GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocE in Pseudomonas putida KT2440

Align Amino-acid permease RocE (characterized)
to candidate PP_0660 PP_0660 S-methyl-L-methionine transporter

Query= SwissProt::P39137
         (467 letters)



>lcl|FitnessBrowser__Putida:PP_0660 PP_0660 S-methyl-L-methionine
           transporter
          Length = 479

 Score =  469 bits (1206), Expect = e-136
 Identities = 218/465 (46%), Positives = 327/465 (70%), Gaps = 1/465 (0%)

Query: 3   TNQDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFL 62
           T   + +  ++ M++RH+ M++LGGVIGTG FL +G+T+NQAGPLGAV++Y++G  +++L
Sbjct: 8   TRNASAHTFKQDMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPLGAVIAYILGAIMVYL 67

Query: 63  TMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRW 122
            M+CLGELAV  P  GSF +YAT+++ P  G+   W+YWL W V    EF +AG LM RW
Sbjct: 68  VMMCLGELAVHMPEVGSFSSYATRYLGPGTGYMVAWMYWLTWTVAIGSEFTAAGILMVRW 127

Query: 123 FPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDL 182
           FP   VW+W  +F A +FI N I+ ++FAE+EFW S +K+L ++ F+++GG A+ G  ++
Sbjct: 128 FPDTPVWMWSALFGAAVFISNIISVRSFAETEFWLSLVKVLAVIAFLVVGGGAILGGFEI 187

Query: 183 KGGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSI 242
           +    A  L +F  +GLFP G  ++ +T++ V FAF GTELIG+AAGE++DPEK +P++I
Sbjct: 188 QQAHSAG-LGNFTREGLFPTGFWSIAMTLLAVAFAFSGTELIGIAAGETKDPEKNVPKAI 246

Query: 243 KQTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLS 302
           + TV R  +FF+ +I V+A ++P +QAGV+ESPFV VF  IGIPYAADIMNFVI+ ALLS
Sbjct: 247 RTTVLRLALFFIGTIFVLATLLPREQAGVIESPFVMVFAMIGIPYAADIMNFVIITALLS 306

Query: 303 VANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETV 362
            ANSGLYA++R+L+ ++++G   +     ++RG P  +++++MA    SLL+     +T+
Sbjct: 307 AANSGLYAASRMLWTLSDQGNMPRRYATLSRRGTPFNAIVLSMAGGMASLLSSVFAPDTI 366

Query: 363 YMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTV 422
           Y+ L+S++G++  V WI+I+ SQI FRR YI  GGK+EDLKF+   YP +PL  +    +
Sbjct: 367 YLALVSISGLAVVVVWISIAASQIAFRRHYIASGGKLEDLKFRVRGYPFVPLGAIFCCVL 426

Query: 423 VLISLAFDPEQRIALYCGVPFMIICYIIYHVVIKKRQQANRQLEL 467
             + +AFDP QR+ALY G+PF+  CY+ Y +  K R +    LE+
Sbjct: 427 ACVGIAFDPAQRVALYFGLPFIAWCYLAYWLTCKYRSRRTAPLEI 471


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: 595
Number of extensions: 21
Number of successful extensions: 2
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: 479
Length adjustment: 33
Effective length of query: 434
Effective length of database: 446
Effective search space:   193564
Effective search space used:   193564
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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