GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG_Sm in Klebsiella michiganensis M5al

Align MalG, 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_RS03240 BWI76_RS03240 maltodextrin ABC transporter permease

Query= TCDB::Q8DT26
         (278 letters)



>FitnessBrowser__Koxy:BWI76_RS03240
          Length = 277

 Score =  207 bits (527), Expect = 2e-58
 Identities = 108/268 (40%), Positives = 168/268 (62%), Gaps = 5/268 (1%)

Query: 12  IYALLILLSFIWLFPIIWVILTSFRGEGTAYVPYIIPKTWTLDNYIKLFTNSSFPFGRWF 71
           +Y  L+L + + L P+IW +++S +     +       ++TL++Y  L T +  P+ +W+
Sbjct: 13  VYLFLLLNALVVLGPVIWTVMSSLKPGNNLFSSGFTEISFTLEHYHNLLTGT--PYLKWY 70

Query: 72  LNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGFMSMIAVYYILK 131
            NT I++T   ++S  +    A+  SR +FK +   L   LVL MFP F+SM A+Y +L 
Sbjct: 71  KNTFILATCNMLISLVVVTITAFIFSRYRFKAKKKILMSILVLQMFPAFLSMTAIYILLS 130

Query: 132 ALNLTQTLTSLVLVYSSGAA-LTFYIAKGFFDTIPYSLDESAMIDGATRKDIFLKITLPL 190
            +NL  T   L+LVY +G+     ++ KG+FD IP SLDE+A IDGA    IF +I LPL
Sbjct: 131 KMNLIDTYIGLLLVYVTGSLPFMTWLVKGYFDAIPTSLDEAAKIDGAGHLTIFFEIILPL 190

Query: 191 SKPIIVYTALLAFIAPWIDFIFAQVILGDATSKYTVAIGLFSMLQADTINNWFMAFAAGS 250
           +KPI+V+ AL++F  PW+DFI   +IL  +  K T+AIG+FS + +++  N F  FAAG+
Sbjct: 191 AKPILVFVALVSFTGPWMDFILPTLIL-RSEDKMTLAIGIFSWISSNSAEN-FTLFAAGA 248

Query: 251 VLIAIPITILFIFMQKYYVEGITGGSVK 278
           +L+A+PIT+LFI  QK+   G+  G+VK
Sbjct: 249 LLVAVPITLLFIVTQKHITTGLVSGAVK 276


Lambda     K      H
   0.330    0.142    0.428 

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: 250
Number of extensions: 13
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: 278
Length of database: 277
Length adjustment: 25
Effective length of query: 253
Effective length of database: 252
Effective search space:    63756
Effective search space used:    63756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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