GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Acidovorax sp. GW101-3H11

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Ac3H11_4630 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:A0A165KC86
         (260 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4630 Branched-chain
           amino acid transport ATP-binding protein LivG (TC
           3.A.1.4.1)
          Length = 274

 Score =  221 bits (563), Expect = 1e-62
 Identities = 112/257 (43%), Positives = 165/257 (64%), Gaps = 1/257 (0%)

Query: 2   TEKSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTP 61
           T+K  +V+L V  IS RFGG++AL+D+   +K  ++  +IGPNGAGK++  N I G+YTP
Sbjct: 16  TKKIGDVILDVKNISLRFGGVKALTDISFNVKEHEIRAIIGPNGAGKSSMLNCINGVYTP 75

Query: 62  DAGTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAV 121
             G+    GK +      +VA+ G+ARTFQN+ LF  M+ ++N+M GR+++  S LF   
Sbjct: 76  QDGSITFRGKTFSHMNSRQVAEMGVARTFQNLALFKGMSVIDNIMTGRNLKIKSNLFLQA 135

Query: 122 FRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIAL 181
            R    + EE A  ++ + ++D++ I  F       L YG Q+R+++ RALA +PQ++ L
Sbjct: 136 LRLGPAEREEMAHREKVEHIIDFLEIQAFRKTPVGQLPYGLQKRVDLGRALAMEPQVLLL 195

Query: 182 DEPAAGMNATEKVQL-RELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGN 240
           DEP AGMN  EK  + R ++D       TI+LIEHD+ +VM + DRV VLDYGK+I +G 
Sbjct: 196 DEPMAGMNVEEKQDMCRFILDVNDEFGTTIVLIEHDMGVVMDISDRVVVLDYGKKIGDGT 255

Query: 241 PAEVQKNEKVIEAYLGT 257
           P EV+ N+ VI AYLGT
Sbjct: 256 PDEVRNNQDVISAYLGT 272


Lambda     K      H
   0.319    0.137    0.384 

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: 201
Number of extensions: 6
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: 260
Length of database: 274
Length adjustment: 25
Effective length of query: 235
Effective length of database: 249
Effective search space:    58515
Effective search space used:    58515
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 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, 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