GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocE in Burkholderia phytofirmans PsJN

Align Amino-acid permease RocE (characterized)
to candidate BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein

Query= SwissProt::P39137
         (467 letters)



>FitnessBrowser__BFirm:BPHYT_RS21680
          Length = 476

 Score =  292 bits (748), Expect = 1e-83
 Identities = 153/454 (33%), Positives = 256/454 (56%), Gaps = 10/454 (2%)

Query: 10  QLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGE 69
           +L+  +K RH+ MI+LGGVIG G F+G+G  + QAGP  AVLS+L+ G ++ L M  LGE
Sbjct: 9   ELKAGLKQRHMTMIALGGVIGAGLFVGSGVVVQQAGP-AAVLSFLITGALVVLVMRMLGE 67

Query: 70  LAVAFPVSGSFQTYAT------KFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWF 123
           +A A P  GSF  YA       +      GF  GW+YW  W +  A+E ++  +L+Q W 
Sbjct: 68  MACAMPAVGSFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGAKLVQFWL 127

Query: 124 PHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLK 183
           P +  W   LV    +   N ++  ++ E EFWF+ IK+  I++F+ LGG  + GL    
Sbjct: 128 PDVPAWAISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYVLGLWPAA 187

Query: 184 GGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIK 243
               A   T     GL P GI  +L   +     + G E++ +AA E+++P K + ++  
Sbjct: 188 KHVTAVLPTLLSHGGLMPKGIGPVLSGAVAATGFYFGAEIVTIAAAEAQEPAKAVAKATN 247

Query: 244 QTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSV 303
             + R LVF+V SI+++  ++PW    +  +P+V+  + +GIP AA +MN ++L A+LS 
Sbjct: 248 SVITRVLVFYVGSILLVVALVPWNSPKMA-TPYVSALDAMGIPAAASVMNAIVLTAVLSA 306

Query: 304 ANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVY 363
            NSGLYA++R+++A+   G A  AL K N+RGVP+ ++++       S++  +   +TV+
Sbjct: 307 LNSGLYAASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFGYASVVMSYVSPDTVF 366

Query: 364 MVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVV 423
             L++  G  A   ++ I++SQ+  R +  R+    E L+ +   YP L  + +     +
Sbjct: 367 AFLVNSYGTVAIFVYVLIAISQLKLRARIERDAP--EKLRVRMWCYPYLTWVAIIGMVGI 424

Query: 424 LISLAFDPEQRIALYCGVPFMIICYIIYHVVIKK 457
           L+++AF PEQR  L+ GV  + +  + Y + ++K
Sbjct: 425 LVAMAFIPEQRQPLWFGVASLGVLLLAYLLRVRK 458


Lambda     K      H
   0.329    0.142    0.438 

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: 515
Number of extensions: 28
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: 467
Length of database: 476
Length adjustment: 33
Effective length of query: 434
Effective length of database: 443
Effective search space:   192262
Effective search space used:   192262
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 (21.8 bits)
S2: 51 (24.3 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