GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruB in Psychromonas ossibalaenae JAMM 0738

Align Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr (characterized)
to candidate WP_019614809.1 G327_RS0110890 fused PTS fructose transporter subunit IIA/HPr protein

Query= SwissProt::P69811
         (376 letters)



>NCBI__GCF_000381745.1:WP_019614809.1
          Length = 373

 Score =  323 bits (827), Expect = 6e-93
 Identities = 173/374 (46%), Positives = 247/374 (66%), Gaps = 4/374 (1%)

Query: 1   MFQLSVQDIHPGEKAGDKEEAIRQVAAALVQAGNVAEGYVNGMLAREQQTSTFLGNGIAI 60
           M  ++  DI   + A +K++AI+ +A +LV+   V   Y++GMLARE Q STFLGNGIAI
Sbjct: 1   MLSINSSDIVLSQAAENKQQAIQSIANSLVEKTYVEAAYLDGMLAREAQNSTFLGNGIAI 60

Query: 61  PHGTTDTRDQVLKTGVQVFQFPEGVTWGDGQVAYVAIGIAASSDEHLGLLRQLTHVLSDD 120
           PHGTT+TRD+V +TGV V  FP+GV WG+    Y+AIGIAA SD+HL +L+QLT VLS +
Sbjct: 61  PHGTTETRDKVKQTGVIVHHFPQGVDWGNDNTVYLAIGIAAQSDQHLAILKQLTKVLSAE 120

Query: 121 SVAEQLKSATTAEELRALLMGEKQSEQLKLDNEMLTLDIVASDLLTLQALNAARLKEAGA 180
            + +QLK A+TA+ + +LL GE QSE L  + +++ L+  ASDLL L A+ A  +K  GA
Sbjct: 121 GIEQQLKEASTAQGIVSLLNGEMQSETL-FNADLIQLNFPASDLLQLTAVAAGLIKNQGA 179

Query: 181 VDATFVTKAINEQPLNLGQGIWLSDSAEGNLRSAIAVSRAANAFDVDGETAAMLVSVAMN 240
           V ++F+   I +Q   LGQG+WL+ S+ G  ++A++   A+ +F + G+    L+ +A N
Sbjct: 180 VQSSFIADVIAKQASYLGQGLWLNSSSTGISKTAVSFVSASESFQLQGKPVQGLLCIASN 239

Query: 241 DDQPIAVLKRLADLLLDNKADRLLKADAATLLALLTSDDAPTDDVLSAEFVVRNEHGLHA 300
               +  L  L DL+   + ++L  A    ++ LLT +       +   F ++N HGLHA
Sbjct: 240 SQLHLKNLNILIDLIHKQQIEQLFDASEEQVITLLTQEKLEGSQQI---FTIKNPHGLHA 296

Query: 301 RPGTMLVNTIKQFNSDITVTNLDGTGKPANGRSLMKVVALGVKKGHRLRFTAQGADAEQA 360
           RPG MLV+  K+F + I +TNL+GTGK AN +SLMKV+  GV+ GH+L+F AQG DAE+A
Sbjct: 297 RPGAMLVHVAKKFKAKIQMTNLNGTGKSANAKSLMKVMTQGVQFGHQLQFVAQGEDAEEA 356

Query: 361 LKAIGDAIAAGLGE 374
           L AIG AI  GLGE
Sbjct: 357 LHAIGQAINEGLGE 370


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: 368
Number of extensions: 16
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: 373
Length adjustment: 30
Effective length of query: 346
Effective length of database: 343
Effective search space:   118678
Effective search space used:   118678
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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