GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3607107 Dshi_0529
           Monosaccharide-transporting ATPase (RefSeq)
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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