GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pseudomonas stutzeri RCH2

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate GFF3784 Psest_3853 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::Q8DQH8
         (254 letters)



>FitnessBrowser__psRCH2:GFF3784
          Length = 266

 Score =  166 bits (419), Expect = 6e-46
 Identities = 96/249 (38%), Positives = 147/249 (59%), Gaps = 7/249 (2%)

Query: 3   LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62
           +L  + L K FGG  AV +V L++   ++  LIGPNGAGKTT+FNLLT   +PS G++ L
Sbjct: 21  MLSARGLRKEFGGFVAVNNVDLDVRHAQVHALIGPNGAGKTTVFNLLTKFLQPSAGSIRL 80

Query: 63  DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122
             H +    P K+A +GL R+FQ   +F  LTVLDNV +A        + T F  LP   
Sbjct: 81  LDHDITRTDPAKVARMGLVRSFQISAVFPHLTVLDNVRVAL--QRPGGLATQFW-LP--M 135

Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182
           +S   L  +AL+L++   L      LA +LSYG++R LEI   LA EPK+L LDEP AGM
Sbjct: 136 RSLNRLNERALQLIESVGLADKRHELAADLSYGRKRVLEIATTLALEPKVLLLDEPMAGM 195

Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242
             ++   + E+IR +  +    ++++EH++ +V ++  ++ VL+ G ++  G    +  +
Sbjct: 196 GHEDVHVVAEIIREVATQ--RAVLMVEHNLKVVADLCHQVTVLQRGEILTSGDYRTVSQD 253

Query: 243 KRVIEAYLG 251
           +RV  AY+G
Sbjct: 254 ERVRVAYMG 262


Lambda     K      H
   0.319    0.139    0.385 

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: 166
Number of extensions: 5
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: 254
Length of database: 266
Length adjustment: 24
Effective length of query: 230
Effective length of database: 242
Effective search space:    55660
Effective search space used:    55660
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 (21.7 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