GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Dinoroseobacter shibae DFL-12

Align Fructose import permease protein FrcC (characterized)
to candidate 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__Dino:3609042
          Length = 328

 Score =  152 bits (383), Expect = 2e-41
 Identities = 92/301 (30%), Positives = 161/301 (53%), Gaps = 13/301 (4%)

Query: 56  VLSLIAFGVILGGKFFS-----AFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIM 110
           +L L+A G+ +   F S     A+ ++          ++  A  L+I++  IDLSV +I+
Sbjct: 26  LLLLVAIGIFVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLIISGEIDLSVASII 85

Query: 111 VLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLA 170
            L+S  MG         P L V+ GLGVG LCG  NG LV RM LP  +VT+G   +   
Sbjct: 86  ALASTAMGAAVQMGVGTPGL-VLIGLGVGLLCGAFNGVLVTRMGLPSIVVTIGTMSLFRG 144

Query: 171 SNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAW 230
            +++   ++  R    S       +FGQ +     V ++ +V+  ++  +   +L++T +
Sbjct: 145 ISYIVLGDQAFRGYPES-----FSWFGQGYVWW--VISFELVLFAIIAVIYAMLLHKTNF 197

Query: 231 GRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANI 290
           GR VYA+G++   A  +G+ V R+   ++ L+GL+  +A   L  R+GS  P+      +
Sbjct: 198 GRAVYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARLGSTRPSIAMGWEL 257

Query: 291 ESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVA 350
           E +T VV+GG+S+ GG G+I+G++  A ++G+ + GL L+        ++IG L+I  +A
Sbjct: 258 EVVTMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVMSIVIGALLIGVIA 317

Query: 351 I 351
           +
Sbjct: 318 L 318


Lambda     K      H
   0.327    0.141    0.420 

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: 356
Number of extensions: 28
Number of successful extensions: 4
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: 360
Length of database: 328
Length adjustment: 29
Effective length of query: 331
Effective length of database: 299
Effective search space:    98969
Effective search space used:    98969
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 (21.7 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