GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Phaeobacter inhibens BS107

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 GFF3831 PGA1_262p02350 histidine transport ATP-binding protein HisP

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Phaeo:GFF3831
          Length = 281

 Score =  227 bits (579), Expect = 2e-64
 Identities = 120/261 (45%), Positives = 170/261 (65%), Gaps = 10/261 (3%)

Query: 2   AEAPAKKLTVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIR 61
           AE P +  T +    A+ + +++K +G   VL+ ++L   +G+ + I G SGSGKSTM+R
Sbjct: 23  AETPVEPHTQAE---AIRVCDLHKSFGSLEVLKGVSLTAKQGDVVAIIGGSGSGKSTMLR 79

Query: 62  CINRLEEHQKGKIVVDGTELTN-------DLKKIDEVRREVGMVFQHFNLFPHLTILENC 114
           CIN LE    G+IV+ G  +         D ++I+ +R  + MVFQ FNL+ H T+LEN 
Sbjct: 80  CINFLETPNSGEIVIAGETVAMRQDGSPADRRQIERIRTRLAMVFQQFNLWTHRTLLENV 139

Query: 115 TLAPIWVRKMPKKQAEEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIM 174
              P+ V K+P+ +A   A   L RV + ++A+ +P  LSGGQQQR AIAR+L ++P +M
Sbjct: 140 IEVPVHVLKVPRSEAIHRAHELLARVGLGDKADAFPAFLSGGQQQRAAIARALAVDPNVM 199

Query: 175 LFDEPTSALDPEMIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQN 234
           LFDEPTSALDPE++ EVL  +  LA EG TML VTHEM FAR+VAN V+++ +G+I EQ 
Sbjct: 200 LFDEPTSALDPELVGEVLTVIRDLAAEGRTMLLVTHEMKFAREVANHVVYLFEGRIEEQG 259

Query: 235 EPAAFFDNPQHERTKLFLSQI 255
            P+  F NP+ ER K FLS +
Sbjct: 260 PPSEVFGNPKSERLKQFLSSV 280


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: 187
Number of extensions: 6
Number of successful extensions: 2
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: 281
Length adjustment: 25
Effective length of query: 232
Effective length of database: 256
Effective search space:    59392
Effective search space used:    59392
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: 47 (22.7 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