GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Bap2 in Burkholderia phytofirmans PsJN

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter

Query= TCDB::Q2VQZ4
         (536 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS15500 BPHYT_RS15500 aromatic
           amino acid transporter
          Length = 461

 Score =  226 bits (575), Expect = 2e-63
 Identities = 144/422 (34%), Positives = 210/422 (49%), Gaps = 12/422 (2%)

Query: 32  GLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAE 91
           GLK+ LKNRH+Q+IA+GGAIG GLF+GS   LQ  GP+ +++GY I GI+       L E
Sbjct: 9   GLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPS-MILGYAIGGIIAFMIMRQLGE 67

Query: 92  MAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMA 151
           M    PV G+F  +  ++     GF  GW Y + ++ V   EL A    I +W   +   
Sbjct: 68  MVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWWPGVPTW 127

Query: 152 VWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIGVK 211
           V   V   ++  I +  V+ YGE EF  +IIK+ A +G I+ G  +   G G        
Sbjct: 128 VSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHGGPQASITN 187

Query: 212 YWRDPGAFT-SFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAIF 270
            W   G F   F G   +  V  FSFGG E++G+ AAE+  P+KSIP A  QV +RI IF
Sbjct: 188 LWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQVIYRILIF 247

Query: 271 YILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSVA 330
           YI +L ++  + P N+   + A G     SPFV+     G  +  +++N V+  A LSV 
Sbjct: 248 YICSLTVLLSLYPWNE---VAAGG-----SPFVMIFSQIGSTLTANVLNVVVLTAALSVY 299

Query: 331 NSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIFG 390
           NS  + ++R +  +AE+  AP     +D +G P   + L         I       E  G
Sbjct: 300 NSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALG 359

Query: 391 WLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFG--VAGSYLGLGLNIL 448
            L+AL     +  W  I L H++ R  M A G  L    +  P    +  +++ L L IL
Sbjct: 360 LLMALVVAALVLNWALISLTHLKSRKAMVAAGETLVFKSFWFPVSNWICLAFMALILVIL 419

Query: 449 AL 450
           A+
Sbjct: 420 AM 421


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: 582
Number of extensions: 26
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: 461
Length adjustment: 34
Effective length of query: 502
Effective length of database: 427
Effective search space:   214354
Effective search space used:   214354
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