GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Klebsiella michiganensis M5al

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BWI76_RS26335 BWI76_RS26335 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Koxy:BWI76_RS26335
          Length = 255

 Score =  231 bits (589), Expect = 1e-65
 Identities = 114/252 (45%), Positives = 169/252 (67%), Gaps = 1/252 (0%)

Query: 6   NEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGT 65
           ++ +L V G+  RFGGL A+++V + ++  ++  LIGPNGAGKTT FN +TG Y P  GT
Sbjct: 2   SQPLLSVNGLMMRFGGLLAVNNVSLELREREIVSLIGPNGAGKTTVFNCLTGFYKPTGGT 61

Query: 66  FELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTK 125
             L  +  E     ++A+ G+ RTFQ++RLF EMT +EN++V +H +  +G+F  + +T 
Sbjct: 62  IMLRDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGVFSGLLKTP 121

Query: 126 GFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185
            F+  ++    RA   L+ +G+ + A+ +A  L+YGDQRRLEIAR + T P+++ LDEPA
Sbjct: 122 SFRRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPA 181

Query: 186 AGMNATEKVQLRELIDRIR-NDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244
           AG+N  E  +L ELI  +R + N TILLIEHD+KLVMG+ DR+ V++ G  +A G P E+
Sbjct: 182 AGLNPKETKELDELIAELRSHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEEI 241

Query: 245 QKNEKVIEAYLG 256
           + N  VI AYLG
Sbjct: 242 RNNPDVIRAYLG 253


Lambda     K      H
   0.319    0.137    0.384 

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: 190
Number of extensions: 6
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: 260
Length of database: 255
Length adjustment: 24
Effective length of query: 236
Effective length of database: 231
Effective search space:    54516
Effective search space used:    54516
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 (21.7 bits)
S2: 47 (22.7 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