Alignments for a candidate for dhaK' in Tatumella morbirosei LMG 23360

GapMind for catabolism of small carbon sources

Alignments for a candidate for dhaK' in Tatumella morbirosei LMG 23360

Align Triokinase/FMN cyclase; Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing); EC 2.7.1.28; EC 2.7.1.29; EC 4.6.1.15 (characterized)
to candidate WP_038021922.1 HA49_RS08100 dihydroxyacetone kinase family protein

Query= SwissProt::Q4KLZ6
         (578 letters)



>NCBI__GCF_000757425.2:WP_038021922.1
          Length = 586

 Score =  238 bits (607), Expect = 5e-67
 Identities = 172/574 (29%), Positives = 287/574 (50%), Gaps = 22/574 (3%)

Query: 14  AGDALAGFVACNPDLQLLQGYRVALRSDLDSLKGRVALLSGGGSGHEPAHAGFIGKGMLT 73
           A + +AGFV  N    +++     +  +  S  G VA++ GGGSGH PA AG +G+G+  
Sbjct: 12  AKEMVAGFV--NAHSSMVRQVPGGVVRNTKSKPGSVAVVVGGGSGHYPAFAGLVGQGLAH 69

Query: 74  GVIAGAVFASPAVGSILAAIRAVAQAGTAGTLLIVKNYTGDRLNFGLAMEQAKAEGISVE 133
           G   G +FASP+   I +  RA    G  G LL+  NY GD L+FGLA E+ +AEGI  E
Sbjct: 70  GAAMGNLFASPSAQQICSVARAANNGG--GVLLMFGNYAGDVLHFGLACERLRAEGIPCE 127

Query: 134 MVVIEDD-SAFTVLKKAGRRGLCGTILIHKVAGALAEEGMGLEEITKKVSVIAKAIGTLG 192
           ++ + DD S+  + ++  RRG+ G +++ K A A AE G  L E+            TLG
Sbjct: 128 VMPVTDDISSAPLAERTKRRGVAGDLVVFKTAAAAAERGDSLAEVLAVARHANDNTRTLG 187

Query: 193 VSLSPCSVPGTK-PTFELAADEMELGLGIHGEAGVRRIKLVPVDQIVTLMLDHMTDT--S 249
           ++ S C  PG + P F +   +M  GLGIHGE G+  + +    +I + +   + +    
Sbjct: 188 LAFSGCKFPGAEQPLFTVPEGKMGFGLGIHGEPGISELPVSSSHEIASKLATKLLEERPE 247

Query: 250 NISHVPVKSGSSVVLMVNNLGGLSFLELGIIADAAIRLLEGRGVKVARALVGTFMSALEM 309
           +IS  P   G+ + +++N LG + + EL ++ +    LLE  GV++    +G F+++ +M
Sbjct: 248 SISQTP---GARLGVIINGLGSVKYEELFVLWNDIQPLLEKAGVELVDIQIGEFVTSFDM 304

Query: 310 RGVSLTLMLVDEPLLKLIDAETNAKAWPHMSKVSVTGRNRIRAAPTEPAEAPEATAAGGV 369
            G S++ +  +  + +L  A     A+   S +     + ++   +   + PEAT     
Sbjct: 305 AGFSVSFVWFEGEIEELWLAPATTPAFSRGSVLRHEPLDPVQLQQSGEVKIPEATEEAKT 364

Query: 370 ASKQMTLVLDRISTTLIGLEEHLNALDRAAGDGDCGSTHSR----AAKAIQGWLKEGPTP 425
           A++   ++L+ + T L    + L  +D  AGDGD G    R    A KA    L +G   
Sbjct: 365 AAENTMVILNALETLLTEKCDELGQIDAIAGDGDHGIGMLRGVVAACKAANQVLDQG--- 421

Query: 426 ASPAQVLSKLSVLLLEKMGGSSGALYGLFLTAAAQPLKANTDLPAWSAAMDAGLKA---M 482
           A    +L   +    +  GG+SGA++G+ L      L  N++ P  ++     ++A   +
Sbjct: 422 AGVGFLLQTAADAWSDDAGGTSGAIWGVILNTLGTTL-GNSEKPTVTSVAKGVVQANHGV 480

Query: 483 QKYGKAAPGDRTMLDSLWAAAQELQAWKSPGASLLPVLTKAVKSAEAAAEATKNMEAGAG 542
             +GKA PGD+T++D L   ++ L +  + G SL     KA   AE +A  T  +    G
Sbjct: 481 MHFGKAKPGDKTLVDVLLPFSEALDSAAAEGLSLADAWHKAALVAEKSAAETAQLVPKIG 540

Query: 543 RASYISSAQLDQPDPGAVAAAAIFRAILEVLQTK 576
           RA  ++   +  PD GAV+ A +   + + L  K
Sbjct: 541 RARPLAERSVGTPDAGAVSLALMIATVDKHLSHK 574


Lambda     K      H
   0.316    0.131    0.366 

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: 691
Number of extensions: 37
Number of successful extensions: 7
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: 578
Length of database: 586
Length adjustment: 36
Effective length of query: 542
Effective length of database: 550
Effective search space:   298100
Effective search space used:   298100
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: 41 (21.6 bits)
S2: 53 (25.0 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources