GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruB in Pseudomonas stutzeri RCH2

Align Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr (characterized)
to candidate GFF3291 Psest_3355 phosphoenolpyruvate-protein phosphotransferase

Query= SwissProt::P69811
         (376 letters)



>FitnessBrowser__psRCH2:GFF3291
          Length = 960

 Score =  235 bits (600), Expect = 3e-66
 Identities = 144/374 (38%), Positives = 202/374 (54%), Gaps = 3/374 (0%)

Query: 1   MFQLSVQDIHPGEKAGDKEEAIRQVAAALVQAGNVAEGYVNGMLAREQQTSTFLGNGIAI 60
           M +L+ Q IH  + A DK  A+  +   LV  G VA GY+ G+ ARE Q STFLG GIAI
Sbjct: 1   MLELNAQHIHMHQAAADKPAALALLGEVLVADGLVAAGYLEGLRAREAQGSTFLGQGIAI 60

Query: 61  PHGTTDTRDQVLKTGVQVFQFPEGVTWGDGQVAYVAIGIAASSDEHLGLLRQLTHVLSDD 120
           PHGT +TRDQV  TGV++  FP GV WG+GQ+ Y+AIGIAA SDEHL LL+ LT  L + 
Sbjct: 61  PHGTPETRDQVFTTGVRLLHFPAGVDWGNGQLVYLAIGIAARSDEHLRLLQLLTRALGEG 120

Query: 121 SVAEQLKSATTAEELRALLMGEKQSEQLKLDNEMLTLDIVASDLLTLQALNAARLKEAGA 180
            ++E L+ A + E +  LL G  Q+  L LD E+++L + A D   L       LK A  
Sbjct: 121 DLSEGLQQAESPEAIIGLLQGAPQA--LALDGELVSLGVAADDFDELAWQGVKLLKRAQC 178

Query: 181 VDATFVTKAINEQPLNLGQGIWLSDSAEGNLRSAIAVSRAANAFDVDGETAAMLVSVAMN 240
           V+  F       Q L LG G+W   S +   R  +A     +  +  G+    L  +A  
Sbjct: 179 VEPGFNASLPLGQSLPLGDGLWWLSSEQSVQRPGLAFVTPVSNLEHQGQPLNGLFVLASM 238

Query: 241 DDQPIAVLKRLADLLLDNKADRLLKADAATLLALLTSDDAPTDDVLSAEFVVRNEHGLHA 300
            +   A+L+RL +LL++ +   L +A ++  +      D P  D  SA+  + N HGLHA
Sbjct: 239 GEAHQAMLERLCNLLIEGRGQELSQATSSRTVLEALGGDVPA-DWPSAQVPLANAHGLHA 297

Query: 301 RPGTMLVNTIKQFNSDITVTNLDGTGKPANGRSLMKVVALGVKKGHRLRFTAQGADAEQA 360
           RP  +L    + F  +I V          + +SL K++A+G  +G  L F A+ A A  A
Sbjct: 298 RPAKVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQLLEFMAEPAIASDA 357

Query: 361 LKAIGDAIAAGLGE 374
           L A+  A+  GLGE
Sbjct: 358 LPALVRAVEEGLGE 371


Lambda     K      H
   0.314    0.130    0.353 

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: 752
Number of extensions: 40
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: 376
Length of database: 960
Length adjustment: 37
Effective length of query: 339
Effective length of database: 923
Effective search space:   312897
Effective search space used:   312897
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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 (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:

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