GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pseudomonas stutzeri RCH2

Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate GFF3784 Psest_3853 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::P0A9S7
         (255 letters)



>FitnessBrowser__psRCH2:GFF3784
          Length = 266

 Score =  160 bits (404), Expect = 3e-44
 Identities = 91/251 (36%), Positives = 151/251 (60%), Gaps = 11/251 (4%)

Query: 5   LLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILL 64
           +LS  GL   FGG +AVNNV+L++   ++ +LIGPNGAGKTTVFN LT F +P+ G+I L
Sbjct: 21  MLSARGLRKEFGGFVAVNNVDLDVRHAQVHALIGPNGAGKTTVFNLLTKFLQPSAGSIRL 80

Query: 65  RDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSF- 123
            D  +      ++ARMG+VR+FQ   +F  +TV++N+ VA  +        G L T  + 
Sbjct: 81  LDHDITRTDPAKVARMGLVRSFQISAVFPHLTVLDNVRVALQR-------PGGLATQFWL 133

Query: 124 -RRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAA 182
             R+ +   +RA   +E +GL +  +  A++L+YG +R LEIA  +  +P++L+LDEP A
Sbjct: 134 PMRSLNRLNERALQLIESVGLADKRHELAADLSYGRKRVLEIATTLALEPKVLLLDEPMA 193

Query: 183 GLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIR 242
           G+  ++   + E+I E+       +L++EH++K+V  +  ++ V+ +G  L +G    + 
Sbjct: 194 GMGHEDVHVVAEIIREVATQR--AVLMVEHNLKVVADLCHQVTVLQRGEILTSGDYRTVS 251

Query: 243 NNPDVIRAYLG 253
            +  V  AY+G
Sbjct: 252 QDERVRVAYMG 262


Lambda     K      H
   0.320    0.137    0.395 

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: 165
Number of extensions: 7
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: 255
Length of database: 266
Length adjustment: 24
Effective length of query: 231
Effective length of database: 242
Effective search space:    55902
Effective search space used:    55902
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