GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Bap2 in Dyella japonica UNC79MFTsu3.2

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily

Query= TCDB::Q2VQZ4
         (536 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2630 N515DRAFT_2630 amino
           acid/polyamine/organocation transporter, APC superfamily
          Length = 454

 Score =  228 bits (581), Expect = 4e-64
 Identities = 142/429 (33%), Positives = 219/429 (51%), Gaps = 24/429 (5%)

Query: 30  NGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLAL 89
           N  L++ L+ RH++++A+G AIG GLF+GS  A++  GPA +L+ YL+ G+ +     AL
Sbjct: 4   NDSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPA-ILLSYLLGGVAIFIIMRAL 62

Query: 90  AEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDIN 149
            EMAV  PV G+F  Y   ++ P  G+  GW Y   WL     E+ A  + +  W  D+ 
Sbjct: 63  GEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVP 122

Query: 150 MAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGY-I 208
             +W    LV +  + +  V+ YGE EF  ++IK+   V  I+ G  +   G+G+QG   
Sbjct: 123 QWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGVPT 182

Query: 209 GVKYWRDPGAF--TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWR 266
           G+      G F     KG      +  F++ G EM+GL A E+ NP+KSIP A   VFWR
Sbjct: 183 GISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVFWR 242

Query: 267 IAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAV 326
           I IFY+  LF++  I P N+          T  SPFV+  +  GIK    I+N V+  A 
Sbjct: 243 ILIFYVGALFVIMSIYPWNE--------LGTHGSPFVMTFERLGIKSAAGIINFVVLTAA 294

Query: 327 LSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIA---FG-LLAYIGAA 382
           LS  N   + + R +  +A++  AP  F      G P   V++ +    FG LL Y+  A
Sbjct: 295 LSSCNGGIYSTGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPA 354

Query: 383 PQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGM-KAQGINLGLIPYKTPFGVAGSYL 441
               ++F W+ +    G ++ WG + +  ++ R G+ +AQ   L    ++ PF    SYL
Sbjct: 355 ----KVFVWVTSAATFGAIWTWGIVLITQMKYRRGLSEAQRSQL---VFRMPFFPYASYL 407

Query: 442 GLGLNILAL 450
            L   +L +
Sbjct: 408 ALAFLVLVV 416


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: 638
Number of extensions: 36
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: 454
Length adjustment: 34
Effective length of query: 502
Effective length of database: 420
Effective search space:   210840
Effective search space used:   210840
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, 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