GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ptsS 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::P12655
         (664 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 =  366 bits (939), Expect = e-105
 Identities = 195/475 (41%), Positives = 303/475 (63%), Gaps = 14/475 (2%)

Query: 2   DYSKVASEVITAVG-KDNLVAAAHCATRLRLVLKDDSKVDQKALDKNADVKGTFKTDGQY 60
           DY  + +E++ ++G  DNL  AAHC TRLRL LKD S VD   L++   VKG+F T G +
Sbjct: 4   DYPNIVTELLHSLGGSDNLEQAAHCVTRLRLALKDPSLVDSATLNQIDLVKGSFYTGGLF 63

Query: 61  QVIIGPGDVNFVYDEIIKQTGLTEVSTDDLKKIAASGKKFNPIMALIKLLSDIFVPIIPA 120
           QV+IGPG+V  VY E+ +QTGL   +  D+K+ +A   K +P+  L+++ SD+F+PI+PA
Sbjct: 64  QVVIGPGEVEKVYAELRRQTGLAVSTIADVKQKSAD--KIHPMQRLVRVFSDVFMPILPA 121

Query: 121 LVAGGLLMALNNFLTSEGLF-GTKSLVQQFPIIKGSSDMIQLMSAAPFWFLPILVGISAA 179
           L+  GLLM +NN + ++G+F   K+L+  +P + G   +I LM+   F FLP LVG SAA
Sbjct: 122 LIIAGLLMGINNLIGAKGMFIEGKTLLDAYPKLDGLWSLINLMANTSFVFLPALVGWSAA 181

Query: 180 KRFGANQFLGASIGMIMVAPGAANIIGLAANAPISKAATIGAYTGFWNIFGL-HVTQASY 238
           KRFG ++ LG  +G+++V P   N    A N   + A   G    +++I G+  + +  Y
Sbjct: 182 KRFGGSEILGIVLGLMLVHPDLLN----AWNYGKAVAGLEGQSLPYFDILGMFQIEKVGY 237

Query: 239 TYQVIPVLVAVWLLSILEKFFHKRLPSAVDFTFTPLLSVIITGFLTFIVIGPVMKEVSDW 298
             Q++P+L+A +++S++EK+   R+P+AV     P+ ++++TG L   VIGPV + +   
Sbjct: 238 QGQILPILMAAYVMSVIEKWLRARVPNAVQLLVVPITTIVVTGVLALAVIGPVTRHLGIL 297

Query: 299 LTNGIVWLYDTTGFLGMGVFGALYSPVVMTGLHQSFPAIETQLISAFQNGTGHGDFIFVT 358
           +T G+V L+D    +G  +FG LY+P+V+TG+H  F A++ QLIS     T  G FI+  
Sbjct: 298 ITEGVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLIS-----TQGGTFIWPM 352

Query: 359 ASMANVAQGAATFAIYFLTKDKKMKGLSSSSGVSALLGITEPALFGVNLKYRFPFFCALI 418
             M+N+AQG+A  A++++T+  + K ++S+S +SA  GITEPA+FGVNL+Y+FPF+ ALI
Sbjct: 353 IVMSNLAQGSAALAVFYMTRSVRDKSMASTSAISAYFGITEPAMFGVNLRYKFPFYAALI 412

Query: 419 GSASAAAIAGLLQVVAVSLGSAGFLGFLSIKASSIPFYVVCELISFAIAFAVTYG 473
           GSA       L +V A ++G  G  GF+SI    IP +VV  +I+  + F +T G
Sbjct: 413 GSALGCIFLSLNKVQASAIGVGGLPGFISIIPQFIPMFVVGMVIAMVVPFVLTCG 467


Lambda     K      H
   0.320    0.135    0.384 

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: 30
Number of successful extensions: 5
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: 664
Length of database: 480
Length adjustment: 36
Effective length of query: 628
Effective length of database: 444
Effective search space:   278832
Effective search space used:   278832
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 (21.8 bits)
S2: 53 (25.0 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