GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Pseudomonas stutzeri RCH2

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF3784 Psest_3853 ABC-type branched-chain amino acid transport systems, ATPase component

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__psRCH2:GFF3784
          Length = 266

 Score =  134 bits (336), Expect = 3e-36
 Identities = 88/264 (33%), Positives = 139/264 (52%), Gaps = 16/264 (6%)

Query: 9   TPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRL 68
           T +L+   L   FGG VAVN+V     + ++ A+IGPNGAGKTT+FN +T F  P+ G +
Sbjct: 19  TVMLSARGLRKEFGGFVAVNNVDLDVRHAQVHALIGPNGAGKTTVFNLLTKFLQPSAGSI 78

Query: 69  TLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFS 128
            L   D     + R    +++ +  + R+FQ   +F  ++VL+N+ VA    L R  G +
Sbjct: 79  RLLDHD-----ITRTDPAKVA-RMGLVRSFQISAVFPHLTVLDNVRVA----LQRPGGLA 128

Query: 129 IAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPV 188
               L + S  R    A+ L    ++ V L +     A +L YG +R LEIA  +  EP 
Sbjct: 129 TQFWLPMRSLNRLNERALQL----IESVGLADKRHELAADLSYGRKRVLEIATTLALEPK 184

Query: 189 MLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKI 248
           +L LDEP AG+   +   +A+++  +  +    VL++EH++ VV  +   V VL  G  +
Sbjct: 185 VLLLDEPMAGMGHEDVHVVAEIIREVATQR--AVLMVEHNLKVVADLCHQVTVLQRGEIL 242

Query: 249 SDGDPAFVKNDPAVIRAYLGEEED 272
           + GD   V  D  V  AY+G ++D
Sbjct: 243 TSGDYRTVSQDERVRVAYMGTDDD 266


Lambda     K      H
   0.319    0.137    0.397 

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: 192
Number of extensions: 18
Number of successful extensions: 4
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: 294
Length of database: 266
Length adjustment: 26
Effective length of query: 268
Effective length of database: 240
Effective search space:    64320
Effective search space used:    64320
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: 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