GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Sphingomonas koreensis DSMZ 15582

Align D-2-hydroxyglutarate--pyruvate transhydrogenase DLD2; D-2HG--pyruvate transhydrogenase DLD2; Actin-interacting protein 2; D-lactate dehydrogenase [cytochrome] 2, mitochondrial; D-lactate ferricytochrome C oxidoreductase; D-LCR; EC 1.1.99.40; EC 1.1.2.4 (characterized)
to candidate Ga0059261_1691 Ga0059261_1691 FAD/FMN-containing dehydrogenases

Query= SwissProt::P46681
         (530 letters)



>FitnessBrowser__Korea:Ga0059261_1691
          Length = 484

 Score =  228 bits (580), Expect = 5e-64
 Identities = 138/441 (31%), Positives = 229/441 (51%), Gaps = 14/441 (3%)

Query: 93  DWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGG-SVPI-FDELIL 150
           D    +   ++ V RP+S  +V+ ++     + IA+VPQGGNTGLVGG +VP     L+L
Sbjct: 45  DMTGNWPSGAQAVARPRSTAEVARLVQAAAAQGIAIVPQGGNTGLVGGCAVPAETPALLL 104

Query: 151 SLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGVVATNA 210
           S   L  IR  D  +  +  +AG IL      V    +  PL LG++GS  +GG+V+TNA
Sbjct: 105 STRRLRSIRAIDLHAPAVIAEAGCILAEVQEAVAAHGFTIPLGLGSEGSATIGGLVSTNA 164

Query: 211 GGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIGIITGV 270
           GG+R LR+G +   VLGLEVV+P+G++ N + ++ K+N GYDLKQLFIG EGT+G++T  
Sbjct: 165 GGIRALRHGVMRNQVLGLEVVLPDGRVWNGLRTLAKNNMGYDLKQLFIGGEGTLGVVTAA 224

Query: 271 SILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKSQVLAKSQLKDA 330
           ++  VP  +     +L+VE       +    R  L +++++FE +  +      + +   
Sbjct: 225 ALRLVPASRQIETLWLAVEDPAAALALLGALRTALGDLVTSFELIQRRGVEWGMAAVPGL 284

Query: 331 AFPLEDEHPFYILIETSGSNKDHD-DSKLETFLENVMEEGIVTDGVVAQDETELQNLWKW 389
             P    H +++L E + +       + +E  L +V E+G+  DG++A+ E + + LW+ 
Sbjct: 285 RVPDSGAHGWFVLAEVATAATGLPLRAAVEAALADVFEQGLALDGMLAESEAQRRELWRI 344

Query: 390 REMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIGYGHVG 449
           RE +     A       DV++PL  +        A L E E       P    +G+GH+G
Sbjct: 345 REAVVVGKAAGKPSISVDVAVPLGQV-------PAFLVETEAAAAGLLPGCETLGFGHLG 397

Query: 450 DGNLHLNV----AVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYIGYSKSP 505
           DGN+H +V       E      + +   V        G++ AEHG+G + +  +  +   
Sbjct: 398 DGNIHFSVHRGANDTERFAGTAEAIAAKVEAIALRLGGTICAEHGVGRRMRAAVADALDA 457

Query: 506 EEVKMMKDLKVHYDPNGILNP 526
            E+ +++ +K   DP+  +NP
Sbjct: 458 AELDLIRAVKRALDPHNRMNP 478


Lambda     K      H
   0.316    0.135    0.385 

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: 487
Number of extensions: 24
Number of successful extensions: 5
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: 530
Length of database: 484
Length adjustment: 34
Effective length of query: 496
Effective length of database: 450
Effective search space:   223200
Effective search space used:   223200
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: 52 (24.6 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