GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Dyella japonica UNC79MFTsu3.2

Align Fructose import permease protein FrcC (characterized)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2415
          Length = 337

 Score =  135 bits (340), Expect = 2e-36
 Identities = 98/320 (30%), Positives = 159/320 (49%), Gaps = 20/320 (6%)

Query: 48  AAVPLIVLVLSLIAF----GVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGID 103
           A VPL+V ++  +A     GV+  G       + L++   A + IV    T VIL  GID
Sbjct: 23  AQVPLLVTLVLFVAMAGAGGVLYHGFLTPQVFLNLLIDN-AFLCIVAVGMTFVILAGGID 81

Query: 104 LSVGAIMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLG 163
           LSVGA++  S+V++ +   R+G+PP  ++   L VG   G   G L+ R +L PF+VTL 
Sbjct: 82  LSVGAVVAFSTVLLAELVQRHGWPPLAAIALVLAVGTGFGAGMGVLIQRFRLQPFVVTLA 141

Query: 164 MWQIVLASNFLYSANETIRAQDISANASILQFFGQNFRI---GNAVFTYGVVVMVLLVCL 220
              +      L S +     Q   A+ +       N R+   G ++ + G +V + +V  
Sbjct: 142 GMFLARGVATLISVDSIDIDQPWLASVA-------NLRLPLGGGSMLSVGALVALAVVAA 194

Query: 221 LWYVLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAG--WALIGRIG 278
              +   +++GR VYA+G    +A+L G+ V   ++ +Y LSG   ALAG  + L    G
Sbjct: 195 GALLAGASSFGRTVYAIGGSESSARLMGLPVDATVVRVYALSGFCAALAGVVYTLYMLSG 254

Query: 279 SVSPTAGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMG-TDPQWT 337
                 G    +++I AVVIGG  L GG G ++G L G L++G+    +   G     WT
Sbjct: 255 YSQHALG--LELDAIAAVVIGGTVLAGGSGYVLGTLLGVLVLGLIQTLIVFDGELSSWWT 312

Query: 338 YLLIGLLIIIAVAIDQWIRK 357
            ++IG L++    + +  R+
Sbjct: 313 RIVIGALLLAFCLLQRLFRR 332


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: 372
Number of extensions: 25
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: 337
Length adjustment: 29
Effective length of query: 331
Effective length of database: 308
Effective search space:   101948
Effective search space used:   101948
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