GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araWsh in Klebsiella michiganensis M5al

Align Inner-membrane translocator (characterized, see rationale)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease

Query= uniprot:A0KWY6
         (405 letters)



>FitnessBrowser__Koxy:BWI76_RS14865
          Length = 339

 Score =  184 bits (467), Expect = 3e-51
 Identities = 116/322 (36%), Positives = 182/322 (56%), Gaps = 8/322 (2%)

Query: 64  WPLLALSILLLANLFIDSSFF-NISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGG 122
           W  + + I+LL  L + S+F  N +  D+     L++I    +  A+L+ GM+ VI T G
Sbjct: 22  WDRVGILIVLLVLLILMSTFAPNFNRVDN-----LLNIARSISVNAILAAGMTFVILTSG 76

Query: 123 IDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVAT 182
           IDLSVG+++A++G V   +  +  I     I AG+ VG L G +NG L ++L + P + T
Sbjct: 77  IDLSVGSIVAVSGVVSV-VAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVT 135

Query: 183 LLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLLRKTA 242
           L  M   RG+A  I +GQ I      F  +G G  +G+P+PV I++ +   +  +L +T 
Sbjct: 136 LGTMTFLRGMAYTITEGQPIVSSSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFILERTR 195

Query: 243 LGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGLWL 302
            G  I AVG NA+A+R  G+  K +    Y IAG+CA LAG+I  A +  +    AG   
Sbjct: 196 FGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQP-TAGTGY 254

Query: 303 ELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIVILTV 362
           ELDA+ AVV+GG +L GGR  +I +++G++I+  L+T +I+  +P    LLIK IVI+  
Sbjct: 255 ELDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIVIILA 314

Query: 363 LLLQSAKFRRQLSALFKSKRHA 384
           + +   K   +L   ++ K  A
Sbjct: 315 VAIDGLKQHPELFTFWRKKEIA 336


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: 314
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: 405
Length of database: 339
Length adjustment: 30
Effective length of query: 375
Effective length of database: 309
Effective search space:   115875
Effective search space used:   115875
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