GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Bap2 in Pseudomonas putida KT2440

Align Valine amino-acid permease; Branched-chain amino-acid permease 3 (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein

Query= SwissProt::P41815
         (604 letters)



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

 Score =  184 bits (468), Expect = 5e-51
 Identities = 125/398 (31%), Positives = 203/398 (51%), Gaps = 17/398 (4%)

Query: 86  LKKSMKSRHVVMMSLGTGIGTGLLVANAKGLSLAGPGSLVIGYVMVSFVTYFMVQAAGEM 145
           L++ +K+RH+ +++LG  IGTGL +  A+ + LAGP S+++GY +   + + +++  GEM
Sbjct: 10  LQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGP-SVLLGYAIAGLMAFLIMRQLGEM 68

Query: 146 GVTYPTLPGNFNAYNSIFISKSFGFATTWLFCIQWLTVLPLELITSSMTVKYWNDTINAD 205
            V  P + G+F+ +   + S+  GF + W + + ++ V   EL    + V+YW       
Sbjct: 69  VVEEP-VAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDFPTW 127

Query: 206 VFIVIFYVFLLFIHFFGVKAYGETEFIFNSCKILMVAGFIILSV-VINCGGAGVDGYIGG 264
               IF+V +  I+   VK YGE EF F   K++ +   I     ++  G  G D  +  
Sbjct: 128 ATAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMIGFGAWLLGSGHGGPDASVAN 187

Query: 265 KYWRDPGSFAEGSGATRFKGICYILVSAYFSFGGIELFVLSINEQSNPRKSTPVAAKRSV 324
             W+  G F  G       G+   L    FSFGG+EL  ++  E  NPR+S P A  + V
Sbjct: 188 -LWQYGGFFPNG-----VTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQVV 241

Query: 325 YRILIIYLLTMILIGFNVPHNNDQLMGSGGSATHASPYVLAASIHKVRVIPHIINAVILI 384
           YRILI Y+  + ++    P    Q +  GGS     P+V+        ++  I+N V+L 
Sbjct: 242 YRILIFYIGALAVLLSLYPW---QKVVQGGS-----PFVMIFHELDSDLVATILNIVVLT 293

Query: 385 SVISVANSALYAAPRLMCSLAQQGYAPKFLNYIDREGRPLRALVVCSLVGVVGFVACSPQ 444
           + +SV NS +YA  R++  LA QG AP+ L  + R G PL AL V +    +  +     
Sbjct: 294 AALSVYNSCVYANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLM 353

Query: 445 EEQAFTWLAAIAGLSELFTWSGIMLSHIRFRKAMKVQG 482
              AF  L A+A  + +  W+ I ++H++FRKA    G
Sbjct: 354 PGGAFGLLMALAVSALVINWASISITHLKFRKAKLAAG 391


Lambda     K      H
   0.324    0.138    0.420 

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: 593
Number of extensions: 25
Number of successful extensions: 6
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: 604
Length of database: 453
Length adjustment: 35
Effective length of query: 569
Effective length of database: 418
Effective search space:   237842
Effective search space used:   237842
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, 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