GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Cupriavidus basilensis 4G11

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate RR42_RS13775 RR42_RS13775 sugar ABC transporter permease

Query= reanno::Smeli:SMc03063
         (380 letters)



>FitnessBrowser__Cup4G11:RR42_RS13775
          Length = 277

 Score =  122 bits (305), Expect = 2e-32
 Identities = 74/232 (31%), Positives = 122/232 (52%), Gaps = 7/232 (3%)

Query: 146 PPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLA 205
           P  FTL++Y  + +       ++NS+     +TVI I +A  AAYA +   F G   +  
Sbjct: 53  PNDFTLEHYKTIFTDPSWYSGYINSMIYVAMNTVISITVALPAAYAFSRYRFIGDKHVFF 112

Query: 206 VVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAG 265
            ++   + P  + L+P  QLY  +G        T++G+ LAH  F +PLA+++L  +M+G
Sbjct: 113 WLLTNRMTPPAVFLLPFFQLYTTIGLM-----DTHLGVALAHLVFNVPLAVWILEGFMSG 167

Query: 266 LPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDK 325
           +PREI E+A VDG S    F+ I LPL    +   A F F+++W +LL+A          
Sbjct: 168 VPREIDETAYVDGYSFGRFFITIFLPLIKAGVGVAAFFCFMFSWVELLLARTLTSVNAKP 227

Query: 326 LVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSV 377
           +V T  +   + + G +W +L A+  +TIV   IV + ++ Y+ +G   G V
Sbjct: 228 IVAT--MTRTVSASGMDWGVLAAAGVLTIVPGGIVIWFVRHYIAKGFAMGRV 277


Lambda     K      H
   0.324    0.139    0.418 

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: 259
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: 380
Length of database: 277
Length adjustment: 28
Effective length of query: 352
Effective length of database: 249
Effective search space:    87648
Effective search space used:    87648
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 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