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_3727 PP_3727 Amino-acid permease RocE

Query= SwissProt::P39137
         (467 letters)



>lcl|FitnessBrowser__Putida:PP_3727 PP_3727 Amino-acid permease RocE
          Length = 468

 Score =  529 bits (1362), Expect = e-155
 Identities = 243/452 (53%), Positives = 343/452 (75%)

Query: 10  QLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGE 69
           QL R +KSRH+FM+SLGGVIGTG F+G+G TINQ GP+GA+L+YLV G +M+L M+CLGE
Sbjct: 9   QLTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLVAGLLMYLVMVCLGE 68

Query: 70  LAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVW 129
           L+V  PVSGSFQ +ATK+I PA GF  GW+YW+ WA T  +EF +AG LM RWFP + +W
Sbjct: 69  LSVQMPVSGSFQAHATKYIGPATGFMIGWVYWMSWATTVGLEFTAAGMLMTRWFPEVPIW 128

Query: 130 IWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAP 189
            W  +F  ++F LNA+ T+AF E+E+WFSGIK+  IL FI++G   +FG I L  G  AP
Sbjct: 129 YWSALFVVVLFGLNALATRAFGEAEYWFSGIKVATILGFIVIGLLVIFGAIPLSSGAPAP 188

Query: 190 FLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRT 249
            L +   + LFP+G+ A+   M+TV +AFQG E++GVAAGE+E PEK+IPR+++  V+R 
Sbjct: 189 MLNNLVGESLFPHGLSAVFAVMMTVVYAFQGCEIMGVAAGETEHPEKSIPRAVRNVVFRV 248

Query: 250 LVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGLY 309
           L+F+VL+I V++ ++P +QAG++ESPFV VF+ +GIPYAAD+MNFVIL A+LSV NSGLY
Sbjct: 249 LIFYVLAIAVLSAIVPHEQAGLMESPFVQVFDMVGIPYAADLMNFVILTAILSVGNSGLY 308

Query: 310 ASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLSL 369
           ASTRIL+AM+  G A K+L   ++RGVP+ +L +T+  A +SL+T F  A+T++MVL+++
Sbjct: 309 ASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALISLMTSFVAADTLFMVLMAV 368

Query: 370 AGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISLAF 429
           +GMS  V WI I+L+Q  FR+ ++R+GG+++DLK+K PLYP++PL+ +TL + + + LA 
Sbjct: 369 SGMSGTVTWIVIALAQYRFRKAWLRDGGQLQDLKYKAPLYPLVPLLCITLCSSLFVFLAL 428

Query: 430 DPEQRIALYCGVPFMIICYIIYHVVIKKRQQA 461
           D  QR +LY G  F+ +CY  Y  V ++RQ A
Sbjct: 429 DETQRPSLYWGFGFIALCYAAYFFVNRRRQGA 460


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: 661
Number of extensions: 26
Number of successful extensions: 1
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: 468
Length adjustment: 33
Effective length of query: 434
Effective length of database: 435
Effective search space:   188790
Effective search space used:   188790
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