GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Burkholderia phytofirmans PsJN

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 BPHYT_RS04435 BPHYT_RS04435 ABC transporter

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__BFirm:BPHYT_RS04435
          Length = 646

 Score =  213 bits (541), Expect = 1e-59
 Identities = 114/249 (45%), Positives = 156/249 (62%), Gaps = 1/249 (0%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           IL++ G+ M+F GL A+N V+L V+   +  +IGPNG+GK+T+ N LTG Y PT G +  
Sbjct: 391 ILQLRGILMQFSGLKALNDVDLTVQRGTIHGLIGPNGSGKSTMMNVLTGIYVPTAGTLEY 450

Query: 65  DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124
            G  + G    +IA  G+ RTFQNV+LF EMTA+EN+LV  H   N N       +  +R
Sbjct: 451 RGASLAGKTSAQIALSGIARTFQNVQLFGEMTALENVLVGLHHTFNANLADVGLMSSRYR 510

Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
           R ER A E A   L  V L   A   A  L YG+QR LEIAR +   P++L+LDEPAAGL
Sbjct: 511 REERAARERAFGMLRFVGLDNVAAEEARNLPYGKQRLLEIARALALDPQLLLLDEPAAGL 570

Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244
              +  +L A+I K+R +H +TV+LIEH M +VMS+ D + V++ G  +A+G P  I+ N
Sbjct: 571 TAPDIKELVAIIRKVR-DHGITVVLIEHHMDVVMSVCDRVSVLDFGQKIAEGKPADIQSN 629

Query: 245 PDVIKAYLG 253
             VI+AYLG
Sbjct: 630 EKVIEAYLG 638


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: 376
Number of extensions: 17
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: 646
Length adjustment: 31
Effective length of query: 224
Effective length of database: 615
Effective search space:   137760
Effective search space used:   137760
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: 50 (23.9 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 (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