GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1639
          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:

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