GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pseudomonas fluorescens FW300-N2E2

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf6N2E2_1433 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1433
          Length = 260

 Score =  200 bits (508), Expect = 3e-56
 Identities = 110/258 (42%), Positives = 161/258 (62%), Gaps = 9/258 (3%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           LL+++H+S+ F G+ A+ D SF    G+I ALIGPNGAGK+++ N I+G Y+   G I F
Sbjct: 9   LLELDHISLSFKGVKAVTDISFRVAAGEICALIGPNGAGKSSLLNVISGVYQAQDGHIRF 68

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
           +++  ++    R  D  +     +ARTFQNI LF G++VL+N+L  ++   +K     I 
Sbjct: 69  DRQERRRM---RPHDVAVRG---IARTFQNIALFKGMSVLDNVLTGRN---LKRRSTWIE 119

Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193
             + +G  + E     E A   +    L    D   G LPYG Q+R+E+ARA+   P LL
Sbjct: 120 QALRIGRARTEDDRQREAAERVIAFLHLQPWRDTLVGTLPYGLQKRVELARALAAEPRLL 179

Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253
            LDEP AG+N  E   ++  +  I  E GT+++LIEHD+ VVM+ISDHVVVL+YG+KI D
Sbjct: 180 LLDEPMAGMNADEKQQMSRFIVDINRELGTTVVLIEHDIGVVMDISDHVVVLDYGRKIGD 239

Query: 254 GTPDHVKNDPRVIAAYLG 271
           G+P+ V+ +P VI+AYLG
Sbjct: 240 GSPEDVRQNPEVISAYLG 257


Lambda     K      H
   0.318    0.136    0.386 

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: 193
Number of extensions: 11
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: 292
Length of database: 260
Length adjustment: 25
Effective length of query: 267
Effective length of database: 235
Effective search space:    62745
Effective search space used:    62745
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 (21.7 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