GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Pseudomonas putida KT2440

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate PP_1059 PP_1059 Uncharacterized amino acid permease YtnA

Query= TCDB::Q2VQZ4
         (536 letters)



>FitnessBrowser__Putida:PP_1059
          Length = 472

 Score =  230 bits (587), Expect = 8e-65
 Identities = 141/429 (32%), Positives = 219/429 (51%), Gaps = 18/429 (4%)

Query: 26  GEVKNGG-LKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLC 84
           G+   GG LK++L  RH++++A+G  IG GLF+GS  A++  GPA +++ Y+I G+ +L 
Sbjct: 10  GQATEGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPA-IMLSYIIGGLAILV 68

Query: 85  TCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFW 144
              AL EMAV  PV G+F  Y   ++ P  GF  GW Y   WL     E+ A +I +  W
Sbjct: 69  IMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAIYMGIW 128

Query: 145 REDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGD 204
             D+   +W    L  +  + +  V+ +GE EF  ++IKI   +  ++ GI I   G G+
Sbjct: 129 FPDVPRWIWALAALGSMGAVNLVAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGN 188

Query: 205 QGY-IGVKYWRDPGAF--TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASK 261
            G  +G+      G F      G      +  F++ G EM+GL A E+ NP+K+IP A  
Sbjct: 189 DGVAVGISNLWSNGGFMPNGVTGVLMSLQMVMFAYLGVEMIGLTAGEARNPQKTIPQAIG 248

Query: 262 QVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAV 321
            VFWRI +FY+  LF++  I P N+   +G+ G     SPFV+  +  GIK    I+N V
Sbjct: 249 SVFWRILLFYVGALFVILSIYPWNE---IGSQG-----SPFVMTFERLGIKTAAGIINFV 300

Query: 322 ITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGA 381
           +  A LS  N   F + R + ++A+   AP  F      G P   ++L I   LL  +  
Sbjct: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAAFARTSKNGVPRNALLLSIGALLLGVLAN 360

Query: 382 APQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGM-----KAQGINLGLIPYKTPFGV 436
                ++F W+ ++   G ++ W  I LA ++ RAG+     KA    + L P  +   +
Sbjct: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRAGLTTAERKALKYRMWLWPLSSYLAL 420

Query: 437 AGSYLGLGL 445
           A   L +GL
Sbjct: 421 AFLVLVVGL 429


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: 645
Number of extensions: 39
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: 472
Length adjustment: 34
Effective length of query: 502
Effective length of database: 438
Effective search space:   219876
Effective search space used:   219876
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