GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaK in Cupriavidus basilensis 4G11

Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate RR42_RS30500 RR42_RS30500 4-hydroxybenzoate transporter

Query= SwissProt::Q51955
         (448 letters)



>FitnessBrowser__Cup4G11:RR42_RS30500
          Length = 447

 Score =  392 bits (1007), Expect = e-113
 Identities = 204/423 (48%), Positives = 279/423 (65%), Gaps = 4/423 (0%)

Query: 11  SLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVM 70
           S+ +  FI++QPLS +Q  +V+LCFLIV +DG DTAA+GFIAPA+  EW +  A L P+ 
Sbjct: 6   SIGITEFIDRQPLSAFQVTIVVLCFLIVAIDGFDTAAIGFIAPAIRAEWQLTPAHLAPLF 65

Query: 71  SAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLG 130
            A L G++ GA   GPLADRFGRK VL+  VL FG  SLA A++ ++  L+ LRFLTGLG
Sbjct: 66  GAGLTGLMAGAFLFGPLADRFGRKNVLLFCVLFFGVASLACAFSGSLWGLVALRFLTGLG 125

Query: 131 LGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGG 190
           LG  MPN  TL SEY P + +S LVT+MFCGF +G A GG  SA +I  +GW ++L++GG
Sbjct: 126 LGGAMPNTITLTSEYCPAKRRSFLVTTMFCGFTIGSALGGLASASLIEEHGWRAVLLLGG 185

Query: 191 VLPLLLALVLMVW-LPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAA 249
           VLPLLL L L+VW LPES R+LV+  +  +K+   L  IAP+     GS  V +++A   
Sbjct: 186 VLPLLL-LPLLVWKLPESVRYLVLSGKHPEKVAAILERIAPRERVAPGSIVVADKRAPG- 243

Query: 250 RSVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQF 309
            S  A +F      GT+LLWLT+FM L+++YLL+SWLPTL+R +G S++ AA +  +FQ 
Sbjct: 244 -SPVAHLFKPELVRGTLLLWLTFFMSLLVIYLLSSWLPTLLRATGISLKTAALVTMMFQV 302

Query: 310 GGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGA 369
           GG L A+ +GW MDR NPH V+   Y LAGVF  A+G       +    V  AG C++G+
Sbjct: 303 GGTLGAIVLGWLMDRANPHYVLAASYALAGVFITAIGSLTTAPWLAGVAVFAAGFCISGS 362

Query: 370 QSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPA 429
           Q    +L+A +YPT  RATGVSW  G+GR G+++G+  G T+L +G     +   + +PA
Sbjct: 363 QVGANALSAAYYPTDCRATGVSWANGVGRMGSVVGSVGGGTMLSMGLTMPALFLMVGIPA 422

Query: 430 ALA 432
            +A
Sbjct: 423 VMA 425


Lambda     K      H
   0.325    0.140    0.424 

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: 604
Number of extensions: 35
Number of successful extensions: 3
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: 448
Length of database: 447
Length adjustment: 33
Effective length of query: 415
Effective length of database: 414
Effective search space:   171810
Effective search space used:   171810
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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