GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_1799 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1799
          Length = 351

 Score =  125 bits (313), Expect = 2e-33
 Identities = 81/245 (33%), Positives = 130/245 (53%), Gaps = 20/245 (8%)

Query: 1   MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60
           MS  ILE   +   +G   AV  VNL + E ++V  +GP+G GKTT+   + G    +GG
Sbjct: 1   MSGLILE--NVEKHYGSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGG 58

Query: 61  LIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKT 120
            IRLDGE+I   P H +   G+V  FQ++ LF  MT  EN+             A   K 
Sbjct: 59  EIRLDGEDIGHTPAH-LRNFGMV--FQSLALFPHMTVGENI-------------AYPLKL 102

Query: 121 PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180
               +++++A       LE + L    NR    L+ GQ++R+ IAR +   P+IL+LDEP
Sbjct: 103 RGVSKADQQAR--VVELLELIQLQAMINRPVAKLSGGQRQRVAIARAIANHPKILLLDEP 160

Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240
            + L+ K  + ++  I +L+   N+T +++ HD +  M+++D +VV+ +      GTP +
Sbjct: 161 LSALDAKLRESMQVEIRQLQQRLNITTIMVTHDQREAMTMADIVVVLGEHKVQQVGTPIE 220

Query: 241 IRDNP 245
           I  +P
Sbjct: 221 IYRHP 225


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: 205
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: 351
Length adjustment: 27
Effective length of query: 228
Effective length of database: 324
Effective search space:    73872
Effective search space used:    73872
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: 48 (23.1 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