GapMind for catabolism of small carbon sources

 

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

Align Lysine permease LysP (characterized)
to candidate Pf1N1B4_1580 Histidine transport protein (permease)

Query= SwissProt::A2RNZ6
         (508 letters)



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

 Score =  281 bits (720), Expect = 3e-80
 Identities = 160/451 (35%), Positives = 261/451 (57%), Gaps = 24/451 (5%)

Query: 33  VKRALKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFLMTSLGEM 92
           +KR L +RH+  +ALG  IGTGLF  S   I  AGP   L AY++ GA V+ +M +LGEM
Sbjct: 8   LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGP-AVLLAYLIGGAAVFMVMRALGEM 66

Query: 93  ATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFWLPDVPSWI 152
           A + P +GSF  Y + Y+ P  GF LGW Y     I    D+TA  + + FW P+V  WI
Sbjct: 67  AVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVDRWI 126

Query: 153 FSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGF-LSIFGIMGGHIDVAKN 211
           + L  + +V  +N  +VK FGE E+WLS +K+  +V  ++ GF + +FGI       A +
Sbjct: 127 WVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGAQATD 186

Query: 212 LS-VGNHGFVGGLGSFTTG-GGILGVLLVAGFSFQGTELLGITAGEAENPEKSIPKAMNS 269
           +S + +HG     G    G GG++    V  F+F G E++G+TAGEA++P++ +P+A+N+
Sbjct: 187 ISNLWSHG-----GFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINA 241

Query: 270 IFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASIMNAVVLT 329
           +  RIL+FY+L++ V+ +I P+     +G      SPF  +F+ +G S AA+I+N VV++
Sbjct: 242 VPLRILLFYVLTMLVLMSIFPWQQ---IGSQG---SPFVQIFDNLGISSAATILNIVVIS 295

Query: 330 SVVSAANSGMYASTRMLYSLAKDGGAPKIFSKTSKNGIPFIALLATTAVALL-TFLTSIY 388
           + VSA NS ++ + RM+Y LA+ G APK F++ S+NG+P++ ++  ++  LL   L  + 
Sbjct: 296 AAVSAINSDIFGAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLI 355

Query: 389 GVSFFTLLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFPFGPI--LA 446
             + F L+ S +       W+ I  +    RR+  A+   V +L +    +P+ P+  +A
Sbjct: 356 PENVFLLIASVATFATVWVWLMILFTQVAMRRSMSAE--QVAQLKFPVPFWPYAPMAAIA 413

Query: 447 LIMTVLVTLGQDP----MLLFGKTWVQGVVM 473
            ++ +   LG  P     L+ G  W+  +V+
Sbjct: 414 FMLFIFGVLGYFPDTQAALIVGVVWIVLLVL 444


Lambda     K      H
   0.326    0.141    0.422 

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: 601
Number of extensions: 35
Number of successful extensions: 6
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: 508
Length of database: 469
Length adjustment: 34
Effective length of query: 474
Effective length of database: 435
Effective search space:   206190
Effective search space used:   206190
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: 52 (24.6 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