GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Phaeobacter inhibens BS107

Align Fructose import permease protein FrcC (characterized)
to candidate GFF2275 PGA1_c23070 putative ribose transport system permease protein

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__Phaeo:GFF2275
          Length = 333

 Score =  138 bits (348), Expect = 2e-37
 Identities = 100/313 (31%), Positives = 160/313 (51%), Gaps = 24/313 (7%)

Query: 55  LVLSLIAFGVILGGKFFS----AF----TMTLILQQVAIVGIVGAAQTLVILTAGIDLSV 106
           +VL LI F V   G+FFS    AF     M L+L+Q A +GI+    T+V++   IDLSV
Sbjct: 19  IVLELIFFSV--AGEFFSVSDKAFMDTDNMLLLLKQSAPIGIIAMGMTIVMVNGNIDLSV 76

Query: 107 GAIMVLSSVIM------GQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIV 160
           GAI  + ++I+        F     +   ++    L  G + G ING +V +  +  FIV
Sbjct: 77  GAIYAICAIILLDSMTWTMFAGLGNWVIPVAWCLALLTGVVLGAINGLIVWKTGVDAFIV 136

Query: 161 TLGMWQIVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCL 220
           TLG         F+Y+  +         N +++ F    F +G    T+ ++V+ + +  
Sbjct: 137 TLGSMLGYRGLVFMYNGEQPTS----HLNWTLVDFAEAQF-LGLHTATWFLLVVTVAI-- 189

Query: 221 LWYVLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSV 280
            W+++NRT  GR  YA+G++ EAA  AG+ V   ++  + + G + AL+        GSV
Sbjct: 190 -WFLMNRTVHGRNAYAIGNNREAAVNAGIRVGPHMMINFMIIGFLAALSAVVFYSESGSV 248

Query: 281 SPTAGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLL 340
           +P  GQ   +  ITAVV+GG  L GG GSI+    G + + +   GL  +G D     L+
Sbjct: 249 NPNDGQLYELWVITAVVLGGTKLTGGAGSIVSTFGGVIAIQLLRKGLAHIGADTSTVNLV 308

Query: 341 IGLLIIIAVAIDQ 353
           IGL++I  + +D+
Sbjct: 309 IGLILIAVLFLDR 321


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: 340
Number of extensions: 19
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: 360
Length of database: 333
Length adjustment: 29
Effective length of query: 331
Effective length of database: 304
Effective search space:   100624
Effective search space used:   100624
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