GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Pseudomonas putida KT2440

Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate PP_4495 PP_4495 aromatic amino acid transport protein

Query= uniprot:Q4KIP0
         (466 letters)



>lcl|FitnessBrowser__Putida:PP_4495 PP_4495 aromatic amino acid
           transport protein
          Length = 472

 Score =  686 bits (1770), Expect = 0.0
 Identities = 327/459 (71%), Positives = 394/459 (85%)

Query: 3   QTLKQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIM 62
           Q +  GELKRGLKNRHIQLIALGGAIGTGLFLGSAGV+KSAGPSMILGYAI GFIAF+IM
Sbjct: 4   QNMHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVMKSAGPSMILGYAICGFIAFMIM 63

Query: 63  RQLGEMIVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWP 122
           RQLGEMIVEEPVAGSFSHFAH YWGG+ GFL+GWN WVLY+LVGM+EL+AVGKYV +WWP
Sbjct: 64  RQLGEMIVEEPVAGSFSHFAHTYWGGFAGFLSGWNCWVLYILVGMSELSAVGKYVHYWWP 123

Query: 123 EIPTWVSAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYMLFSGSGGSQ 182
           EIPTWV+AA FFVL+N IN+MNVKFFGEAEFWFAIIKVVAIV MI LG Y+L SGSGG +
Sbjct: 124 EIPTWVTAAAFFVLINAINLMNVKFFGEAEFWFAIIKVVAIVSMIGLGAYLLTSGSGGPE 183

Query: 183 ASVSNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQVVY 242
           A+V+NLW+HGGFFPNG +GL+MA+AFIMFSFGGLE++G TAAEA +P+ VIPKAINQV+Y
Sbjct: 184 ATVANLWTHGGFFPNGVSGLVMALAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIY 243

Query: 243 RVLIFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVVLT 302
           R+LIFYVGAL VLLSL PWD L+ S++A G +Y SSPFV++FSL+GSD AA +LNFVVLT
Sbjct: 244 RILIFYVGALVVLLSLTPWDNLVASIDASGGSYGSSPFVQVFSLLGSDVAANLLNFVVLT 303

Query: 303 AALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNYLA 362
           AALSVYNSG YCN+RML G+AEQGDAP +L K++K+GVP+ ++ +SA +T + VL+NYL 
Sbjct: 304 AALSVYNSGTYCNARMLLGMAEQGDAPASLAKVDKRGVPVRSILVSAAVTFVAVLLNYLM 363

Query: 363 PHEALELLFALVVAALMINWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYLCLAFMV 422
           P  ALELL +LVVA L+INWA+IS +HL+FR+ +   G  P FKA W P  NY+ LAF+V
Sbjct: 364 PQNALELLMSLVVATLVINWAMISYSHLKFRQHLDRTGQKPLFKALWYPYGNYVVLAFVV 423

Query: 423 MIVGVMWMIPGIRASVYAIPVWVLVIWGFYLLSRAKKAS 461
           +I+G+M MIPGI+ SVYAIPVW+L +   Y++   ++ +
Sbjct: 424 LILGIMLMIPGIQVSVYAIPVWLLAMLVVYMVKSRRQVN 462


Lambda     K      H
   0.327    0.141    0.440 

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: 805
Number of extensions: 42
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: 466
Length of database: 472
Length adjustment: 33
Effective length of query: 433
Effective length of database: 439
Effective search space:   190087
Effective search space used:   190087
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