GapMind for catabolism of small carbon sources

 

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

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

Query= SwissProt::Q8G845
         (340 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2415
          Length = 337

 Score =  227 bits (578), Expect = 4e-64
 Identities = 135/327 (41%), Positives = 195/327 (59%), Gaps = 8/327 (2%)

Query: 6   ANKVKAPKKGFKLDRQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIIL 65
           A    A ++ +   R  +P L  +V+F+ M   G  L+  ++      +L ID+A+L I+
Sbjct: 8   ATSAAAGRRPWWRRRAQVPLLVTLVLFVAMAGAGGVLYHGFLTPQVFLNLLIDNAFLCIV 67

Query: 66  AVAMTLPILTGGIDLSVGAIVAITAVVGLKLANA-GVPAFLVMIIMLLIGAVFGLLAGTL 124
           AV MT  IL GGIDLSVGA+VA + V+  +L    G P    + ++L +G  FG   G L
Sbjct: 68  AVGMTFVILAGGIDLSVGAVVAFSTVLLAELVQRHGWPPLAAIALVLAVGTGFGAGMGVL 127

Query: 125 IEEFNMQPFIATLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSF 184
           I+ F +QPF+ TL+ MFLARG+A++IS DS+   Q     ++++V  +     +      
Sbjct: 128 IQRFRLQPFVVTLAGMFLARGVATLISVDSIDIDQ----PWLASVANL--RLPLGGGSML 181

Query: 185 NVGVIIALVVVVFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAA 244
           +VG ++AL VV  G +    +  GRT+YAIGGS SSA LMGLPV  T   +Y  S   AA
Sbjct: 182 SVGALVALAVVAAGALLAGASSFGRTVYAIGGSESSARLMGLPVDATVVRVYALSGFCAA 241

Query: 245 LASIVYTANIGSAKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPL- 303
           LA +VYT  + S  +   +G ELDA+A+VVIGGT++ GG GYVLG++LG LV  ++  L 
Sbjct: 242 LAGVVYTLYMLSGYSQHALGLELDAIAAVVIGGTVLAGGSGYVLGTLLGVLVLGLIQTLI 301

Query: 304 TSDFGVPAEWTTIVIGLMILVFVVLQR 330
             D  + + WT IVIG ++L F +LQR
Sbjct: 302 VFDGELSSWWTRIVIGALLLAFCLLQR 328


Lambda     K      H
   0.327    0.142    0.400 

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: 285
Number of extensions: 10
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: 340
Length of database: 337
Length adjustment: 28
Effective length of query: 312
Effective length of database: 309
Effective search space:    96408
Effective search space used:    96408
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