GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Pseudomonas putida KT2440

Align Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)
to candidate PP_5031 PP_5031 proline (histidine) APC transporter

Query= TCDB::P15993
         (457 letters)



>lcl|FitnessBrowser__Putida:PP_5031 PP_5031 proline (histidine) APC
           transporter
          Length = 467

 Score =  387 bits (994), Expect = e-112
 Identities = 198/445 (44%), Positives = 281/445 (63%), Gaps = 5/445 (1%)

Query: 6   QHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQ 65
           Q  + LKRGL  RHI+ +ALG AIGTGLF GSAS IQ AGP ++L Y I G   F++MR 
Sbjct: 2   QQAQGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRA 61

Query: 66  LGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEI 125
           LGEM V  PVAGSF H+A  Y G  AGF  GW Y    V+VA+A++TA G Y+ FW+PE+
Sbjct: 62  LGEMAVHNPVAGSFGHYATTYLGPMAGFILGWTYAFEMVIVAIADVTAFGIYMGFWFPEV 121

Query: 126 PTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSG----NGG 181
             W+       +I  +NL NVKVFGEMEFW +++KV A+VAMI+ G  ++  G      G
Sbjct: 122 ARWIWVLGIVFLIGGLNLCNVKVFGEMEFWLSLLKVGAIVAMILAGLGIMAFGFSQVGTG 181

Query: 182 PQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQV 241
               +SNL+D GGF+P+G  GL+   A++MF+FGG+E++G+TA EA +P++ IPKA N V
Sbjct: 182 HAVGMSNLFDHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVIPKAINAV 241

Query: 242 IYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYN 301
             RIL+FY+ +L VL+ L PW ++ +  SPFV IF  LG    A  LN+VV++AA+S  N
Sbjct: 242 PLRILLFYVLTLFVLMCLYPWPQIGSQGSPFVQIFSNLGIGSAAAVLNVVVISAAISAIN 301

Query: 302 SCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGL 361
           S ++   RM++GLAQQG+AP+  + + K GVP  T++V      + VL+NYL PE+ F L
Sbjct: 302 SDIFGAGRMMYGLAQQGHAPRGFSKLSKHGVPWMTVVVMGAALLIGVLLNYLIPENVFLL 361

Query: 362 LMALVVSALVINWAMISLAHMKFRRA-KQEQGVVTRFPALLYPLGNWICLLFMAAVLVIM 420
           + ++   A V  W MI L  +  RR+  +EQ    +FP   +P G  + + FM  +  ++
Sbjct: 362 IASIATFATVWVWLMILLTQVAMRRSMSREQVAQLKFPVPFWPYGPAMAIAFMVFIFGVL 421

Query: 421 LMTPGMAISVYLIPVWLIVLGIGYL 445
              P    ++ +  +W++ L   YL
Sbjct: 422 GYFPDTQAALIVGVIWVVFLVASYL 446


Lambda     K      H
   0.328    0.141    0.434 

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: 689
Number of extensions: 41
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: 457
Length of database: 467
Length adjustment: 33
Effective length of query: 424
Effective length of database: 434
Effective search space:   184016
Effective search space used:   184016
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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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 paper from 2022 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