GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12055 in Klebsiella michiganensis M5al

Align Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate BWI76_RS07235 BWI76_RS07235 hypothetical protein

Query= uniprot:A0A1N7UEK0
         (335 letters)



>FitnessBrowser__Koxy:BWI76_RS07235
          Length = 307

 Score =  155 bits (391), Expect = 2e-42
 Identities = 95/281 (33%), Positives = 149/281 (53%), Gaps = 10/281 (3%)

Query: 10  TAALSLLACSIAMAADGKTYKVGAAVYGLKGQFMQNWVRELKEHPAVKDGTVQLTVFDGN 69
           T   SL+AC +      K   VG ++      F+   +R   +    KDG V+  V D  
Sbjct: 6   TVVASLIACMLPAVVMAKDISVGVSMALFDDNFL-TILRTAMQKEMQKDG-VKAQVEDAK 63

Query: 70  YDALTQNNQIENMVTQRYDAILFVPIDTKAGVGTVKAAMSNDVVVIASNTKVADA---SV 126
            D   Q  Q++N + Q  DAI+  P+DT A    +  A    + +I  N +        +
Sbjct: 64  GDVSQQLQQVQNFIGQGVDAIIVNPVDTNAVKPIMDQATKAGIPLIFVNRRPQAQLTDKM 123

Query: 127 PYVGNDDVEGGRLQAQAMVDKLNGKGNVVIIQGPIGQSAQIDREKGELEVLGKHPDIKII 186
            YVG+D V  GRLQ +A+   +NGKGNV I+ G +   +  DR KG  EV+ K+PDIKI+
Sbjct: 124 AYVGSDSVLAGRLQMEALAKAMNGKGNVAILLGDLANESTRDRTKGVEEVVAKYPDIKIV 183

Query: 187 EKKTANWDRAQALALTEDWLNAHPKGINGVIAQNDDMALGAVQALKSHGLTSKDVPVTSI 246
           +K+TA + R  A+ +  +W+ +  + I  + + ND+MA+GA+QAL   G     + +  +
Sbjct: 184 QKQTAKFTRNDAVDVVSNWMTS-GEDIQAIASNNDEMAIGALQAL---GKNPNHILIAGV 239

Query: 247 DGMPDAIQAAKKDE-VTTFLQDAQAQSQGALDVALRALAGK 286
           DG PDA+Q  K  + + T  QDA+ Q +GA+D A++   G+
Sbjct: 240 DGTPDALQMLKNGKMIATIFQDAKGQGEGAVDAAIKLANGE 280


Lambda     K      H
   0.314    0.130    0.373 

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: 285
Number of extensions: 24
Number of successful extensions: 5
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: 335
Length of database: 307
Length adjustment: 28
Effective length of query: 307
Effective length of database: 279
Effective search space:    85653
Effective search space used:    85653
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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