GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Burkholderia phytofirmans PsJN

Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease

Query= uniprot:A0A0C4YP23
         (465 letters)



>FitnessBrowser__BFirm:BPHYT_RS07280
          Length = 466

 Score =  313 bits (801), Expect = 1e-89
 Identities = 162/449 (36%), Positives = 257/449 (57%), Gaps = 2/449 (0%)

Query: 13  LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMV 72
           L+RGL    + +IA+GGAIGTGLFLG    I  AGPSVL+ YA+  +IA  +M  L EM 
Sbjct: 18  LQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGPSVLVSYAIGALIALLLMGCLAEMT 77

Query: 73  VDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWAS 132
           V  P +GSF  +A  Y   +AGF+  + YW   +     E++A+ +Y++YW+P +P W  
Sbjct: 78  VAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTAIAVYMKYWFPAVPGWYW 137

Query: 133 ALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGTAGPQASVSNLW 192
            +GF   +  IN  SVK FG +E+ FS++K++AIVG I+ G Y++    A      +N  
Sbjct: 138 IVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAYVVFGAPADSTIGFANYT 197

Query: 193 QHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRILIFYV 252
            HGGFFP G+ G+ +A+ V +FS+  +E++ + A EA +P+K I +A    ++R++ FY+
Sbjct: 198 SHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKAITRAFRATMFRLVFFYL 257

Query: 253 GALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYNSGVYCNSRM 312
             L ++L++ PW    T  SPFV +  A +    A V+N V+L AALS  NS +Y  +RM
Sbjct: 258 LTLALMLAIVPWNAAGTDESPFVRVMAATHVPGAAGVINFVILVAALSAMNSQLYITTRM 317

Query: 313 LFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFELLMGLVVSAL 372
           +F L++ G AP+ L  +N +G+P+AAL +S +  A   V+N   P  +F L+M + +   
Sbjct: 318 MFSLSRAGYAPRKLGALNGKGVPVAALWLSTIGIALATVLNVVYPDASFVLMMSVSMFGA 377

Query: 373 IINWAMISIIHLKFRRDKRAAGQETRFKSLGYPLTNYVCLAFLAGILYVMYLTPGLRISV 432
           +  W MI + H  FR   R  G    F+  GYP T+ +    +   L   + T   R+++
Sbjct: 378 MFTWLMIFVTHFFFRH--RHQGAPLAFRMWGYPGTSALGAGLMVSALVTTWFTREFRMTL 435

Query: 433 YLIPAWLAVLGLSYRLRQKQKRAEPALPE 461
            +   ++  L + Y +  +++  E A  E
Sbjct: 436 VIGVPFIVSLLVVYFVWYRKRAVEGAAAE 464


Lambda     K      H
   0.326    0.140    0.426 

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: 599
Number of extensions: 25
Number of successful extensions: 3
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: 465
Length of database: 466
Length adjustment: 33
Effective length of query: 432
Effective length of database: 433
Effective search space:   187056
Effective search space used:   187056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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