GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Pseudomonas fluorescens FW300-N2E2

Align AapM, 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 Pf6N2E2_1799 ABC transporter permease protein

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1799
          Length = 292

 Score =  104 bits (260), Expect = 3e-27
 Identities = 60/171 (35%), Positives = 103/171 (60%), Gaps = 11/171 (6%)

Query: 171 LWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFM- 229
           +WG L+ T+V++ + +A+ +  G++ A+ R S  P++R + + +  + RG PLI  L + 
Sbjct: 73  MWG-LLNTVVMAVLAMALGIVFGVITAIMRMSANPILRYVALIYTWLFRGTPLILQLLLW 131

Query: 230 ---ASVMLPLFLPTGWNVDKL------LRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEG 280
              A +   + +P  + +D +      + AL+G+SI   AY AEV+R GL ++  GQ+E 
Sbjct: 132 FNLALIFPTIGIPGLFEMDTVSLMTPFVAALLGLSINQGAYTAEVVRAGLLSVDTGQYEA 191

Query: 281 ADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLL 331
           A S+G+   Q  R II+PQA++++IP + N FIG  K TSL ++I   +LL
Sbjct: 192 AKSIGMPRLQALRRIILPQAMRIIIPPVGNEFIGMVKMTSLASVIQYSELL 242


Lambda     K      H
   0.330    0.145    0.469 

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: 287
Number of extensions: 12
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: 384
Length of database: 292
Length adjustment: 28
Effective length of query: 356
Effective length of database: 264
Effective search space:    93984
Effective search space used:    93984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 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