GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1580 Histidine transport protein (permease)

Query= TCDB::P15993
         (457 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580 Histidine transport
           protein (permease)
          Length = 469

 Score =  392 bits (1007), Expect = e-113
 Identities = 205/452 (45%), Positives = 287/452 (63%), Gaps = 5/452 (1%)

Query: 5   QQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMR 64
           QQ  + LKRGL  RHI+ +ALG AIGTGLF GSAS IQ AGP ++L Y I G   F++MR
Sbjct: 2   QQPAKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMR 61

Query: 65  QLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPE 124
            LGEM V  PVAGSF  +A  Y G  AGF  GW Y    V+V MA++TA G Y+ FW+PE
Sbjct: 62  ALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPE 121

Query: 125 IPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFG-GWLLF--SGNGG 181
           +  W+       V+  +NL NVKVFGEMEFW +++KV A+VAMI+ G G +LF  S   G
Sbjct: 122 VDRWIWVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPG 181

Query: 182 PQAT-VSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQ 240
            QAT +SNLW  GGF+P+G  GL+   A++MF+FGG+E++G+TA EA +P++ +P+A N 
Sbjct: 182 AQATDISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINA 241

Query: 241 VIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVY 300
           V  RIL+FY+ ++ VL+S+ PW ++ +  SPFV IF  LG +  A  LNIVV++AA+S  
Sbjct: 242 VPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSAI 301

Query: 301 NSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFG 360
           NS ++   RM++GLAQQG+APK  A + + GVP  T++V +    L VL+NYL PE+ F 
Sbjct: 302 NSDIFGAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPENVFL 361

Query: 361 LLMALVVSALVINWAMISLAHMKFRRA-KQEQGVVTRFPALLYPLGNWICLLFMAAVLVI 419
           L+ ++   A V  W MI    +  RR+   EQ    +FP   +P      + FM  +  +
Sbjct: 362 LIASVATFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFIFGV 421

Query: 420 MLMTPGMAISVYLIPVWLIVLGIGYLFKEKTA 451
           +   P    ++ +  VW+++L + YL   K A
Sbjct: 422 LGYFPDTQAALIVGVVWIVLLVLAYLTWVKPA 453


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: 680
Number of extensions: 43
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: 469
Length adjustment: 33
Effective length of query: 424
Effective length of database: 436
Effective search space:   184864
Effective search space used:   184864
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, 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