GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaK' in Azospirillum brasilense Sp245

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 AZOBR_RS23290 AZOBR_RS23290 dihydroxyacetone kinase subunit K

Query= SwissProt::F1RKQ4
         (579 letters)



>FitnessBrowser__azobra:AZOBR_RS23290
          Length = 332

 Score =  204 bits (520), Expect = 3e-57
 Identities = 119/335 (35%), Positives = 188/335 (56%), Gaps = 9/335 (2%)

Query: 4   KKLVNSVAGCADDALAGLVACNPSLQLLQGHRVALRSDLDSLKGRVALLSGGGSGHEPAH 63
           KKL+N  A   D+ L GL A +PSL         +R    +  G+V +++GGGSGH P  
Sbjct: 2   KKLINDPAHYVDEMLDGLCAAHPSLMRDGPAGRVIRRTEGARAGKVGIVTGGGSGHLPLF 61

Query: 64  AGFIGKGMLTGVIAGAVFTSPAVGSILAAIRAVAQAGTVGTLLIVKNYTGDRLNFGLARE 123
            G++G G++     G VF  P V S +AAI+A    G  G L +  NY GDR+NF +A E
Sbjct: 62  TGYVGPGLVDACSIGNVFEGPTVDSCMAAIKAAD--GGRGVLRLYGNYGGDRMNFDMAGE 119

Query: 124 QARAEGIPVEMVVVGDDSAFTV-LKKAGRRGLCGTVLIHKVAGALAEAGVGLEEITNRVS 182
               EG+ +  V+  DD A     +++ RRG+ G V  +K+AGA A+ G  L E+T   +
Sbjct: 120 FLEEEGLELSTVLGTDDIASAAPAERSKRRGVAGIVYAYKIAGARADEGASLAEVTAAAA 179

Query: 183 VVAKAMGTLGVSLSSCSVPGS-RPTFELSADEVELGLGIHGEAGVLRIKMATADEIVAHM 241
              +   T+G +LSSC +PG+  P+F ++  E+E+G+GIHGE G+ R  +  AD +   M
Sbjct: 180 KAVERTRTIGCALSSCQIPGAAEPSFRIAPSEMEMGIGIHGEPGIWRDTLKPADAVADEM 239

Query: 242 LNHMTDSSNVSHVPVQSGSSVVLMVNNLGGLSYLELGIIADAAVRFLEGRGVKIARALVG 301
           ++ +     ++  P  SG+ V ++VN+LG     EL I+       L+  G+ + + LVG
Sbjct: 240 VDRL-----LAERPEGSGNRVSVLVNSLGATPLEELFILYRRIAERLDKAGLAVVQPLVG 294

Query: 302 TFMSALEMPGVSLTLLLVDEPLLKLIDAETTAAAW 336
            +++++EM GVSL+L  +D+ L +L+ A  +   W
Sbjct: 295 PYVTSMEMTGVSLSLCFLDDELERLLAAPASCPFW 329


Lambda     K      H
   0.315    0.131    0.367 

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: 447
Number of extensions: 20
Number of successful extensions: 6
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: 579
Length of database: 332
Length adjustment: 32
Effective length of query: 547
Effective length of database: 300
Effective search space:   164100
Effective search space used:   164100
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: 51 (24.3 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