GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kgtP in Pseudomonas fluorescens FW300-N2E2

Align Alpha-ketoglutarate permease (characterized)
to candidate Pf6N2E2_1930 L-Proline/Glycine betaine transporter ProP

Query= SwissProt::P0AEX3
         (432 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1930
          Length = 456

 Score =  209 bits (533), Expect = 1e-58
 Identities = 141/424 (33%), Positives = 212/424 (50%), Gaps = 22/424 (5%)

Query: 12  LTSSDTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAA 71
           +T + T     ++   + GN  E +DF V+ F     +  FFP  + T  LL T  V+A 
Sbjct: 1   MTKTKTTSSRRSLAAGAIGNFGEIYDFAVFGFSIPILSVHFFPGSDRTAALLSTFAVYAV 60

Query: 72  GFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLLLAR 131
            F+ RP+GG +FG +AD+ GR + M ++V +M  G+ +I  LP Y TIG  AP LLLL R
Sbjct: 61  AFVARPLGGLMFGYLADRLGRIRVMAMTVWLMALGTAIIGLLPTYATIGIAAPLLLLLCR 120

Query: 132 LFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLV---VVVLQHTME 188
           + QGL++GGE   S +Y+ E A E R+G++  F   TLI   L   +V   VV LQ    
Sbjct: 121 IAQGLALGGETTGSTSYIVESAPENRRGYWLGF---TLIFSHLPNAVVAGLVVALQLGAG 177

Query: 189 DAALREWGWRIPFALGAVLAVVALWLRRQLDETSQ-QETRALKEAGSLK----------G 237
           D A  +W WRIPF LG ++ VV  WLRR +DE  + ++ R   +A  +K          G
Sbjct: 178 DQAYSDWAWRIPFLLGGIIGVVGFWLRRNIDEPEEYKQARQASKASKIKKNPLIAAIRCG 237

Query: 238 LWRNRRAFIMVLGFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQP 297
             R      MV    + G+   Y    +M  +L+    + +  A      A+ V   + P
Sbjct: 238 GLRGMLHVFMVQPVFSVGA---YLLLGFMYTFLIEVGKLDSTSALISNAIAVIVLSALLP 294

Query: 298 LIGALSDKIGRRTSMLCFGSLAAIFTVPILSALQNVSSPYAAFGLVMCALLIVSFYTSIS 357
           L G LSD+ GR+  +    +  A+   P +    + S   A  G  + A  +   Y + S
Sbjct: 295 LGGLLSDRFGRKRVLTFGAAWIALSAYPAMYLAASGSFASAVAGQTLLAAGL-GIYGAAS 353

Query: 358 GILKAEMFPAQVRALGVGLSYAVANAIFGGSAEYVALSL-KSIGMETAFFWYVTLMAVVA 416
            +  AE FP   RA G  +SY  + A+FGG+   +A  L ++ G   A  +YVTL+AV+ 
Sbjct: 354 FVAAAEFFPTSFRATGHAISYQTSVAMFGGTCPLIAAYLSQAFGSPLAPAFYVTLIAVLC 413

Query: 417 FLVS 420
            + +
Sbjct: 414 LITT 417


Lambda     K      H
   0.328    0.138    0.419 

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: 527
Number of extensions: 27
Number of successful extensions: 4
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: 432
Length of database: 456
Length adjustment: 32
Effective length of query: 400
Effective length of database: 424
Effective search space:   169600
Effective search space used:   169600
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.

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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