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

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources