GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proW in Pseudomonas putida KT2440

Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate PP_3559 PP_3559 glycine betaine ABC transporter (permease)

Query= SwissProt::P14176
         (354 letters)



>FitnessBrowser__Putida:PP_3559
          Length = 282

 Score =  238 bits (608), Expect = 1e-67
 Identities = 121/262 (46%), Positives = 183/262 (69%), Gaps = 1/262 (0%)

Query: 72  IDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALIAWQISGVGMGVATLV 131
           +DW+V ++    + +   +  +L G + LL  +P  + +++  L+AW  S   +  A LV
Sbjct: 21  VDWLVLNYGDHLRSLSDQLLQLLVGLENLLRLLPWWLLLLLVGLLAWHASRSLLRSAVLV 80

Query: 132 SLIA-IGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKIIRPLLDAMQTT 190
           +L+A IG +G W + + TLALVL +   C+++G+PLGI LA  P A +++ P+LD MQT 
Sbjct: 81  ALLALIGMLGLWDKLLQTLALVLVSTGLCVLVGVPLGILLAARPLARRLLLPVLDVMQTL 140

Query: 191 PAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRSFGASPRQ 250
           PAFVYL+P++MLFG+G VP V  T+I+ALPP++RLT LG++Q+   L++A+   GAS  Q
Sbjct: 141 PAFVYLIPVLMLFGLGKVPAVFATLIYALPPLVRLTELGLSQIDPSLLQAAHGLGASRWQ 200

Query: 251 MLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGRLDMGLATVGG 310
            L ++ LPLA+P+IMAG+NQ++M+ALSMVV+ASMI   GLG+ VL GI  L++G     G
Sbjct: 201 RLRRIALPLALPSIMAGLNQSVMMALSMVVVASMIGARGLGEDVLAGIQTLNVGQGMEAG 260

Query: 311 VGIVILAIILDRLTQAVGRDSR 332
           + IV LA+++DR++QA GR SR
Sbjct: 261 LAIVALAMVIDRISQAYGRSSR 282


Lambda     K      H
   0.326    0.141    0.435 

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: 298
Number of extensions: 10
Number of successful extensions: 1
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: 354
Length of database: 282
Length adjustment: 27
Effective length of query: 327
Effective length of database: 255
Effective search space:    83385
Effective search space used:    83385
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 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