GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Klebsiella michiganensis M5al

Align Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized)
to candidate BWI76_RS03240 BWI76_RS03240 maltodextrin ABC transporter permease

Query= TCDB::Q9KZ08
         (303 letters)



>FitnessBrowser__Koxy:BWI76_RS03240
          Length = 277

 Score =  184 bits (468), Expect = 2e-51
 Identities = 99/272 (36%), Positives = 156/272 (57%), Gaps = 2/272 (0%)

Query: 32  SRAASLASHGVLTLASLVALFPVAWLVYLSLGPDKNDYLHPGRIWSKMTFDNYAFVLQDT 91
           S+  ++  +  L L +LV L PV W V  SL P  N+    G      T ++Y  +L  T
Sbjct: 6   SKIMTILVYLFLLLNALVVLGPVIWTVMSSLKPG-NNLFSSGFTEISFTLEHYHNLLTGT 64

Query: 92  NFFDWLKSSLIVSLGTTVIGVLVAATTGYAVSRMRFPGYRKLMWVLLVTQMFPIAVLIVP 151
            +  W K++ I++    +I ++V   T +  SR RF   +K++  +LV QMFP  + +  
Sbjct: 65  PYLKWYKNTFILATCNMLISLVVVTITAFIFSRYRFKAKKKILMSILVLQMFPAFLSMTA 124

Query: 152 MYQILSKLQLIDNYFGLILVYCSTAVPYCAWLLKGYFDTIPFEIDEAGRVDGLTPFGTFF 211
           +Y +LSK+ LID Y GL+LVY + ++P+  WL+KGYFD IP  +DEA ++DG      FF
Sbjct: 125 IYILLSKMNLIDTYIGLLLVYVTGSLPFMTWLVKGYFDAIPTSLDEAAKIDGAGHLTIFF 184

Query: 212 RLILPLARPGLAVAGFYSFITAFGEVAFASTFMLSDTKYTFAVGLQSFVSEHDAQR-NLM 270
            +ILPLA+P L      SF   + +    +  + S+ K T A+G+ S++S + A+   L 
Sbjct: 185 EIILPLAKPILVFVALVSFTGPWMDFILPTLILRSEDKMTLAIGIFSWISSNSAENFTLF 244

Query: 271 AATAVLVAIPVSAFFYLVQKNLVTGLTAGGTK 302
           AA A+LVA+P++  F + QK++ TGL +G  K
Sbjct: 245 AAGALLVAVPITLLFIVTQKHITTGLVSGAVK 276


Lambda     K      H
   0.326    0.139    0.422 

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: 259
Number of extensions: 13
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: 303
Length of database: 277
Length adjustment: 26
Effective length of query: 277
Effective length of database: 251
Effective search space:    69527
Effective search space used:    69527
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 (21.6 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