Alignments for a candidate for dhaK' in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for dhaK' in Klebsiella michiganensis M5al

Align glycerone kinase; EC 2.7.1.29 (characterized)
to candidate BWI76_RS24610 BWI76_RS24610 dihydroxyacetone kinase

Query= CharProtDB::CH_008528
         (552 letters)



>FitnessBrowser__Koxy:BWI76_RS24610
          Length = 549

 Score =  900 bits (2326), Expect = 0.0
 Identities = 460/548 (83%), Positives = 501/548 (91%)

Query: 1   MSQFFFNQRTHLVSDVIDGAIIASPWNNLARLESDPAIRIVVRRDLNKNNVAVISGGGSG 60
           MSQFFFNQR +LV+DVI+G IIASPWNNLARLESDPAIR+VVRRDL+KNNVAVISGGGSG
Sbjct: 1   MSQFFFNQRANLVNDVIEGTIIASPWNNLARLESDPAIRVVVRRDLDKNNVAVISGGGSG 60

Query: 61  HEPAHVGFIGKGMLTAAVCGDVFASPSVDAVLTAIQAVTGEAGCLLIVKNYTGDRLNFGL 120
           HEPAH GF+GKGMLTAAVCGD+FASPSVDAVLTAIQAVTG+AGCLLIVKNYTGDRLNFGL
Sbjct: 61  HEPAHAGFVGKGMLTAAVCGDLFASPSVDAVLTAIQAVTGDAGCLLIVKNYTGDRLNFGL 120

Query: 121 AAEKARRLGYNVEMLIVGDDISLPDNKHPRGIAGTILVHKIAGYFAERGYNLATVLREAQ 180
           AAEKARR+GYNVEMLIVGDDISLPDNKHPRGIAGTILVHK+AGYFAERG+NLATVLREAQ
Sbjct: 121 AAEKARRMGYNVEMLIVGDDISLPDNKHPRGIAGTILVHKVAGYFAERGHNLATVLREAQ 180

Query: 181 YAASNTFSLGVALSSCHLPQETDAAPRHHPGHAELGMGIHGEPGASVIDTQNSAQVVNLM 240
           YAA +TFSLG+AL+SCHLPQ+ + APRHH   AELGMGIHGEPGASVI TQNSA++V LM
Sbjct: 181 YAAGHTFSLGLALASCHLPQDAETAPRHHADQAELGMGIHGEPGASVIATQNSAEIVTLM 240

Query: 241 VDKLLAALPETGRLAVMINNLGGVSVAEMAIITRELASSPLHSRIDWLIGPASLVTALDM 300
            +KL AALPETGRLAVMINNLGGVS+AEMAI+TRELA +PL  RIDWLIGPASLVTALDM
Sbjct: 241 AEKLSAALPETGRLAVMINNLGGVSIAEMAILTRELAHTPLQQRIDWLIGPASLVTALDM 300

Query: 301 KGFSLTAIVLEESIEKALLTEVETSNWPTPVPPREITCVVSSHASARVEFQPSANALVAG 360
           KGFSLTAIVLEESIEKALL+ VET+ W TPV PREI+ + SS  S RVEF+PS N++VA 
Sbjct: 301 KGFSLTAIVLEESIEKALLSAVETAGWQTPVQPREISVMPSSLRSTRVEFEPSENSVVAD 360

Query: 361 IVELVTATLSDLETHLNALDAKVGDGDTGSTFAAAAREIASLLHRQQLPLNNLATLFALI 420
            VE VT TLSDLE  LNALDAKVGDGDTGSTFAA AR+IA LL R+QLPL NLATL ALI
Sbjct: 361 YVERVTGTLSDLEADLNALDAKVGDGDTGSTFAAGARDIADLLQRRQLPLANLATLLALI 420

Query: 421 GERLTVVMGGSSGVLMSIFFTAAGQKLEQGANVVEALNTGLAQMKFYGGADEGDRTMIDA 480
           GERLTVVMGGSSGVLMSIFFTAAGQKLEQGA+V EALN GLAQMKFYGGADEGDRTMIDA
Sbjct: 421 GERLTVVMGGSSGVLMSIFFTAAGQKLEQGASVAEALNAGLAQMKFYGGADEGDRTMIDA 480

Query: 481 LQPALTSLLAQPKNLQAAFDAAQAGAERTCLSSKANAGRASYLSSESLLGNMDPGAQRLA 540
           LQPAL +L A+P+NLQAAF AAQAGA+RT  +SKANAGRASYL+S+SL GNMDPGA  +A
Sbjct: 481 LQPALAALAAEPENLQAAFAAAQAGADRTLHASKANAGRASYLNSDSLRGNMDPGAHAVA 540

Query: 541 MVFKALAE 548
           MVFKALA+
Sbjct: 541 MVFKALAQ 548


Lambda     K      H
   0.317    0.132    0.373 

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: 984
Number of extensions: 23
Number of successful extensions: 1
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: 552
Length of database: 549
Length adjustment: 36
Effective length of query: 516
Effective length of database: 513
Effective search space:   264708
Effective search space used:   264708
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 (21.7 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 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