GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braF in Pseudomonas fluorescens FW300-N2E2

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf6N2E2_2925 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:Q1MCU2
         (292 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2925 Branched-chain amino
           acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
          Length = 255

 Score =  258 bits (658), Expect = 1e-73
 Identities = 131/258 (50%), Positives = 177/258 (68%), Gaps = 9/258 (3%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           +LKVE+LSM+FGGL+A+N  +   K   + ALIGPNGAGKTTVFNC+TGFY+PT G I  
Sbjct: 5   ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
           + +      ++ LP   I ++  V RTFQN+RLF  +T +ENLL+AQH  L   +     
Sbjct: 65  DGEP-----IQGLPGHHIARKG-VVRTFQNVRLFKDMTAVENLLIAQHRHL---NTNFFA 115

Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193
           GL     +++   EA+E A +WL+K +L + A+ PAG L YG QRRLEIAR M T P +L
Sbjct: 116 GLFKTPAFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRIL 175

Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253
            LDEPAAGLNP+E+  L AL+  +R E   ++LLIEHDM +VM ISDH+VV+  G  ++D
Sbjct: 176 MLDEPAAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLAD 235

Query: 254 GTPDHVKNDPRVIAAYLG 271
           GTP+ ++++P VI AYLG
Sbjct: 236 GTPEQIRDNPEVIKAYLG 253


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: 217
Number of extensions: 5
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: 255
Length adjustment: 25
Effective length of query: 267
Effective length of database: 230
Effective search space:    61410
Effective search space used:    61410
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 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