GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaK in Herbaspirillum seropedicae SmR1

Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate HSERO_RS05600 HSERO_RS05600 4-hydroxybenzoate transporter

Query= SwissProt::Q51955
         (448 letters)



>FitnessBrowser__HerbieS:HSERO_RS05600
          Length = 447

 Score =  339 bits (870), Expect = 9e-98
 Identities = 170/426 (39%), Positives = 260/426 (61%), Gaps = 1/426 (0%)

Query: 11  SLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVM 70
           ++ V   + Q     +Q+ ++LLC L + +DG D  AMG++APA+  +WG+ +ASLGPV 
Sbjct: 11  TVHVDQVVEQGRFGAFQFGLLLLCGLCLIIDGFDVQAMGYVAPAIIADWGVSKASLGPVF 70

Query: 71  SAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLG 130
            A L GM+ G+L   P+ DR+GR+ VL+ + L F    LA+   T +DQLLVLRF+TG G
Sbjct: 71  GAGLFGMLLGSLVLTPVGDRYGRRPVLILSTLFFALCMLATPMVTTLDQLLVLRFITGFG 130

Query: 131 LGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGG 190
           LG+ MPNA  L+ E++P   +   +  + CGF +G A GGF+SA +IPAYGWH++  +GG
Sbjct: 131 LGSIMPNAMALVGEFSPSSSRVTRMMLVSCGFTVGAAAGGFVSAALIPAYGWHAVFWVGG 190

Query: 191 VLPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAAR 250
            +PL+L L ++VWLPES +FLV+  R   ++ + L  + P +V +  +  V ++      
Sbjct: 191 AVPLVLGLAMLVWLPESIQFLVLHRRPRTQVARWLRKLDPNIVIDDKTEVVVKETKAEGM 250

Query: 251 SVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFG 310
            V A+   G  G+ T+LLWL  FM L+ +Y L++WLPTL+RD+G S   A  IG   Q G
Sbjct: 251 PVAALFRDGRAGV-TVLLWLISFMNLINLYFLSNWLPTLIRDAGYSTSMAVLIGTSLQVG 309

Query: 311 GVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGAQ 370
           GV+  + +G  + R+   +V+G  +LLA +    +G+      +L   V++AG C+ G Q
Sbjct: 310 GVIGTLSLGRFIQRFGFTRVLGSCFLLACLSIALIGKLATVPALLFVAVIVAGFCIVGGQ 369

Query: 371 SAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPAA 430
            A+ +LA  FYPT  R+TG+ W LGIGR G+++G   G  L+ L W    +  A  VPA 
Sbjct: 370 PAVNALAGTFYPTTLRSTGIGWALGIGRIGSVVGPVIGGQLIALQWTNASLFLAAAVPAL 429

Query: 431 LATVGV 436
           ++ + +
Sbjct: 430 ISALTI 435


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: 568
Number of extensions: 27
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