GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruG in Dinoroseobacter shibae DFL-12

Align Fructose import permease protein FruG (characterized)
to candidate 3607107 Dshi_0529 Monosaccharide-transporting ATPase (RefSeq)

Query= SwissProt::Q8G845
         (340 letters)



>FitnessBrowser__Dino:3607107
          Length = 333

 Score =  124 bits (310), Expect = 4e-33
 Identities = 93/306 (30%), Positives = 149/306 (48%), Gaps = 10/306 (3%)

Query: 25  TLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGA 84
           TL A VI +L   +       ++ +  +S L      + ILAV   L +++GGID+S  A
Sbjct: 15  TLVAGVI-MLFCFVATVSDPRFLTITTVSDLLRASIVIGILAVGAMLVLVSGGIDVSFTA 73

Query: 85  IVAITAVVGLKLANA---GVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMF 141
           I          L+      +P  ++ +I ++ GA  G + G  I    +   I TL T+ 
Sbjct: 74  IAVFAMYSSTVLSLTIWPEIPWPVIFVISVVFGAALGAINGFFIAFLGLPTLIVTLGTLS 133

Query: 142 LARG-LASIISTDSLTF--PQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFG 198
           + RG L + I +  ++   P   DFS     +      +  N  S     +  L V+V  
Sbjct: 134 IFRGFLLTFIGSQRISDLPPSMRDFS---RGVIARGTTEAGNFYSIPWAALALLFVIVLT 190

Query: 199 YVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAK 258
           +  L  T  GR+IYAIGGS  SA  +G+ VK TQ+ +Y+    LA LA I++ +    A 
Sbjct: 191 WFILKKTMLGRSIYAIGGSVESARRIGINVKWTQFFVYVYVGALAGLAGIIHGSVGRMAD 250

Query: 259 NTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIVI 318
               VG EL  +A+VV+GG  + GG+G + G++LG  +  I+       G+P  W ++ I
Sbjct: 251 PFSLVGLELSVIAAVVLGGARLIGGYGTLTGTMLGVALIVIVQNSLIVIGIPTTWQSVTI 310

Query: 319 GLMILV 324
           G++IL+
Sbjct: 311 GILILL 316


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: 282
Number of extensions: 16
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: 340
Length of database: 333
Length adjustment: 28
Effective length of query: 312
Effective length of database: 305
Effective search space:    95160
Effective search space used:    95160
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