GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kgtP in Pseudomonas fluorescens GW456-L13

Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate PfGW456L13_3155 L-Proline/Glycine betaine transporter ProP

Query= uniprot:D8J257
         (457 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3155
          Length = 429

 Score =  235 bits (599), Expect = 2e-66
 Identities = 144/413 (34%), Positives = 218/413 (52%), Gaps = 12/413 (2%)

Query: 23  ILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTAGVFAAGFLMRPIGGWLF 82
           I+ A  GN VEWFDF VY F A   A  FFP GD ++ LL T  VFA  F  RP+GG  F
Sbjct: 2   IVAAGIGNFVEWFDFAVYGFLATTIAQQFFPSGDASAALLKTFAVFAVAFAFRPLGGIFF 61

Query: 83  GRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPALLLLARLFQGLSVGGEYG 142
           G + D+ GRK ++ +++L+M G +  + ++PTYA IG  AP LL L R  QG S GGEY 
Sbjct: 62  GMLGDRIGRKRTLAMTILLMAGATTLIGLLPTYAAIGVMAPILLSLIRCAQGFSAGGEYA 121

Query: 143 TSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQWLTKAELMAWGWRVPFVL 202
            +  Y+ E AP+ +R ++ SF  V+       A +V + ++  L+   + +WGWR+PF++
Sbjct: 122 GACAYLMEHAPSDKRAWYGSFIPVSTFSAFAAAAVVAYALEASLSAEAMGSWGWRLPFLI 181

Query: 203 GAVGALVAMYLRSSLAETSSAGARKKKDA---GTLKGLLQHKRAFLNVVG-FTAGGSLMF 258
            A   LV +YLR  L ET +  A  ++ A     LK  L++  A +  +G F +  +L F
Sbjct: 182 AAPLGLVGLYLRWKLDETPAFQAVTQEHAVAHSPLKETLRNHGAAICCLGAFVSLTALSF 241

Query: 259 YTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGAISDKIGRRNSMLCFAFFG 318
           Y FTTY   YL    G+    A  V   AL     + P+ G  SD++GRR +++      
Sbjct: 242 YMFTTYFATYLQVAGGLSRATALLVSLIALLFAAAICPLAGLYSDRVGRRVTVMTACALL 301

Query: 319 MVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTS-ISGLIKAEMFPPEVRALGVGLSY 377
           +V  +P   FL   S    A  + ++ L I +     ++  + +E FP   R     ++Y
Sbjct: 302 IVVVYP--SFLMASSGSFAASIVGVMLLAIGAVLCGVVTAALLSETFPTRTRYTASAITY 359

Query: 378 AVGNAIFGGSAEFVA---LSLKSAGIESAFYWYVSALCLVALIISLRMPDPQR 427
            +   +FGG+A  VA   +S   + +  AF  Y+ A+ L+AL   L +P+  R
Sbjct: 360 NMAYTLFGGTAPLVATWLISTTGSNLSPAF--YLIAIALLALAGGLALPETSR 410


Lambda     K      H
   0.325    0.138    0.418 

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: 530
Number of extensions: 32
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: 457
Length of database: 429
Length adjustment: 32
Effective length of query: 425
Effective length of database: 397
Effective search space:   168725
Effective search space used:   168725
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