GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Caulobacter crescentus NA1000

Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate CCNA_01001 CCNA_01001 ribokinase

Query= SwissProt::Q0JGZ6
         (323 letters)



>FitnessBrowser__Caulo:CCNA_01001
          Length = 303

 Score = 88.2 bits (217), Expect = 2e-22
 Identities = 94/308 (30%), Positives = 135/308 (43%), Gaps = 38/308 (12%)

Query: 21  TVAGVSLAEAPAFVKAPGGAPANVAIAVARLGGGAAFVGKLGDDEFGRMLAAILRDNGVD 80
           TVAG+SL     F+   GG  AN A+A AR+G     +G +G D+ G  L A L   GV 
Sbjct: 26  TVAGLSLE---LFL---GGKGANQAVAAARMGVATRLMGAVGGDDSGAGLKAKLAGYGVQ 79

Query: 81  DGGVVFDAGARTALAFVTLRADGEREFMFYRNPSADMLLTHAELNVELIKRAAVFHYGSI 140
            G VV   G  T  A V +    E   M      A+ ++T  ++    I+   V     +
Sbjct: 80  VGDVVELPGVPTGQAHVWVANSAEN--MIVVTAGANAMVTPQQVAATTIEGQRVL----L 133

Query: 141 SLIAEPCRSAH-LRAMEIAKEAGALLSYDPNLREALWPSREEARTKILSIWDQADIVKVS 199
             +  P  +   L     AK A  +L+  P L +              +++   DI+ V+
Sbjct: 134 CQLETPATAIETLFRAGSAKGALRILNAAPALPQG------------AALFPLTDILIVN 181

Query: 200 EVELEFLTGID----SVEDDVV--MKLWRPTMKLLLVTLGDQGCKYYARDFRGAVPSYKV 253
           + EL     +D     +E+  V   KL     + ++VTLG  G     RD    V   KV
Sbjct: 182 QTELATYAKLDREPVKLEEVSVAARKLMSRPDQTIIVTLGAAGAAVVRRDEAFLVEGKKV 241

Query: 254 QQVDTTGAGDAFVGALLRRIVQDPSSLQDQKKLEEAIKFANACGAITATKKGAIPSLPTE 313
           + VDT GAGD F GAL        ++L     L EA++ ANA  A++  K GA PS+P  
Sbjct: 242 KAVDTVGAGDCFCGAL-------AATLAAGMDLAEAVETANAAAALSVQKAGAAPSMPNR 294

Query: 314 VEVLKLME 321
            EV   +E
Sbjct: 295 REVEAFLE 302


Lambda     K      H
   0.320    0.136    0.388 

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: 224
Number of extensions: 16
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: 323
Length of database: 303
Length adjustment: 27
Effective length of query: 296
Effective length of database: 276
Effective search space:    81696
Effective search space used:    81696
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 (21.8 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