GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araWsh in Sinorhizobium meliloti 1021

Align Inner-membrane translocator (characterized, see rationale)
to candidate SM_b20352 SM_b20352 sugar ABC transporter permease

Query= uniprot:A0KWY6
         (405 letters)



>FitnessBrowser__Smeli:SM_b20352
          Length = 354

 Score =  170 bits (430), Expect = 7e-47
 Identities = 105/315 (33%), Positives = 178/315 (56%), Gaps = 21/315 (6%)

Query: 77  LFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGIDLSVGAVMAIAGA 136
           LF   +FF+I   +     +LI +    A  A L++GM+ VI TGGIDLSVG+++ + G 
Sbjct: 31  LFAVVAFFSIFAPNFLSTANLILMSKHVALNAFLAMGMTFVIITGGIDLSVGSIVGLCGM 90

Query: 137 VCANLLL---------VPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVATLLLMV 187
           V   L+L             ++V V    L VG++ G +NG L++ L + P +ATL  + 
Sbjct: 91  VAGGLILNGIDLQFGYTVYFNVVEVCLITLAVGIVIGAVNGLLITKLNVAPFIATLGTLY 150

Query: 188 AGRGVAQLINQGQIITFQH---------PGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLL 238
             RG A L + GQ  TF +          GFA +G G+ LGLP+ +W++I +   +  + 
Sbjct: 151 VARGFALLSSGGQ--TFPNLVGKPELATTGFAFLGSGRLLGLPVSIWVLIVVALAAAYVA 208

Query: 239 RKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNA 298
           R T +G  I AVG N +A+R  GI    +K+F Y  +G CAA+ G++ ++++  S     
Sbjct: 209 RYTPIGRHIFAVGGNERAARMSGIRVDRVKMFVYMFSGFCAAIVGLVISSELMASHP-AT 267

Query: 299 GLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIV 358
           G   EL+A+ A V+GG +++GGR ++  +++GA +I  L+  +++ G+ + + ++IK IV
Sbjct: 268 GNSFELNAIAAAVLGGTSMSGGRGTIGGTIIGAFVIGILSDGLVMMGISSFWQMVIKGIV 327

Query: 359 ILTVLLLQSAKFRRQ 373
           I+  +++  A+ R Q
Sbjct: 328 IIVAVVVDQAQRRLQ 342


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: 316
Number of extensions: 14
Number of successful extensions: 4
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: 354
Length adjustment: 30
Effective length of query: 375
Effective length of database: 324
Effective search space:   121500
Effective search space used:   121500
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: 50 (23.9 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