GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_2630
          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 (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