GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araWsh in Escherichia coli BW25113

Align Inner-membrane translocator (characterized, see rationale)
to candidate 18255 b4230 predicted sugar transporter subunit: membrane component of ABC superfamily (RefSeq)

Query= uniprot:A0KWY6
         (405 letters)



>FitnessBrowser__Keio:18255
          Length = 341

 Score =  335 bits (858), Expect = 2e-96
 Identities = 184/320 (57%), Positives = 234/320 (73%), Gaps = 6/320 (1%)

Query: 56  STSMGRYLWP-----LLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALL 110
           +T   R+ WP     L+AL ++LL +  +   F+ +  QD RL+GS IDILNR+APVALL
Sbjct: 10  TTPKRRFRWPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALL 69

Query: 111 SIGMSLVIATGGIDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGL 170
           +IGM+LVIATGGIDLSVGAVMAIAGA  A  + V   SL  V+ + L  G+LAG  NG L
Sbjct: 70  AIGMTLVIATGGIDLSVGAVMAIAGATTA-AMTVAGFSLPIVLLSALGTGILAGLWNGIL 128

Query: 171 VSFLGIQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGM 230
           V+ L IQP VATL+LMVAGRGVAQLI  GQI+TF  P  +  G G  L LP PV I +  
Sbjct: 129 VAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLT 188

Query: 231 LTFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADI 290
           L    LL RKTALG+FIEAVG N +A++  G+N + I +  Y ++GLCAA+AG+I  ADI
Sbjct: 189 LILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADI 248

Query: 291 QGSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKF 350
           +G+DANNAGLWLELDA+LAVVIGG +L GGRF+L+LSVVGALIIQ + T I++SG P + 
Sbjct: 249 RGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEM 308

Query: 351 NLLIKAIVILTVLLLQSAKF 370
           N ++KA+V+L VL++QS +F
Sbjct: 309 NQVVKAVVVLCVLIVQSQRF 328


Lambda     K      H
   0.323    0.136    0.379 

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: 399
Number of extensions: 19
Number of successful extensions: 2
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: 405
Length of database: 341
Length adjustment: 30
Effective length of query: 375
Effective length of database: 311
Effective search space:   116625
Effective search space used:   116625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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