDSSGVRGA WLW
Sbjct: 233 CDLIDPDIIVLGGGMSNVDALYERLPAAIAPHVFSDIFETPVRKAVHGDSSGVRGAVWLW 292

Query: 300 PQE 302
           P E
Sbjct: 293 PPE 295


Lambda     K      H
   0.318    0.137    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: 327
Number of extensions: 19
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: 302
Length of database: 296
Length adjustment: 27
Effective length of query: 275
Effective length of database: 269
Effective search space:    73975
Effective search space used:    73975
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 (21.7 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