GapMind for catabolism of small carbon sources

 

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

Align protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized)
to candidate Pf1N1B4_836 PTS system, trehalose-specific IIB component (EC 2.7.1.69) / PTS system, trehalose-specific IIC component (EC 2.7.1.69)

Query= BRENDA::P51184
         (480 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_836 PTS system,
           trehalose-specific IIB component (EC 2.7.1.69) / PTS
           system, trehalose-specific IIC component (EC 2.7.1.69)
          Length = 480

 Score =  447 bits (1149), Expect = e-130
 Identities = 218/474 (45%), Positives = 331/474 (69%), Gaps = 9/474 (1%)

Query: 2   NYKKSAENILQALGGEDNVEAMTHCATRLRLVLKDEGLVDEKALGDMDVVKGTFSTGGQY 61
           +Y      +L +LGG DN+E   HC TRLRL LKD  LVD   L  +D+VKG+F TGG +
Sbjct: 4   DYPNIVTELLHSLGGSDNLEQAAHCVTRLRLALKDPSLVDSATLNQIDLVKGSFYTGGLF 63

Query: 62  QVIIGSGTVNKVFSELEKITGKEASSVSEVKTQGTKNMNPFQRFVKMLSDIFVPIIPAIV 121
           QV+IG G V KV++EL + TG   S++++VK +    ++P QR V++ SD+F+PI+PA++
Sbjct: 64  QVVIGPGEVEKVYAELRRQTGLAVSTIADVKQKSADKIHPMQRLVRVFSDVFMPILPALI 123

Query: 122 AGGLLMGINNILTAPGIFYDNQSLIEVQNQFSGLAEMINIFANAPFTLLPILIGFSAAKR 181
             GLLMGINN++ A G+F + ++L++   +  GL  +IN+ AN  F  LP L+G+SAAKR
Sbjct: 124 IAGLLMGINNLIGAKGMFIEGKTLLDAYPKLDGLWSLINLMANTSFVFLPALVGWSAAKR 183

Query: 182 FGGNAYLGAALGMILVHPELMSAYDYPKALEA--GKEIPHWNLFGL-EINQVGYQGQVLP 238
           FGG+  LG  LG++LVHP+L++A++Y KA+    G+ +P++++ G+ +I +VGYQGQ+LP
Sbjct: 184 FGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGLEGQSLPYFDILGMFQIEKVGYQGQILP 243

Query: 239 MLVATYILATIEKGLRKVIPTVLDNLLTPLLAILSTGFITFSFVGPLTRTLGYWLSDGLT 298
           +L+A Y+++ IEK LR  +P  +  L+ P+  I+ TG +  + +GP+TR LG  +++G+ 
Sbjct: 244 ILMAAYVMSVIEKWLRARVPNAVQLLVVPITTIVVTGVLALAVIGPVTRHLGILITEGVV 303

Query: 299 WLYEFGGAIGGLIFGLLYAPIVITGMHHSFIAIETQLIADSSSTGGSFIFPIATMSNIAQ 358
            L++    +GG IFGLLYAP+VITGMHH F+A++ QLI   S+ GG+FI+P+  MSN+AQ
Sbjct: 304 TLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLI---STQGGTFIWPMIVMSNLAQ 360

Query: 359 GAAALAAFFIIKENKKLKGVASAAGVSALLGITEPAMFGVNLKLRYPFIGAIVGSGIGSA 418
           G+AALA F++ +  +  K +AS + +SA  GITEPAMFGVNL+ ++PF  A++GS +G  
Sbjct: 361 GSAALAVFYMTRSVRD-KSMASTSAISAYFGITEPAMFGVNLRYKFPFYAALIGSALGCI 419

Query: 419 YIAFFKVKAIALGTAGIPGFISISGQNNGWLHYGIAMIIAFIVAFGVTYALSYR 472
           +++  KV+A A+G  G+PGFISI  Q      + + M+IA +V F +T  LS R
Sbjct: 420 FLSLNKVQASAIGVGGLPGFISIIPQFIPM--FVVGMVIAMVVPFVLTCGLSMR 471


Lambda     K      H
   0.322    0.140    0.406 

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: 610
Number of extensions: 21
Number of successful extensions: 4
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: 480
Length of database: 480
Length adjustment: 34
Effective length of query: 446
Effective length of database: 446
Effective search space:   198916
Effective search space used:   198916
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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