GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Klebsiella michiganensis M5al

Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BWI76_RS07235 BWI76_RS07235 hypothetical protein

Query= TCDB::P0AEE5
         (332 letters)



>FitnessBrowser__Koxy:BWI76_RS07235
          Length = 307

 Score =  149 bits (376), Expect = 9e-41
 Identities = 102/329 (31%), Positives = 180/329 (54%), Gaps = 28/329 (8%)

Query: 1   MNKKVLTLSAVMASMLFGAAAHAADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLL 60
           MN K   +++++A ML  A   A D  +GV++  +DDNF++++R A++++ +    V+  
Sbjct: 1   MNIKKTVVASLIACML-PAVVMAKDISVGVSMALFDDNFLTILRTAMQKEMQK-DGVKAQ 58

Query: 61  MNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRK 120
           + D++ D S+Q  Q+   + +GV A+ +N VD  A   ++++A    +P++F N+ P  +
Sbjct: 59  VEDAKGDVSQQLQQVQNFIGQGVDAIIVNPVDTNAVKPIMDQATKAGIPLIFVNRRPQAQ 118

Query: 121 ALDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEA 180
                DK  YVG+DS  +G +Q + +AK         +N  G +   +L G+  +     
Sbjct: 119 LT---DKMAYVGSDSVLAGRLQMEALAK--------AMNGKGNV--AILLGDLANESTRD 165

Query: 181 RTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMG 240
           RT  V +E+  K    + +Q  TA +    A D +  W++  +   I+ + +NND MA+G
Sbjct: 166 RTKGV-EEVVAKYPDIKIVQKQTAKFTRNDAVDVVSNWMT--SGEDIQAIASNNDEMAIG 222

Query: 241 AVEALKAHNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLADGKG 300
           A++AL   N + I + GVD  P+AL ++K+G +  T+  DA  Q +   D A  LA+G+ 
Sbjct: 223 ALQAL-GKNPNHILIAGVDGTPDALQMLKNGKMIATIFQDAKGQGEGAVDAAIKLANGE- 280

Query: 301 AADGTNWKIDNKVVRVPYVGVDKDNLAEF 329
                  K++ KV+ VPY  + KDN+AEF
Sbjct: 281 -------KVE-KVIDVPYQLITKDNMAEF 301


Lambda     K      H
   0.313    0.129    0.363 

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: 275
Number of extensions: 25
Number of successful extensions: 6
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: 332
Length of database: 307
Length adjustment: 28
Effective length of query: 304
Effective length of database: 279
Effective search space:    84816
Effective search space used:    84816
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