GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocE in Pseudomonas putida KT2440

Align arginine permease (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein

Query= CharProtDB::CH_091699
         (590 letters)



>lcl|FitnessBrowser__Putida:PP_0927 PP_0927 aromatic amino acid
           transport protein
          Length = 453

 Score =  246 bits (629), Expect = 1e-69
 Identities = 163/465 (35%), Positives = 246/465 (52%), Gaps = 33/465 (7%)

Query: 84  VKRELKQRHIGMIALGGTIGTGLFIGLSTPLTNAGPVGALISYLFMGSLAYSVTQSLGEM 143
           ++R LK RHI +IALGG IGTGLF+G++  +  AGP   L+ Y   G +A+ + + LGEM
Sbjct: 10  LQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGP-SVLLGYAIAGLMAFLIMRQLGEM 68

Query: 144 ATFIPVTSSFTVFSQRFLSPAFGAANGYMYWFSWAITFALELSVVGQVIQFWTYKVPLAA 203
               PV  SF+ F+ ++ S   G  +G+ YW  + +    EL+ VG  +Q+W    P  A
Sbjct: 69  VVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDFPTWA 128

Query: 204 WISIFWVIITIMNLFPVKYYGEFEFWVASIKVLAIIGFLIYCFCMVCGAGVTGPVG--FR 261
             +IF+V+I ++NL  VK YGE EFW A +KV+AI+  +I     + G+G  GP      
Sbjct: 129 TAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVS-MIGFGAWLLGSGHGGPDASVAN 187

Query: 262 YWRNPGAWGPGIISKDKNEGRFLGWVSSLINAAFTFQGTELVGITAGEAANPRKSVPRAI 321
            W+  G +  G+           G V +L    F+F G ELVGITA EA NPR+S+P+A 
Sbjct: 188 LWQYGGFFPNGV----------TGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKAT 237

Query: 322 KKVVFRILTFYIGSLLFIGLLVPYNDPKLTQSTSYVSTSPFIIAIENSGTKVLPHIFNAV 381
            +VV+RIL FYIG+L  +  L P+   K+ Q       SPF++      + ++  I N V
Sbjct: 238 NQVVYRILIFYIGALAVLLSLYPWQ--KVVQ-----GGSPFVMIFHELDSDLVATILNIV 290

Query: 382 ILTTIISAANSNIYVGSRILFGLSKNKLAPKFLSRTTKGGVPYIAVFVTAAFGALAYMET 441
           +LT  +S  NS +Y  SR+LFGL+    AP+ L + ++ GVP  A+ V+A    L  +  
Sbjct: 291 VLTAALSVYNSCVYANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLIN 350

Query: 442 STGGDKVFEWLLNITGVAGFFAWLFISISHIRFMQALKYRGISRDELPFKAKL-MPGLAY 500
                  F  L+ +   A    W  ISI+H++F +A    GI+    PF   L  P   Y
Sbjct: 351 YLMPGGAFGLLMALAVSALVINWASISITHLKFRKAKLAAGIT----PFYKSLGHPLTNY 406

Query: 501 YAATFMTIIIIIQGFTAFAPKFNGVSFAAAYISIFLFLAVWILFQ 545
               F+ +I+++   T   P    V    A+I++     +W+ F+
Sbjct: 407 LCLAFIVLILVVMYLT--PPIRISVMLIPAWIAV-----LWVAFK 444


Lambda     K      H
   0.325    0.140    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: 691
Number of extensions: 45
Number of successful extensions: 5
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: 590
Length of database: 453
Length adjustment: 35
Effective length of query: 555
Effective length of database: 418
Effective search space:   231990
Effective search space used:   231990
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: 52 (24.6 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