GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Pseudomonas stutzeri RCH2

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases

Query= TCDB::Q2VQZ4
         (536 letters)



>FitnessBrowser__psRCH2:GFF1660
          Length = 464

 Score =  224 bits (570), Expect = 7e-63
 Identities = 141/398 (35%), Positives = 211/398 (53%), Gaps = 9/398 (2%)

Query: 31  GGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALA 90
           G L++ LKNRH+Q+IA+GGAIG GLF+GS G L+  GP+ +++GY I G +       L 
Sbjct: 9   GSLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPS-MILGYAIGGFIAFLIMRQLG 67

Query: 91  EMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINM 150
           EM V  PV G+F  +  ++     GF  GW Y + ++ V   EL A    ++FW  ++  
Sbjct: 68  EMIVEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPT 127

Query: 151 AVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIGV 210
               + F V++  I +  V+ +GE EF  +I+K+ A VG I+LG+ +   G G +     
Sbjct: 128 WATAAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVSGKGGEQASIS 187

Query: 211 KYWRDPGAF-TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAI 269
             W   G F   F G      +  FSFGG E+VG+ AAE+A P+  IP A  QV +RI I
Sbjct: 188 NLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQVVYRILI 247

Query: 270 FYILNLFIVGLILPANDPRL-MGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLS 328
           FYI  L ++  + P +   L +GA+G     SPFV      G      ++N V+  A LS
Sbjct: 248 FYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVVLTAALS 307

Query: 329 VANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLL--AYIGAAPQG- 385
           V NS  + ++R +  +AE+  AP     I+S+G P+  V +     LL  A     PQG 
Sbjct: 308 VYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNYLFPQGA 367

Query: 386 MEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGI 423
           +E+   L++L     +  W  I LAH++ R  M+ QG+
Sbjct: 368 LEL---LMSLAVAALVINWAMISLAHLKFRRAMQQQGV 402


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: 627
Number of extensions: 33
Number of successful extensions: 6
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.

Links

Downloads

Related tools

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