GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Bacteroides thetaiotaomicron VPI-5482

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 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__Btheta:350819
          Length = 463

 Score =  125 bits (315), Expect = 1e-33
 Identities = 79/255 (30%), Positives = 140/255 (54%), Gaps = 20/255 (7%)

Query: 3   RPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLI 62
           + I+EVS ++  FG   A++ V L V++ + V+++GP+G GKTT+   + GF   + G I
Sbjct: 7   KSIIEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEI 66

Query: 63  RLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPA 122
           R+ G+EI   P HK   + V   FQ   LF  +   +N+           F   L KTP 
Sbjct: 67  RISGKEITQTPPHK---RPVNTVFQKYALFPHLNVYDNIA----------FGLKLKKTP- 112

Query: 123 FRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182
            +++  + ++ A   L+ V +T++  R   +L+ GQQ+R+ IAR ++  P +L+LDEP A
Sbjct: 113 -KQTIGKKVKAA---LKMVGMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLA 168

Query: 183 GLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIR 242
            L+ K   D++  + ++     +T + + HD +  +++SD IVV+++G     GTP  I 
Sbjct: 169 ALDLKMRKDMQMELKEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIY 228

Query: 243 DNP--DVIKAYLGEA 255
           + P    +  ++GE+
Sbjct: 229 NEPINSFVADFIGES 243


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: 235
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: 463
Length adjustment: 29
Effective length of query: 226
Effective length of database: 434
Effective search space:    98084
Effective search space used:    98084
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: 49 (23.5 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