GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruF in Caulobacter crescentus NA1000

Align Fructose import permease protein FruF (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP

Query= SwissProt::Q8G846
         (356 letters)



>FitnessBrowser__Caulo:CCNA_00904
          Length = 332

 Score =  137 bits (345), Expect = 4e-37
 Identities = 89/272 (32%), Positives = 146/272 (53%), Gaps = 12/272 (4%)

Query: 59  ITMLQESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAAAMQTLS----NGMNVWL-SI 113
           + +L E + Y +IA GMT VI   GID++VGS++A A  AA   ++    +G   WL ++
Sbjct: 53  LNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIAL 112

Query: 114 LIALAVGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVAG-NEP 172
           L++  +GLA G V G  V++L +  FI TL  M   RG   ++  G       ++G N+ 
Sbjct: 113 LVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDG-----GPISGFNDA 167

Query: 173 LKWFANGFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKIL 232
            +W+ +G IL +P   VI  ++     +  R T  G  + AVG N EA+R++G+    I 
Sbjct: 168 YRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFIT 227

Query: 233 FLVYAISGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSA 292
             VYAI G LA ++G   +A +   + V  G   E+  I +VVIGG SL GG   + G+ 
Sbjct: 228 TSVYAIIGALAGLSGFLLSARLGSAEAV-AGTGYELRVIASVVIGGASLTGGSGGVGGTV 286

Query: 293 VGAVIIAMIRKTIITLGVNAEATPAFFAVVVI 324
           +GA++I ++   ++ L V +        ++++
Sbjct: 287 LGALLIGVLSNGLVMLHVTSYVQQVVIGLIIV 318


Lambda     K      H
   0.325    0.136    0.384 

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: 323
Number of extensions: 25
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: 356
Length of database: 332
Length adjustment: 29
Effective length of query: 327
Effective length of database: 303
Effective search space:    99081
Effective search space used:    99081
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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