GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Paraburkholderia phymatum STM815

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_012405807.1 BPHY_RS32965 amino acid permease

Query= TCDB::Q2VQZ4
         (536 letters)



>NCBI__GCF_000020045.1:WP_012405807.1
          Length = 484

 Score =  195 bits (496), Expect = 3e-54
 Identities = 143/441 (32%), Positives = 214/441 (48%), Gaps = 37/441 (8%)

Query: 37  LKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAEMAVLY 96
           L+ RH+ MI++GG IGAGLFVGS   L   GP A  + YL+ GI++L     L EMA+  
Sbjct: 26  LRQRHVTMISLGGIIGAGLFVGSSATLSTVGPGAC-VSYLVAGIVVLLVMRMLGEMALAV 84

Query: 97  PVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMAVWVS- 155
           P  G+F  Y    +    GF  GW Y   W+ V+  E +A +  ++ W     + VW+  
Sbjct: 85  PGIGSFTEYARIGLGDWAGFTSGWLYWYFWVIVVAVEAVAGAAILQRWTP---VPVWMIG 141

Query: 156 -VFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIGVKYWR 214
            V L V+  I +  V+ YGE EF  + IK+ A + FI++G     G     G      W 
Sbjct: 142 LVLLSVMTLINLMSVKSYGEFEFWFASIKVAAIIVFIVIGAAWVFGLGHTHGA-----WI 196

Query: 215 DPGAFTSFKGFCAVFVVAA-----FSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAI 269
           +  A   F  F  + V AA     F+ GG E+  +AAAES NP KS+   ++ V  R+  
Sbjct: 197 NLTAAKGFLPFGTMSVFAAVPTVIFAVGGAEIATIAAAESDNPAKSVAAMTRSVILRVIT 256

Query: 270 FYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSV 329
           FY+ ++F++  I+P             T  SPFV A++   +     IMNA++ VAVLS 
Sbjct: 257 FYVGSMFLIACIVPWTT--------IVTGHSPFVAALETMRVPGSADIMNAIVLVAVLSA 308

Query: 330 ANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIF 389
            NS  + S+R +  +A R  AP     +     P   V+L    G +A I A      +F
Sbjct: 309 LNSGLYVSSRILFRLAGRGDAPRALLRLTPSRVPRLAVLLSSVVGYIAIIAAIVSPQGVF 368

Query: 390 GWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGL-------IPYKTPFGVAGSYLG 442
            +L+  +G   LFV+ +  LA IR+R  + A+G+   L       + Y     + G  L 
Sbjct: 369 LFLVNASGAVMLFVYLATALAQIRIRRRLAAKGVQPELPMWLFPWLSYAVVAAIVGVLLA 428

Query: 443 LGLN------ILALIASFYTA 457
           +G++      ++A IAS   A
Sbjct: 429 MGMDAELRPQLMASIASLAVA 449


Lambda     K      H
   0.327    0.142    0.442 

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: 607
Number of extensions: 36
Number of successful extensions: 6
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: 536
Length of database: 484
Length adjustment: 34
Effective length of query: 502
Effective length of database: 450
Effective search space:   225900
Effective search space used:   225900
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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