GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Pseudomonas putida KT2440

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__Putida:PP_0411
          Length = 374

 Score =  232 bits (592), Expect = 1e-65
 Identities = 131/316 (41%), Positives = 196/316 (62%), Gaps = 9/316 (2%)

Query: 7   KDIRKSY-GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGE 65
           + ++KSY G   ++  ++LDI++GEF+  +GPSG GK+T L M+AG E  T G++ + G 
Sbjct: 18  RGVQKSYDGESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQLGGR 77

Query: 66  RVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTP 125
            +N+VPP KR I MVFQ+YAL+PHMTV +N+AF + +   SK +I  RV+   +M+QL  
Sbjct: 78  SINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLNMVQLDA 137

Query: 126 YLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSD 185
           +  R P  LSGGQ+QRVA+ RA+   P++ L DEPL  LD  LR   ++EI  + +R+  
Sbjct: 138 FAKRYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIHQRLG- 196

Query: 186 TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPA 245
            T++YVTHDQ EA+T++DR+ V   G I+Q+  P  LYE P N FVA FIG    N I  
Sbjct: 197 VTVVYVTHDQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIGE--NNRISG 254

Query: 246 TITAT-GQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRV---TEADDFLFEGT 301
           T+ A+ G++  V L  G+ V   +  N  + G+  +  +RPE +R+   +E+    F G 
Sbjct: 255 TLLASDGKRCQVQLPRGERVEA-LAVNVGQAGEPVTLSIRPERVRLNGHSESCVNRFSGR 313

Query: 302 VSIVEALGEVTLLYIE 317
           V+    LG+   + +E
Sbjct: 314 VAEFIYLGDHVRVRLE 329


Lambda     K      H
   0.320    0.137    0.387 

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: 355
Number of extensions: 14
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: 362
Length of database: 374
Length adjustment: 30
Effective length of query: 332
Effective length of database: 344
Effective search space:   114208
Effective search space used:   114208
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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