GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate HSERO_RS01340 HSERO_RS01340 sugar ABC transporter permease

Query= reanno::WCS417:GFF4323
         (302 letters)



>FitnessBrowser__HerbieS:HSERO_RS01340
          Length = 311

 Score =  132 bits (331), Expect = 1e-35
 Identities = 85/276 (30%), Positives = 143/276 (51%), Gaps = 6/276 (2%)

Query: 25  LAPSMFIVLVGFYGYILWTFVLSFTNSTFLPTYKWAGLAQYARLFDNDRWWVASKNLAVF 84
           LAP+  + LV     IL+T  LSF +   +   ++ GLA Y  LF    ++ A KN  ++
Sbjct: 42  LAPACVMTLVYVLYPILYTIYLSFFSWDGMTEPRFVGLANYVELFHAPTFYTALKNNVLW 101

Query: 85  GGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAWKWLLNPGMGLDK 144
             MF+ +   +G+ +A++L+QK+     +++++  P  LS +V G  + W  +P  GL  
Sbjct: 102 LLMFL-LAPPMGLAIALYLNQKVIGMRVVKSLFFAPFVLSGVVVGLMYSWFYDPSFGLLS 160

Query: 145 LLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQSIVRAAQIDG 204
           LL   G     +  L D     + ++ AA+W  + + M +FL GL  ++   V AA+++G
Sbjct: 161 LLFGQG-----VPVLGDARYATFGIIFAALWPQTAYCMILFLTGLTALNHDQVEAARMEG 215

Query: 205 ASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYSFT 264
           A    +   V+LP LR   F A ++    A++SFDL++ MT+GGP  SS + A + Y   
Sbjct: 216 AKGWTMLRYVILPQLRSTTFMAFVVSIIGALRSFDLISVMTSGGPYESSTVLAYYAYDQA 275

Query: 265 FSRGQMGMGSASAILMLGAILAIIVPYLYSELRTKR 300
               + G  +A A+ +   +L  IV  L   LR +R
Sbjct: 276 IKYYRQGYSAAVAVTLFAIMLVYIVYQLRRMLRAER 311


Lambda     K      H
   0.330    0.141    0.455 

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: 248
Number of extensions: 15
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: 302
Length of database: 311
Length adjustment: 27
Effective length of query: 275
Effective length of database: 284
Effective search space:    78100
Effective search space used:    78100
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 (21.8 bits)
S2: 48 (23.1 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