GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Paraburkholderia phymatum STM815

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_012400013.1 BPHY_RS03010 amino acid permease

Query= TCDB::Q2VQZ4
         (536 letters)



>NCBI__GCF_000020045.1:WP_012400013.1
          Length = 466

 Score =  224 bits (570), Expect = 7e-63
 Identities = 144/425 (33%), Positives = 211/425 (49%), Gaps = 12/425 (2%)

Query: 29  KNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLA 88
           ++ GLK+ LKNRH+Q+IA+GGAIG GLF+GS G L+  GP+ +++GY I G +       
Sbjct: 10  QHDGLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAIGGFIAFLIMRQ 68

Query: 89  LAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDI 148
           L EM    PV G+F  +  ++     GF  GW Y + ++ V   EL A    + FW   +
Sbjct: 69  LGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHFWWPGV 128

Query: 149 NMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYI 208
              +   V  VV+  I +  V+ YGE EF  +I+K+ A +G I+ G  +   G G     
Sbjct: 129 PAWLSALVCFVVINAINLANVKAYGETEFWFAIVKVVAVMGMIVFGGYLLLSGHGGPQAS 188

Query: 209 GVKYWRDPGAFT-SFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRI 267
               W   G F     G   +  V  FSFGG E++G+ AAE+ +P+KSIP A  QV +RI
Sbjct: 189 ISNLWSQGGFFPHGVHGLFMMLAVIMFSFGGLELIGITAAEADDPQKSIPKAVNQVIYRI 248

Query: 268 AIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVL 327
            IFYI +L ++  + P N      A G     SPFV+     G  +  +++N V+  A L
Sbjct: 249 LIFYICSLIVLLSLYPWNQV----AEG----GSPFVMIFSQIGAGLTANVLNVVVLTAAL 300

Query: 328 SVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGME 387
           SV NS  + ++R +  +AE+  AP     +D +G P   + L         I       +
Sbjct: 301 SVYNSGVYANSRMLYGLAEQGNAPRALLEVDRRGVPYMAIGLSAVATFACVIINYLMPAK 360

Query: 388 IFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFG--VAGSYLGLGL 445
               L+AL     +  W  I L H++ R  M AQG  L       P G  V  +++ L L
Sbjct: 361 ALDVLMALVVAALVLNWSLISLTHLKSRRAMLAQGDTLVFKSLWFPLGNWVCLAFMALIL 420

Query: 446 NILAL 450
            ILAL
Sbjct: 421 VILAL 425


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: 585
Number of extensions: 29
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: 466
Length adjustment: 34
Effective length of query: 502
Effective length of database: 432
Effective search space:   216864
Effective search space used:   216864
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 Apr 09 2024. 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