GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS14865 BWI76_RS14865 ribose ABC
           transporter permease
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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