GapMind for catabolism of small carbon sources

 

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

Align AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Btheta:351279
          Length = 408

 Score =  142 bits (358), Expect = 1e-38
 Identities = 77/226 (34%), Positives = 135/226 (59%), Gaps = 4/226 (1%)

Query: 33  LRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVDGTELT--NDLKKIDE 90
           ++D NL +  GE  VI G SGSGKST++RCINRL     G+++++GT++   +D + +  
Sbjct: 43  VKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDIAKVSDKELLQI 102

Query: 91  VRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFLKRVKIPEQANKYP 150
            R+E+ MVFQ+F L PH ++L N     + ++ + K + E+ AM  ++ V +    N+  
Sbjct: 103 RRKELAMVFQNFGLLPHRSVLHNIAFG-LELQGVKKGEREQKAMESMQLVGLKGYENQMV 161

Query: 151 GQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVGL-AEEGMTMLCVT 209
            +LSGG QQRV +AR+L  NP+++L DE  SALDP +  ++ D ++ L ++   T++ +T
Sbjct: 162 SELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQSKMKKTIVFIT 221

Query: 210 HEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQI 255
           H++  A ++ +R+  M  G+IV+          P +   + F+  +
Sbjct: 222 HDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVERFVENV 267


Lambda     K      H
   0.321    0.135    0.394 

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: 218
Number of extensions: 12
Number of successful extensions: 4
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: 257
Length of database: 408
Length adjustment: 28
Effective length of query: 229
Effective length of database: 380
Effective search space:    87020
Effective search space used:    87020
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 (21.9 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