GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Shewanella oneidensis MR-1

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 203044 SO3960 ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__MR1:203044
          Length = 243

 Score =  142 bits (357), Expect = 8e-39
 Identities = 81/256 (31%), Positives = 142/256 (55%), Gaps = 19/256 (7%)

Query: 1   MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60
           M++  L+   L   +     V  V+L V+  QVV ++GPNGAGKTT F  + G  +   G
Sbjct: 1   MTQITLKAQNLAKSYKSRQVVKDVSLTVKTGQVVGLLGPNGAGKTTTFYMVVGLVKSDKG 60

Query: 61  LIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLL--VAQHRHLNTNFLAGLF 118
            I +D +++   P H  ARKG+    Q   +F+++T  +N++  +   + LN++      
Sbjct: 61  HIFIDDDDLTADPMHLRARKGIGYLPQEASIFRKLTVHDNIMAVLQTRKELNSD------ 114

Query: 119 KTPAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLD 178
                     EA+E     LEE ++T   +    +L+ G++RR+EIAR +   P+ ++LD
Sbjct: 115 -------QREEALE---QLLEEFHITHIRDSQGMSLSGGERRRVEIARALAANPKFILLD 164

Query: 179 EPAAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTP 238
           EP AG++P    D+K +I +L+S   + VL+ +H+++  + + +H  +++ G+ +A+GTP
Sbjct: 165 EPFAGVDPISVIDIKKIIEQLKS-RGLGVLITDHNVRETLDVCEHAYIVSHGSLIAEGTP 223

Query: 239 EQIRDNPDVIKAYLGE 254
            +I DN  V   YLGE
Sbjct: 224 AEILDNQQVRAVYLGE 239


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: 156
Number of extensions: 8
Number of successful extensions: 3
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: 243
Length adjustment: 24
Effective length of query: 231
Effective length of database: 219
Effective search space:    50589
Effective search space used:    50589
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: 46 (22.3 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