GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Pseudomonas stutzeri RCH2

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__psRCH2:GFF857
          Length = 371

 Score =  332 bits (851), Expect = 1e-95
 Identities = 186/363 (51%), Positives = 239/363 (65%), Gaps = 15/363 (4%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           MA + L  + K+Y    +  +I+LDI+ GE +VFVGPSGCGKSTLLR+IAGLE IT G L
Sbjct: 1   MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
            ID   VND+PP  R + MVFQSYALYPHMTV ENM+F LK+A   + EI   VEA AE 
Sbjct: 61  LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           LQL + L+R PK LSGGQRQRVAIGR++VR+PKV+LFDEPLSNLDA LRV  R+EIA+L 
Sbjct: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
           + +  STM+YVTHDQVEAMTLA +IVVL  G IAQVG PL LY  P+N FVA F+GSP+M
Sbjct: 181 QRI-RSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQM 239

Query: 241 NLLPGKIIGTGAQT-TVEMTDGGRAVSDYPSDDSLMGAAVN------VGVRPEDMVEAAP 293
           N +  + I    +T T+E+  G      YP    + G+AV+      +G+RPE  V    
Sbjct: 240 NFVEVRAISASPETVTIELPSG------YPLTLPVDGSAVSPGDPLTLGIRPEHFV-MPD 292

Query: 294 GGDYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHV 353
             D+ F G++ + E LG+  LLY      +D     + G  +  +G+      +  K H+
Sbjct: 293 EADFTFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHL 352

Query: 354 FKD 356
           F++
Sbjct: 353 FRE 355


Lambda     K      H
   0.316    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: 425
Number of extensions: 25
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: 373
Length of database: 371
Length adjustment: 30
Effective length of query: 343
Effective length of database: 341
Effective search space:   116963
Effective search space used:   116963
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 (21.6 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