GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Bap2 in Paraburkholderia bryophila 376MFSha3.1

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family

Query= TCDB::Q2VQZ4
         (536 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04042 H281DRAFT_04042
           aromatic amino acid:proton symporter, AAT family
          Length = 506

 Score =  223 bits (568), Expect = 1e-62
 Identities = 142/426 (33%), Positives = 211/426 (49%), Gaps = 12/426 (2%)

Query: 28  VKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCL 87
           ++  GLK+ LKNRH+Q+IA+GGAIG GLF+GS   LQ  GP+ +++GY I G++      
Sbjct: 50  LQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPS-MILGYAIGGVIAFMIMR 108

Query: 88  ALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWRED 147
            L EM    PV G+F  +  ++     GF  GW Y + ++ V   EL A    + +W   
Sbjct: 109 QLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPG 168

Query: 148 INMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGY 207
           +   V   V    +  I +  V+ YGE EF  +IIK+ A +G I+ G  +   G G    
Sbjct: 169 VPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQA 228

Query: 208 IGVKYWRDPGAFT-SFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWR 266
                W   G F   F G   +  V  FSFGG E++G+ AAE+  P+KSIP A  QV +R
Sbjct: 229 SISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYR 288

Query: 267 IAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAV 326
           I IFYI +L ++  + P N+   + A G     SPFV+     G  +  +++N V+  A 
Sbjct: 289 ILIFYICSLAVLLSLYPWNE---VAAGG-----SPFVMIFSQIGSTLTANVLNVVVLTAA 340

Query: 327 LSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGM 386
           LSV NS  + ++R +  +AE+  AP     +D +G P   + L         I       
Sbjct: 341 LSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPA 400

Query: 387 EIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFG--VAGSYLGLG 444
           E  G L+AL     +  W  I L H++ R  M A G  L    +  P    +  +++ L 
Sbjct: 401 EALGLLMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALI 460

Query: 445 LNILAL 450
           L ILA+
Sbjct: 461 LVILAM 466


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: 615
Number of extensions: 27
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: 506
Length adjustment: 35
Effective length of query: 501
Effective length of database: 471
Effective search space:   235971
Effective search space used:   235971
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 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