GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ansP in Burkholderia phytofirmans PsJN

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein

Query= TCDB::P40812
         (497 letters)



>FitnessBrowser__BFirm:BPHYT_RS21680
          Length = 476

 Score =  273 bits (697), Expect = 1e-77
 Identities = 157/447 (35%), Positives = 248/447 (55%), Gaps = 14/447 (3%)

Query: 33  RQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLHRPSSG 92
           R + MIA+GG IG GLF+G+G  +Q AGPA  L +LI G     ++R LGE+    P+ G
Sbjct: 17  RHMTMIALGGVIGAGLFVGSGVVVQQAGPAAVLSFLITGALVVLVMRMLGEMACAMPAVG 76

Query: 93  SFVSYAREFLGEK------AAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWV 146
           SF  YAR   G K      A ++ GWMY+  W +   V+  A A  + +W    DVP W 
Sbjct: 77  SFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGAKLVQFW--LPDVPAWA 134

Query: 147 FALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLEGNATG-F 205
            +L  L  +   N++ V  + E EFWFA IKV AI++FL +G +++    P   + T   
Sbjct: 135 ISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYVLGLWPAAKHVTAVL 194

Query: 206 HLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIG 265
             +  +GG  P G+ P L         +   E+V  AA E ++P K V KA NSVI R+ 
Sbjct: 195 PTLLSHGGLMPKGIGPVLSGAVAATGFYFGAEIVTIAAAEAQEPAKAVAKATNSVITRVL 254

Query: 266 LFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYC 325
           +FYVGS++L+V L+PWN+ +   +P+V+    +G+P   S+MN +VLTA LS+LNSGLY 
Sbjct: 255 VFYVGSILLVVALVPWNSPKMA-TPYVSALDAMGIPAAASVMNAIVLTAVLSALNSGLYA 313

Query: 326 TGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFA 385
             R++ +++  G AP  +AK++R+ VP   IL   V     V ++Y+ P  VF  ++N  
Sbjct: 314 ASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFGYASVVMSYVSPDTVFAFLVN-- 371

Query: 386 SLGIIASWAFIMVC--QMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFD 443
           S G +A + ++++   Q++LR  I+      +  ++   P+ +W+ ++ ++ +LV MAF 
Sbjct: 372 SYGTVAIFVYVLIAISQLKLRARIERDAPEKLRVRMWCYPYLTWVAIIGMVGILVAMAFI 431

Query: 444 YPNGTYTIASLPLIAILLVAGWFGVRR 470
                     +  + +LL+A    VR+
Sbjct: 432 PEQRQPLWFGVASLGVLLLAYLLRVRK 458


Lambda     K      H
   0.328    0.140    0.434 

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: 690
Number of extensions: 41
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: 497
Length of database: 476
Length adjustment: 34
Effective length of query: 463
Effective length of database: 442
Effective search space:   204646
Effective search space used:   204646
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 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