GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dhaM in Desulfovibrio vulgaris Miyazaki F

Align PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized)
to candidate 8501869 DvMF_2584 phosphoenolpyruvate-protein phosphotransferase (RefSeq)

Query= SwissProt::D4GL26
         (473 letters)



>lcl|FitnessBrowser__Miya:8501869 DvMF_2584
           phosphoenolpyruvate-protein phosphotransferase (RefSeq)
          Length = 846

 Score =  292 bits (748), Expect = 3e-83
 Identities = 196/487 (40%), Positives = 270/487 (55%), Gaps = 39/487 (8%)

Query: 1   MVNLVIVSHSAMLGEGVEMLARQMLTGDNCRIAVAAGIDDPDHPIGTDPIKVMEAIEAVA 60
           MV +V+V+HSA+LG+GV+ L  QM  G    +AVA GIDDP+HPIGTDP++VM AIE V 
Sbjct: 1   MVGIVVVTHSAVLGQGVKELVEQMTQG-RVPLAVAGGIDDPEHPIGTDPMRVMAAIEEVQ 59

Query: 61  DTDHVLVMMDMGSALLSAETALDLLDPVIAEKVRLCAAPLVEGTLAATVSAAAGADIDTV 120
             D VLV+MD+GSAL+SAETALDLL P +A +VRL  APLVEG +AA V A+ GAD+DTV
Sbjct: 60  QGDGVLVLMDLGSALMSAETALDLLPPEVAAQVRLRPAPLVEGVMAAAVQASIGADLDTV 119

Query: 121 IDVAMNALAAKQAQLGITPPA------HAASLPAQAPDSDARSVTVTIRNHHGLHVRPAS 174
           +  A +ALAAK   LG+  P        AA   A A  + +  +T+ + N  GLH RPA+
Sbjct: 120 LREAQSALAAKAELLGMALPQDGGGVDEAAPPAAGATPAASHELTLMVPNRLGLHARPAA 179

Query: 175 RLVAALAGMNADLVLEKQGQCVKPDSLNQIALLQVRCHDAVTLSASGPDAERALAAFESL 234
           R+V AL    AD+ L +  + V   S+N+IA L VR  + +T  A+G DAE+AL A   L
Sbjct: 180 RIVTALGPFVADVQLARGERVVSARSVNRIATLAVRGGETITFRAAGTDAEQALKALADL 239

Query: 235 AAEDFGEHPESMALKTSAST-VE-----KVQGKAVFYPLPLAQ----------------- 271
           AAE+FG+ P+  A K+S  T VE       QG+A    +P A+                 
Sbjct: 240 AAENFGDLPD--ATKSSGRTGVEGPEGPGEQGRAGVAGVPAAKGGVPASPGIAVGPAVWH 297

Query: 272 -------PARHPCSDVGQEERRLQQAIVDTLNDLNALAALAEKKYGASVAAIFSGHYTLL 324
                  P      D   E  RL  A+     +L AL        G   A IF  H  LL
Sbjct: 298 RPAFDAPPPDLAAGDPDSEAARLDGALDAARKELAALERRTAAMAGKQEAEIFVMHRLLL 357

Query: 325 DDPDLFDAACKVIRNDSCCAESAWYQVLMELSQQYQHLDDAYLQARFIDIEDILYRSLCH 384
           DD  +   A + I      AE+AWY V+ + ++ ++ L + Y++ R  D+ D+  R L  
Sbjct: 358 DDATIAGDARQRIAERREPAEAAWYAVIDQAAESFRQLPEGYMRERAADLVDVGARVLRL 417

Query: 385 LKGRDIRLPTPDVPAIIVADDIFPSAVVNLNAQLVKGICLREGSTLSHAAIIAQQAGIAF 444
           L G     P  + P++++A D+ PS + +L+  LV GI   +G   SHAAI+A+  GI  
Sbjct: 418 LTGAPPSGPRLERPSVLLAADLGPSDMAHLDPALVLGIVTAQGGATSHAAILARSMGIPA 477

Query: 445 ICQQGAV 451
           +   GA+
Sbjct: 478 VAGAGAL 484


Lambda     K      H
   0.320    0.133    0.380 

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: 895
Number of extensions: 42
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: 473
Length of database: 846
Length adjustment: 38
Effective length of query: 435
Effective length of database: 808
Effective search space:   351480
Effective search space used:   351480
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: 54 (25.4 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