GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Pseudomonas simiae WCS417

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate GFF1065 PS417_05405 D-alanine/D-serine/glycine permease

Query= TCDB::Q2VQZ4
         (536 letters)



>FitnessBrowser__WCS417:GFF1065
          Length = 472

 Score =  228 bits (580), Expect = 5e-64
 Identities = 140/441 (31%), Positives = 223/441 (50%), Gaps = 16/441 (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  IMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVW 128

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

Query: 205 QGY-IGVKYWRDPGAF--TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASK 261
            G  +G+      G F     +G      +  F++ G EM+GL A E+ NP+K+IP A  
Sbjct: 189 DGVALGISNLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIG 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    S G P   ++L I   LL  +  
Sbjct: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLN 360

Query: 382 APQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGM---KAQGINLGLIPYKTPFGVAG 438
                ++F W+ ++   G ++ W  I LA ++ R  +   +  G+   +  Y     +A 
Sbjct: 361 YLVPEKVFVWVTSIATFGAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLAL 420

Query: 439 SYLGLGLNILALIASFYTALF 459
           ++L L + ++A       AL+
Sbjct: 421 AFLLLVVGLMAYFPDTRIALY 441


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: 674
Number of extensions: 38
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: 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.

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