GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaK in Magnetospirillum magneticum AMB-1

Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate WP_011386821.1 AMB_RS22655 MFS transporter

Query= SwissProt::Q51955
         (448 letters)



>NCBI__GCF_000009985.1:WP_011386821.1
          Length = 453

 Score =  265 bits (676), Expect = 3e-75
 Identities = 147/431 (34%), Positives = 230/431 (53%), Gaps = 6/431 (1%)

Query: 12  LDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMS 71
           ++    I++    ++ W V+    LI+  DG D    G + P L +EW +D    G + S
Sbjct: 4   VNAHKLIDEAKFGKFHWNVLFWTALIIIFDGYDLVIYGVVLPVLMKEWHLDPIQAGTLGS 63

Query: 72  AALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGL 131
            AL GM+FGAL  G L+DRFGRK V+   V++F  F++ + +  +  +  + RF+ GLG+
Sbjct: 64  YALFGMMFGALTFGSLSDRFGRKPVIAVCVVLFSLFTVLNGFVRDTTEFAICRFVAGLGI 123

Query: 132 GAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGGV 191
           G  MPNA  L++EY P+RL+S LV  MF G+++G      +   +IP YGW ++  +  V
Sbjct: 124 GGVMPNAVALMTEYAPKRLRSTLVAVMFSGYSVGGMLSAGLGMTLIPVYGWSAVFFVAAV 183

Query: 192 LPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAARS 251
            PLLL  V++  LPES  FL+   R  +   K L+ + P    + G   +        ++
Sbjct: 184 -PLLLLPVILFLLPESIGFLIKAGRTAEAADK-LARLEPSYKPQPGD-EISFPTGATGQA 240

Query: 252 VFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFGG 311
               +F+G  G+ T++ W+ +FM L++VY L SWLP LM ++G  +  +     +  FG 
Sbjct: 241 SLPALFAGGRGVSTVMFWIAFFMCLLMVYALGSWLPKLMNNAGYGLGSSLSFLLVLNFGA 300

Query: 312 VLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGAQS 371
           +  AVG G   DR N  +V+  F+++A +    +G     + VL  LV +AG    G Q 
Sbjct: 301 IFGAVGGGHIADRMNLKRVLVAFFVIAAISISLLGVKSPTL-VLYVLVAVAGATTIGTQI 359

Query: 372 AMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPAAL 431
            + +  A+FYP   R+TG+ W  G+GR GAILG   G TLL       Q   A  VP  +
Sbjct: 360 LLYAYVAQFYPMAIRSTGIGWASGVGRSGAILGPVLGGTLLAWKLPLMQNFMAFAVPGVI 419

Query: 432 ATV--GVIVKG 440
           A +   ++V+G
Sbjct: 420 AAIAMSLVVRG 430


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: 623
Number of extensions: 33
Number of successful extensions: 7
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: 453
Length adjustment: 33
Effective length of query: 415
Effective length of database: 420
Effective search space:   174300
Effective search space used:   174300
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