GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Klebsiella michiganensis M5al

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 BWI76_RS16795 BWI76_RS16795 amino acid ABC transporter ATPase

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Koxy:BWI76_RS16795
          Length = 240

 Score =  249 bits (636), Expect = 4e-71
 Identities = 125/239 (52%), Positives = 170/239 (71%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           + I N++K +GD HVLR I+  +   E + I GPSGSGKST +RC+N LE   +G++ V+
Sbjct: 2   IHINNLHKRFGDSHVLRGISCDIKPQEVVCIIGPSGSGKSTFLRCMNALETVSEGEVEVN 61

Query: 78  GTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFL 137
           G    +    ++++R  VGMVFQ FNLFPH T+LEN  +AP+ +R M + +A  +A   L
Sbjct: 62  GFAAHDRATDLNKMRESVGMVFQRFNLFPHKTVLENLIMAPMNLRGMARAEAVRLAEELL 121

Query: 138 KRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVG 197
            +V + ++ + +P  LSGGQQQRVAIAR+L M P IMLFDEPTSALDPE++ +VL+ M  
Sbjct: 122 AKVGLSDKRDAWPSSLSGGQQQRVAIARALAMKPSIMLFDEPTSALDPELVGDVLEVMKN 181

Query: 198 LAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQIL 256
           LA EGMTM+ VTHEMGFAR+VA+RVIF+DQG I E+ +PA  F  P + RT  FLS++L
Sbjct: 182 LASEGMTMVIVTHEMGFAREVADRVIFIDQGIIQEEGKPAQIFSAPTNPRTAAFLSKVL 240


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: 192
Number of extensions: 5
Number of successful extensions: 1
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: 240
Length adjustment: 24
Effective length of query: 233
Effective length of database: 216
Effective search space:    50328
Effective search space used:    50328
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: 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