GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pantoea rwandensis LMG 26275

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_084935580.1 HA51_RS15830 ATP-binding cassette domain-containing protein

Query= TCDB::P21629
         (255 letters)



>NCBI__GCF_002095475.1:WP_084935580.1
          Length = 291

 Score =  288 bits (738), Expect = 7e-83
 Identities = 153/283 (54%), Positives = 191/283 (67%), Gaps = 30/283 (10%)

Query: 1   MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60
           MS  IL+V+ L MRFGG+ A+N V+L VE   V S+IGPNGAGKTTVFNCLTGFY+ TGG
Sbjct: 1   MSDAILQVNNLMMRFGGIKALNDVSLSVERGSVTSLIGPNGAGKTTVFNCLTGFYRATGG 60

Query: 61  LIRLDGEE-----IQGL-------------------------PGHKIARKGVVRTFQNVR 90
            I L+  +     IQ L                           H + R G+ RTFQN+R
Sbjct: 61  RIMLNANQRHTDVIQVLGQKIHPQDWLNPARLGSRIWYKMFGGAHLVNRAGLARTFQNIR 120

Query: 91  LFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFRRSEREAMEYAAHWLEEVNLTEFANRS 150
           LF+EM+ VENLLVAQH  +N   LAG+  T  +R +E  A++ A +WLE V+L   ANR 
Sbjct: 121 LFREMSVVENLLVAQHMLVNRQLLAGVMNTRGYREAENRALDRAFYWLENVDLVSSANRL 180

Query: 151 AGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLNPKETDDLKALIAKLRSEHNVTVLLI 210
           AGTL+YGQQRRLEIAR M TRP ++ LDEPAAGLNP ETD L  ++ +LR++H ++VLLI
Sbjct: 181 AGTLSYGQQRRLEIARAMCTRPELICLDEPAAGLNPVETDTLSQILHRLRADHRISVLLI 240

Query: 211 EHDMKLVMSISDHIVVINQGAPLADGTPEQIRDNPDVIKAYLG 253
           EHDM +VM ISDHIVV++ G  +A GTP+QIR +P VI AYLG
Sbjct: 241 EHDMPMVMRISDHIVVLDHGDVIAQGTPQQIRHDPKVIAAYLG 283


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: 220
Number of extensions: 5
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 255
Length of database: 291
Length adjustment: 25
Effective length of query: 230
Effective length of database: 266
Effective search space:    61180
Effective search space used:    61180
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 24 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 (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