GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braF in Desulfovibrio vulgaris Hildenborough

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 206140 DVU0715 branched-chain amino acid ABC transporter, ATP binding protein

Query= TCDB::P21629
         (255 letters)



>lcl|MicrobesOnline__882:206140 DVU0715 branched-chain amino acid
           ABC transporter, ATP binding protein
          Length = 255

 Score =  225 bits (574), Expect = 6e-64
 Identities = 117/249 (46%), Positives = 161/249 (64%), Gaps = 1/249 (0%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           +L +  LT  FGGL+AVN V+  V+E  +V +IGPNGAGKTTVFN +TG Y+P  G I  
Sbjct: 3   LLSLRNLTKTFGGLVAVNSVSFDVDEGSIVGLIGPNGAGKTTVFNLITGNYKPDSGDIFF 62

Query: 65  DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124
           DG  I+GL  H+I + G+ RTFQ +RLF+ M+ +EN+L   H  +     + +  T   R
Sbjct: 63  DGRAIKGLLTHRIVQMGIARTFQTIRLFQNMSVMENVLAGCHCRMTAGVFSAMLGTAGHR 122

Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
           R E+ A+E A   LE V L +  +  A  L+YG QR LEIAR + T PR ++LDEPA G+
Sbjct: 123 REEKRAIERAVRELEFVGLADQHDNLAKNLSYGNQRLLEIARALATDPRFIILDEPAGGM 182

Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244
           N +ET  L   I  +R +  ++VLLIEHDM LVM + + +VV+  GA +A+GTP  I+ +
Sbjct: 183 NDQETAALIGTIRAIR-DRGISVLLIEHDMSLVMKVCEKLVVLEYGALIAEGTPSVIKRD 241

Query: 245 PDVIKAYLG 253
           P VI+AYLG
Sbjct: 242 PRVIEAYLG 250


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: 179
Number of extensions: 7
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: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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