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_01192 CCNA_01192 sugar kinase

Query= reanno::Korea:Ga0059261_1776
         (335 letters)



>FitnessBrowser__Caulo:CCNA_01192
          Length = 307

 Score =  261 bits (668), Expect = 1e-74
 Identities = 142/291 (48%), Positives = 172/291 (59%), Gaps = 4/291 (1%)

Query: 19  LGAVEAGGTKFLCGIADRTGSVLAQTRIPTTTPAETLDAATAFFAEHVARHGPLSAFSVG 78
           + A+E GGTK +         +    RIPTTTPAETL       A   A  G   A  V 
Sbjct: 9   IAAIELGGTKVMVAFGSGPDDLSPPLRIPTTTPAETLARIEDALA---AEQGRFDAIGVA 65

Query: 79  SFGPLSLDPIAPDYGSITSTPKPGWQDVDLLGYFRQMIDAPMALDTDVNCAAVGERLFGS 138
           SFGP+ LDP APD+G I  TPKPGW   D+     +  D P+ALDTDVN AAV E L+G+
Sbjct: 66  SFGPIRLDPAAPDWGHILKTPKPGWSHADVAARLVRRFDRPLALDTDVNGAAVAEGLWGA 125

Query: 139 GRGLDTFCYVTVGTGIGVGLLVGGAPHGGANHPEAGHIRLPRAPGDHDFAGICPFHGDCL 198
            +GL  + YVTVGTG+GVGL+V GAP  G  HPEAGHI + R      F G CPFHGDCL
Sbjct: 126 AKGLGDYAYVTVGTGVGVGLVVNGAPTHGLLHPEAGHILVRRDAALDPFTGSCPFHGDCL 185

Query: 199 EGLACGPAMKARWGAAAETLPGDHPAWDIEADYLAGLCATLTYIVRPDRIILGGGVMESH 258
           EGL  GPA+ AR GA  E+L  D P W + ADYLA L A L  I  P R+I+GGGV  + 
Sbjct: 186 EGLISGPALAARTGAPGESLSKDDPVWALVADYLAQLVANLALIASPRRVIIGGGVGGNP 245

Query: 259 LMHARVRRTLVAKLAGYDASM-RSLDMDEYVVPPTAGPSAGLTGAFALAYR 308
            +  + R  L   LAGY A + +  D+D +V  P  G ++GL GA AL  R
Sbjct: 246 QLLEQTRTRLQTHLAGYLAPLEQRSDIDAFVAAPGLGANSGLLGAVALGLR 296


Lambda     K      H
   0.321    0.139    0.442 

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: 351
Number of extensions: 20
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: 335
Length of database: 307
Length adjustment: 28
Effective length of query: 307
Effective length of database: 279
Effective search space:    85653
Effective search space used:    85653
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