GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Bap2 in Pseudomonas fluorescens FW300-N2E2

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate Pf6N2E2_5459 D-serine/D-alanine/glycine transporter

Query= TCDB::Q2VQZ4
         (536 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5459
           D-serine/D-alanine/glycine transporter
          Length = 473

 Score =  234 bits (596), Expect = 7e-66
 Identities = 140/429 (32%), Positives = 218/429 (50%), Gaps = 15/429 (3%)

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

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

Query: 145 REDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGD 204
             D+   +W    LV +  I +  V+ +GE EF  ++IKI   +  +I G+ I   G G+
Sbjct: 129 FPDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGN 188

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

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

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

Query: 382 APQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVAGSYL 441
                ++F W+ ++   G ++ W  I LA ++ R  + A       + Y+       SYL
Sbjct: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSAS--ERAALKYRMWLYPVSSYL 418

Query: 442 GLGLNILAL 450
            L   +L +
Sbjct: 419 ALAFLVLVV 427


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: 657
Number of extensions: 34
Number of successful extensions: 5
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: 473
Length adjustment: 34
Effective length of query: 502
Effective length of database: 439
Effective search space:   220378
Effective search space used:   220378
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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