GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Pseudomonas stutzeri RCH2

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate GFF1276 Psest_1309 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::P21629
         (255 letters)



>lcl|FitnessBrowser__psRCH2:GFF1276 Psest_1309 ABC-type
           branched-chain amino acid transport systems, ATPase
           component
          Length = 255

 Score =  441 bits (1134), Expect = e-129
 Identities = 221/255 (86%), Positives = 233/255 (91%)

Query: 1   MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60
           MSRPILEV GL MRFGGLLAVN V L V +KQVVSMIGPNGAGKTTVFNCLTGFYQPT G
Sbjct: 1   MSRPILEVRGLMMRFGGLLAVNEVGLTVHDKQVVSMIGPNGAGKTTVFNCLTGFYQPTAG 60

Query: 61  LIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKT 120
            I LDG  I GLPGHKIAR+GVVRTFQNVRLFK+MTAVENLLVAQHRHLNTNFLAGL KT
Sbjct: 61  EILLDGTPIHGLPGHKIARQGVVRTFQNVRLFKDMTAVENLLVAQHRHLNTNFLAGLLKT 120

Query: 121 PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180
           P FR+SER AM++AAHWLE+VNLT+ ANR AGTLAYGQQRRLEIARCMMTRPRILMLDEP
Sbjct: 121 PGFRKSERAAMDFAAHWLEQVNLTDVANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180

Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240
           AAGLNPKET+DLKALIA LR EH VTVLLIEHDMKLVMSISDHI VINQG PLADG+PEQ
Sbjct: 181 AAGLNPKETEDLKALIAMLRDEHGVTVLLIEHDMKLVMSISDHIYVINQGTPLADGSPEQ 240

Query: 241 IRDNPDVIKAYLGEA 255
           +R+NPDVIKAYLGEA
Sbjct: 241 VRNNPDVIKAYLGEA 255


Lambda     K      H
   0.320    0.137    0.391 

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: 309
Number of extensions: 2
Number of successful extensions: 1
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: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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