GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Bap2 in Pseudomonas fluorescens FW300-N1B4

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate Pf1N1B4_1639 transport permease protein of gamma-aminobutyrate

Query= TCDB::Q2VQZ4
         (536 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1639 transport permease
           protein of gamma-aminobutyrate
          Length = 464

 Score =  228 bits (581), Expect = 4e-64
 Identities = 139/402 (34%), Positives = 210/402 (52%), Gaps = 10/402 (2%)

Query: 23  VETGEVKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIML 82
           + + +  + GL+Q LK RH+ M++I G IGAGLFVGSG A+   GPA LL  Y   G ++
Sbjct: 1   MSSSQSSSNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLL-AYAAAGALV 59

Query: 83  LCTCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIR 142
           +     L EMAV  P  G+F TY  R +    GF +GW Y   W+ V+P E  AA+  + 
Sbjct: 60  VLVMRMLGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILH 119

Query: 143 FWREDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGV 202
            W  ++ +  +  V  ++L    +F V+ YGE EF  +++K+ A +GFI LGI+   G +
Sbjct: 120 AWFPNVAIWAFTLVITLLLTATNLFSVKNYGEFEFWFALVKVIAIIGFIGLGILAIFGFL 179

Query: 203 GDQGYIGVKYWRDPGAF--TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMAS 260
                 GV +  D   F            +   FSF GTE+V +AAAES NP + I  A+
Sbjct: 180 PTSQVSGVSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKAT 239

Query: 261 KQVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNA 320
             V WRI +FY++++FIV  ++P NDP L       T        ++  GI     I++ 
Sbjct: 240 NSVIWRIGLFYLVSIFIVVALVPWNDPILASVGSYQT-------VLERMGIPNAKLIVDI 292

Query: 321 VITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIG 380
           V+ VAV S  NS  + ++R + ++ +R  AP   +  +S G P + V+L  A   LA   
Sbjct: 293 VVLVAVTSCLNSALYTASRMMFSLGKRGDAPAVSQRTNSSGTPYWAVMLSTAAAFLAVFA 352

Query: 381 AAPQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQG 422
                  +F +LLA +G   L V+  I ++ +RMR    A+G
Sbjct: 353 NYVAPAAVFEFLLASSGAIALLVYLVIAISQLRMRKQRMARG 394


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: 574
Number of extensions: 28
Number of successful extensions: 4
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: 464
Length adjustment: 34
Effective length of query: 502
Effective length of database: 430
Effective search space:   215860
Effective search space used:   215860
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 preprint 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