GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Methylocystis bryophila S285

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_085770502.1 B1812_RS04380 ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>NCBI__GCF_002117405.1:WP_085770502.1
          Length = 293

 Score =  182 bits (463), Expect = 5e-51
 Identities = 91/250 (36%), Positives = 148/250 (59%)

Query: 6   LEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRLD 65
           L ++ +++ FGG+ A++ ++  V   ++ S+IGPNGAGK+++ N +TG Y+P  G I+LD
Sbjct: 35  LALTNISLSFGGIQALSEIDFSVAAGEICSIIGPNGAGKSSLINVITGLYRPDWGRIQLD 94

Query: 66  GEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFRR 125
                 +P  ++A  GV RTFQN+ LF+ ++  +N+ V +     +++L  +F  P  R 
Sbjct: 95  KNSFSRMPTERLASLGVARTFQNLALFRGLSVFDNIAVGRVSATRSHWLEQVFGLPRARA 154

Query: 126 SEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLN 185
                       L  + L +  NR AGTL YG Q+R+E+AR +  RPR+L+LDEP AG+ 
Sbjct: 155 DRLATEIIVEEMLVFLGLGQVRNRIAGTLPYGMQKRVELARALAIRPRLLLLDEPMAGMT 214

Query: 186 PKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDNP 245
             E  ++   I   R     +++LIEHD+ +VM +SD + V++ G  +ADG P  + ++ 
Sbjct: 215 AGEKAEMGEFIQLTRDRFGASIVLIEHDIGVVMELSDRVAVLDYGRKIADGPPSDVMNDE 274

Query: 246 DVIKAYLGEA 255
            VI AYLG A
Sbjct: 275 AVIDAYLGVA 284


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: 163
Number of extensions: 4
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: 293
Length adjustment: 25
Effective length of query: 230
Effective length of database: 268
Effective search space:    61640
Effective search space used:    61640
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 Apr 09 2024. 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