GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Escherichia coli BW25113

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 14934 b0809 glutamine ABC transporter ATP-binding protein (NCBI)

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Keio:14934
          Length = 240

 Score =  253 bits (646), Expect = 3e-72
 Identities = 128/240 (53%), Positives = 173/240 (72%), Gaps = 4/240 (1%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           +E  N++K +G   VL +I+L + +GE +VI GPSGSGKST++RCIN+LEE   G ++VD
Sbjct: 2   IEFKNVSKHFGPTQVLHNIDLNIAQGEVVVIIGPSGSGKSTLLRCINKLEEITSGDLIVD 61

Query: 78  GTELTNDLKKIDE--VRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMH 135
           G ++ +   K+DE  +R+E GMVFQ F LFPHLT LEN    P+ VR   K++AE++A  
Sbjct: 62  GLKVNDP--KVDERLIRQEAGMVFQQFYLFPHLTALENVMFGPLRVRGANKEEAEKLARE 119

Query: 136 FLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTM 195
            L +V + E+A+ YP +LSGGQQQRVAIAR+L + PK+MLFDEPTSALDPE+  EVL  M
Sbjct: 120 LLAKVGLAERAHHYPSELSGGQQQRVAIARALAVKPKMMLFDEPTSALDPELRHEVLKVM 179

Query: 196 VGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQI 255
             LAEEGMTM+ VTHE+GFA +VA+R+IF+D+G+I E   P     NP  +R + FL  +
Sbjct: 180 QDLAEEGMTMVIVTHEIGFAEKVASRLIFIDKGRIAEDGNPQVLIKNPPSQRLQEFLQHV 239


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: 201
Number of extensions: 4
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