GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Cupriavidus basilensis 4G11

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate RR42_RS11100 RR42_RS11100 gamma-aminobutyrate permease

Query= TCDB::Q2VQZ4
         (536 letters)



>FitnessBrowser__Cup4G11:RR42_RS11100
          Length = 509

 Score =  284 bits (726), Expect = 6e-81
 Identities = 154/473 (32%), Positives = 251/473 (53%), Gaps = 11/473 (2%)

Query: 28  VKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCL 87
           V++  L++ LK RH+ MIAIGGA+G GLFV SG ++ + GP   L+ Y +IG+M+ C   
Sbjct: 13  VEHDDLQRKLKARHLTMIAIGGAVGTGLFVASGASISQAGPGGALLMYCLIGLMVYCLMT 72

Query: 88  ALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWRED 147
           +L E+AV  PV G+F TY   +V+  +GFA+GW Y  +    +  EL AA + +++W   
Sbjct: 73  SLGELAVHMPVAGSFVTYSALYVEEGFGFALGWSYWFSLAVTIAVELAAAQLVMQYWFPH 132

Query: 148 INMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCG---GVGD 204
           ++  VW + FL+++ G+  F VRG+GE E+  ++IK+   + F+  G+++  G   G   
Sbjct: 133 VSGVVWSAGFLLLMFGLNAFSVRGFGEAEYWFALIKVATILIFLAAGLMMIFGIMQGGPQ 192

Query: 205 QGYIGVKYWRDP--GAFTSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQ 262
            G+        P  G   +  G   V ++A FSF GTE VG+AA E+A+P ++IP A +Q
Sbjct: 193 SGWHNFTLGDAPFVGGIPAMFG---VAMIAGFSFQGTETVGVAAGEAADPARTIPRAIRQ 249

Query: 263 VFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVI 322
            FWRI +FY+L + I+G+++P  DP L+     +   SPF L  + AG+     +MNAV+
Sbjct: 250 TFWRILLFYVLAILIIGVLIPYTDPSLLRNDVTDIGVSPFALVFRHAGLAFAAGLMNAVV 309

Query: 323 TVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAA 382
             A+LS   S  + STR +  +A    AP     + + G P   +    A G L ++ + 
Sbjct: 310 LTALLSAGTSSMYASTRILYGLAVSGRAPRALARLSANGVPYVALFATTAVGALCFLSSL 369

Query: 383 PQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVAGSYLG 442
                ++ WLL  +G+     W  I ++H R R G+  QG     + Y++P    G    
Sbjct: 370 FGDKAVYLWLLNTSGMTGFIAWLGIAISHYRFRRGLVHQGYKPSDLAYRSPLYPFGPLFA 429

Query: 443 LGLNILALIASFYTALFPASGASPTAEAFFSSYLAFFSVTLLYLGYKACTRKR 495
           + L ++ ++   Y A     G          +Y+      +L+LGY+   + R
Sbjct: 430 IVLCVVIVLGQNYQAFSDVRG---RWLEIVGTYIGVPLFLVLWLGYRLVKKTR 479


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: 667
Number of extensions: 34
Number of successful extensions: 2
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: 509
Length adjustment: 35
Effective length of query: 501
Effective length of database: 474
Effective search space:   237474
Effective search space used:   237474
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