GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Klebsiella michiganensis M5al

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate BWI76_RS01840 BWI76_RS01840 ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__Koxy:BWI76_RS01840
          Length = 369

 Score =  313 bits (801), Expect = 6e-90
 Identities = 171/340 (50%), Positives = 229/340 (67%), Gaps = 23/340 (6%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M +++L N+ K + +      ++ NL+I D EF+VFVGPSGCGKST LRMIAGLE +T G
Sbjct: 1   MASVQLRNVTKAWGDV--VVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIAGLETVTSG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
           +L I D  MND  P +R I MVFQ+YALYPH+SV ENM+FGLKL   KK+ IN+RV + A
Sbjct: 59  DLLIGDTRMNDVPPAERGIGMVFQSYALYPHLSVAENMSFGLKLAGAKKELINQRVTQVA 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           E+L L   LERKP  LSGGQRQRVA+GR +V + +VFL+DEPLSNLDA LRV MR EI++
Sbjct: 119 EVLQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISR 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H+R+G T IYVTHDQ EAMTLAD+IV++ A          GR+ Q+G P ELY+ PA++
Sbjct: 179 LHKRLGRTMIYVTHDQVEAMTLADKIVVLDA----------GRVAQVGKPLELYHYPADR 228

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKIL---EEKGYLGKKVTLGIRP 297
           FVAGFIGSP MNF  V V    +   + + + LP  Q+  L     +  +G  ++LGIRP
Sbjct: 229 FVAGFIGSPKMNFLPVKVTATAI---EQVQVELPNRQQVWLPVDSARVQVGANMSLGIRP 285

Query: 298 EDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGS 337
           E +    I      + ++  ++ V E LG E+ ++++  S
Sbjct: 286 EHLLPSDIA-----DVTLEGEVQVVEQLGHETQIHIQIPS 320


Lambda     K      H
   0.318    0.135    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: 332
Number of extensions: 9
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: 377
Length of database: 369
Length adjustment: 30
Effective length of query: 347
Effective length of database: 339
Effective search space:   117633
Effective search space used:   117633
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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