GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proY in Pseudomonas putida KT2440

Align Proline-specific permease (ProY) (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein

Query= TCDB::P37460
         (456 letters)



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

 Score =  380 bits (975), Expect = e-110
 Identities = 195/444 (43%), Positives = 275/444 (61%), Gaps = 3/444 (0%)

Query: 6   KLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEM 65
           +L+RGL  RHI+ +ALG AIGTGLF G A  I++AGPSVLL Y I G+ A++IMR LGEM
Sbjct: 9   RLQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFLIMRQLGEM 68

Query: 66  SVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWI 125
            V  P A SFS +A +     AG+++GW Y    ++V +A++TA GIY+  W+P  P W 
Sbjct: 69  VVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDFPTWA 128

Query: 126 WVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIH 185
                 ++I  INL  VKV+GE+EFWF+  KV  I+ MI  G G  + G G+GG    + 
Sbjct: 129 TAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMI--GFGAWLLGSGHGGPDASVA 186

Query: 186 NLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILV 245
           NLW  GGFF NG  G++M+L ++MF++GG+E++GITA EA +P +SIP+A N V  RIL+
Sbjct: 187 NLWQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQVVYRILI 246

Query: 246 FYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGV 305
           FY+G L V++S+YPW +V   GSPFV+ F  +     A+ILN VVLTA+LS  NS V+  
Sbjct: 247 FYIGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIVVLTAALSVYNSCVYAN 306

Query: 306 GRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIASLAT 365
            RML G+A QG AP+   K SR G+P   + V   A    V +NY+MP   F ++ +LA 
Sbjct: 307 SRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPGGAFGLLMALAV 366

Query: 366 FATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGYHPDT 425
            A V  W  I ++ + FR+      +    +K  G  +T    L F+V I+ ++   P  
Sbjct: 367 SALVINWASISITHLKFRKAKLAAGITPF-YKSLGHPLTNYLCLAFIVLILVVMYLTPPI 425

Query: 426 RISLYVGFAWIVLLLIGWIFKRRR 449
           RIS+ +  AWI +L + +  K+ R
Sbjct: 426 RISVMLIPAWIAVLWVAFKLKKAR 449


Lambda     K      H
   0.329    0.143    0.449 

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: 575
Number of extensions: 31
Number of successful extensions: 3
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: 456
Length of database: 453
Length adjustment: 33
Effective length of query: 423
Effective length of database: 420
Effective search space:   177660
Effective search space used:   177660
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.

Links

Downloads

Related tools

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