GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Pseudarthrobacter sulfonivorans Ar51

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_058929813.1 AU252_RS05225 amino acid permease

Query= TCDB::Q2VQZ4
         (536 letters)



>NCBI__GCF_001484605.1:WP_058929813.1
          Length = 470

 Score =  217 bits (553), Expect = 7e-61
 Identities = 138/444 (31%), Positives = 224/444 (50%), Gaps = 31/444 (6%)

Query: 37  LKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAEMAVLY 96
           LK R + M+ +G AIGAGLF+GSG  +Q  GPA +LI YL+ G +++    AL EMA   
Sbjct: 16  LKPRQLTMMGLGSAIGAGLFIGSGAGIQAAGPA-VLISYLVAGTLIILVMWALGEMAAAN 74

Query: 97  PVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMAVWVSV 156
           P +GAF  Y  +   P  G  +GW + L  + V+  E + A+  +      + + +   V
Sbjct: 75  PDSGAFSVYTAKAYGPVAGATVGWLWWLQLVVVIAAEALGAAGLLSTIFPALPVWLMAFV 134

Query: 157 FLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCG---GVGDQGYIGVKYW 213
           F+VVL  + +  V+ +GE EF  +++K+ A VGF+++G  +  G   GV   G     + 
Sbjct: 135 FIVVLTAVNLTSVKNFGEFEFWFALLKVAAIVGFLLVGAALLFGWLPGVQSPGL--ANFT 192

Query: 214 RDPGAFTSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAIFYIL 273
            D  A   F G      V AF+FGGTE+V +AAAE+A P +S+  A + V WRI +FYI 
Sbjct: 193 GDGFAPDGFAGIATALFVVAFAFGGTEIVSVAAAETAEPARSVRTAVRTVLWRILVFYIG 252

Query: 274 NLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSVANSC 333
            +F++  ++P      +G++G     SPF   ++ AG+    + +  V   A+LS  N+ 
Sbjct: 253 AIFVIAAVVP------VGSAGLK---SPFAAVLEAAGMPGAATAITLVAVAALLSALNAN 303

Query: 334 TFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIFGWLL 393
            +G++R   ++A+R  AP     +     P+  V+  +AFG++  +       ++   LL
Sbjct: 304 LYGASRMAYSLADRGEAPRLLASVSKARVPVVAVLASVAFGVVTVVLELAFPEKVLPVLL 363

Query: 394 ALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGL----IPYKTPFGVAGSYLGLGLNILA 449
            + G   L VW S  LA + +R     +G  L L     P+ T FG            L 
Sbjct: 364 NIVGSTCLLVWTSALLAQLALRLRANREGTELPLRMPGFPWLTCFG------------LL 411

Query: 450 LIASFYTALFPASGASPTAEAFFS 473
           ++A+ +T  F    + P   + F+
Sbjct: 412 ILAAIFTVGFIGEDSRPQLLSTFA 435


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: 618
Number of extensions: 36
Number of successful extensions: 4
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: 470
Length adjustment: 34
Effective length of query: 502
Effective length of database: 436
Effective search space:   218872
Effective search space used:   218872
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.

Links

Downloads

Related tools

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