GapMind for catabolism of small carbon sources

 

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

Align Fructose import permease protein FrcC (characterized)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)

Query= SwissProt::Q9F9B1
         (360 letters)



>lcl|FitnessBrowser__Dino:3609043 Dshi_2432
           Monosaccharide-transporting ATPase (RefSeq)
          Length = 327

 Score =  142 bits (357), Expect = 2e-38
 Identities = 94/303 (31%), Positives = 154/303 (50%), Gaps = 9/303 (2%)

Query: 52  LIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMV 111
           LI  +L L+A        F +   +  +    + + ++   Q +VILT  IDLSV A + 
Sbjct: 13  LIAAILLLLALIASRFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVAANLA 72

Query: 112 LSSVIMGQFTFRY-GFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLA 170
           L+ +++        G P  + +   +G+G L G  NG LV ++++PP +VTLG   I   
Sbjct: 73  LTGMVVSMVNVAAPGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLGTMTIFRG 132

Query: 171 SNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAW 230
             FL S  + + + ++S      + F +   +G  V ++   + +L V L   V+ RT  
Sbjct: 133 IIFLISDGKWVNSHEMSP---AFKAFPRAELLGLPVLSW---IAILAVILFTIVMTRTTL 186

Query: 231 GRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIG-SVSPTAGQFAN 289
           GR  YA G +P AA  AG++V +     +T+SG +  L G+  + R   S    AG F  
Sbjct: 187 GRAFYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYVDIAGGF-E 245

Query: 290 IESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAV 349
           ++ + A VIGG+S+ GG G++ G L GAL +G+    L ++   P W   + G  IIIAV
Sbjct: 246 LDVVAACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPFWQLAISGGAIIIAV 305

Query: 350 AID 352
           A++
Sbjct: 306 ALN 308


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: 321
Number of extensions: 21
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: 327
Length adjustment: 29
Effective length of query: 331
Effective length of database: 298
Effective search space:    98638
Effective search space used:    98638
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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