GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguB in Caulobacter crescentus NA1000

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__Caulo:CCNA_00904
          Length = 332

 Score =  167 bits (424), Expect = 3e-46
 Identities = 118/345 (34%), Positives = 174/345 (50%), Gaps = 73/345 (21%)

Query: 53  NLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIVAFVGAIAA-ILTVQWGMNP---FL 108
           N  N++ + S   I+A+GM  VI+ G ID++VGS++AF    AA ++T   G  P    +
Sbjct: 51  NALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLI 110

Query: 109 AALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQV 168
           A L+  +IG   G  QG  + +  +P+FIVTL GM V+RG TL                 
Sbjct: 111 ALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLL---------------- 154

Query: 169 ISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLL 228
                L D G I G N               Y  W                         
Sbjct: 155 -----LNDGGPISGFNDA-------------YRWWG------------------------ 172

Query: 229 ISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGI 288
            SG ILFL          P  +++  ++ A      R T  GR+VYA+GGN +A +LSG+
Sbjct: 173 -SGEILFL----------PVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGV 221

Query: 289 NTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGK 348
           N + ++   +  +G LAGL+G +++ RL SA   AG G+EL VIA+  IGGAS +GG G 
Sbjct: 222 NVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGG 281

Query: 349 ITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDVY 393
           + G V+GA ++GV++NG+ ++ +    QQ+V GL+++AAV FD Y
Sbjct: 282 VGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHY 326


Lambda     K      H
   0.329    0.145    0.422 

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: 476
Number of extensions: 36
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 398
Length of database: 332
Length adjustment: 29
Effective length of query: 369
Effective length of database: 303
Effective search space:   111807
Effective search space used:   111807
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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