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 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__Dino:3609043
          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 (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