GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysP in Pseudomonas putida KT2440

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

Query= CharProtDB::CH_003129
         (489 letters)



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

 Score =  265 bits (678), Expect = 2e-75
 Identities = 150/395 (37%), Positives = 223/395 (56%), Gaps = 16/395 (4%)

Query: 13  LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTSLGEL 72
           L+R LK RH+ +IA+GG+IGTGLF+    TI  AGP   LL Y + GLM + +M  LGE+
Sbjct: 10  LQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPS-VLLGYAIAGLMAFLIMRQLGEM 68

Query: 73  AAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDTPGWI 132
               PV+GSF+ +   Y  E  GF  GWNYW  + +    +L A  + + +W+PD P W 
Sbjct: 69  VVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDFPTWA 128

Query: 133 WSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQPAGWSN 192
            +A+F  VI L+N   V+ +GE E+WF+L+KV  ++  I  G   ++G   G   A  +N
Sbjct: 129 TAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMIGFGA-WLLGSGHGGPDASVAN 187

Query: 193 -WTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFWRILL 251
            W  G   F  G   ++    ++ FSF G EL+GI A E+++P ++IP+A  QV +RIL+
Sbjct: 188 LWQYG-GFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQVVYRILI 246

Query: 252 FYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAVLSA 311
           FY+ A+ ++  + P+    +++        SPF ++F        A ++N V+LTA LS 
Sbjct: 247 FYIGALAVLLSLYPW--QKVVQGG------SPFVMIFHELDSDLVATILNIVVLTAALSV 298

Query: 312 GNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTS--MFGNQT 369
            NS +YA++RML+ LA  G APR   K+SR GVP  AL  +    GLC L +  M G   
Sbjct: 299 YNSCVYANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPGGAF 358

Query: 370 VYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQG 404
             L  L  S +   I W  I+I+H +FR+  +  G
Sbjct: 359 GLLMALAVSALV--INWASISITHLKFRKAKLAAG 391


Lambda     K      H
   0.327    0.142    0.451 

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: 660
Number of extensions: 47
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: 489
Length of database: 453
Length adjustment: 33
Effective length of query: 456
Effective length of database: 420
Effective search space:   191520
Effective search space used:   191520
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 (21.7 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