GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braF in Magnetospirillum magneticum AMB-1

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 WP_011385946.1 AMB_RS18160 ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385946.1 AMB_RS18160 ABC
           transporter ATP-binding protein
          Length = 265

 Score =  195 bits (495), Expect = 9e-55
 Identities = 96/251 (38%), Positives = 157/251 (62%), Gaps = 1/251 (0%)

Query: 4   PILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIR 63
           P+LEV  +++ FGG+ A+  V+ +V + ++ S+IGPNGAGKT++ NC++G Y+PT G + 
Sbjct: 7   PVLEVRDVSLAFGGVRALTEVSFQVNKGELFSIIGPNGAGKTSMLNCVSGRYKPTSGRVF 66

Query: 64  LDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAG-LFKTPA 122
           +DG ++ GL  +  A  G+ RTFQN+ LF  M+ ++N++V +H  L  N   G L+    
Sbjct: 67  MDGRDVTGLSPNVRATLGLGRTFQNLALFGHMSVLDNIMVGRHHLLGNNAATGALYWLSG 126

Query: 123 FRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182
            R+ E          ++ + +       AGTL YG ++R+E+AR M   P++++LDEP A
Sbjct: 127 ARKEELAHRRKVEDIIDFLEIAHIRKAVAGTLPYGLRKRVELARAMAVEPKVILLDEPMA 186

Query: 183 GLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIR 242
           G+N +E +D+   I  L  E  +TV++IEHDM +VM IS  ++V+  G  +A+G P+++ 
Sbjct: 187 GMNLEEKEDMARYIVDLNEEWGMTVIMIEHDMGVVMDISHRVMVLEFGRKIAEGLPDEVM 246

Query: 243 DNPDVIKAYLG 253
           +N  V  AYLG
Sbjct: 247 NNERVKVAYLG 257


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: 178
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: 255
Length of database: 265
Length adjustment: 24
Effective length of query: 231
Effective length of database: 241
Effective search space:    55671
Effective search space used:    55671
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