GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Sphingomonas koreensis DSMZ 15582

Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate Ga0059261_1691 Ga0059261_1691 FAD/FMN-containing dehydrogenases

Query= BRENDA::O23240
         (559 letters)



>FitnessBrowser__Korea:Ga0059261_1691
          Length = 484

 Score =  241 bits (614), Expect = 6e-68
 Identities = 149/479 (31%), Positives = 250/479 (52%), Gaps = 10/479 (2%)

Query: 84  SLIQRNPLFSSLDSKDVSYFKEILGEKNVVEDKERLETANTDWMHKYKGSSKLMLLPKNT 143
           S +   P  +S     +S   E LG    V D++       D    +   ++ +  P++T
Sbjct: 4   SAVTTVPASASPTDPCLSALSETLGADLFVRDEDARAACLRDMTGNWPSGAQAVARPRST 63

Query: 144 QEVSQILEYCDSRRLAVVPQGGNTGLVGG-SVPV-FDEVIVNVGLMNKILSFDEVSGVLV 201
            EV+++++   ++ +A+VPQGGNTGLVGG +VP     ++++   +  I + D  +  ++
Sbjct: 64  AEVARLVQAAAAQGIAIVPQGGNTGLVGGCAVPAETPALLLSTRRLRSIRAIDLHAPAVI 123

Query: 202 CEAGCILENLATFLDTKGFIMPLDLGAKGSCHIGGNVSTNAGGLRLIRYGSLHGTVLGLE 261
            EAGCIL  +   +   GF +PL LG++GS  IGG VSTNAGG+R +R+G +   VLGLE
Sbjct: 124 AEAGCILAEVQEAVAAHGFTIPLGLGSEGSATIGGLVSTNAGGIRALRHGVMRNQVLGLE 183

Query: 262 AVTANGNVLDMLGTLRKDNTGYDLKHLFIGSEGSLGIVTKVSILTQPKLSSVNLAFIACK 321
            V  +G V + L TL K+N GYDLK LFIG EG+LG+VT  ++   P    +   ++A +
Sbjct: 184 VVLPDGRVWNGLRTLAKNNMGYDLKQLFIGGEGTLGVVTAAALRLVPASRQIETLWLAVE 243

Query: 322 DYLSCQKLLVEAKRNLGEILSAFEFLDNNSMDLVLNHLDGVRNPVSSSENFYILIE-TTG 380
           D  +   LL   +  LG+++++FE +    ++  +  + G+R P S +  +++L E  T 
Sbjct: 244 DPAAALALLGALRTALGDLVTSFELIQRRGVEWGMAAVPGLRVPDSGAHGWFVLAEVATA 303

Query: 381 SDETNDREKLEAFLLKSLEKGLVSDGVIAQDINQASSFWRIREGITEALQKAGAVYKYDL 440
           +     R  +EA L    E+GL  DG++A+   Q    WRIRE +             D+
Sbjct: 304 ATGLPLRAAVEAALADVFEQGLALDGMLAESEAQRRELWRIREAVVVGKAAGKPSISVDV 363

Query: 441 SLPVEEIYNIVNDLRGRLGDL---ANVMGYGHLGDGNLHLNI-SAAEYNDKLLGLIEPY- 495
           ++P+ ++   + +       L      +G+GHLGDGN+H ++   A   ++  G  E   
Sbjct: 364 AVPLGQVPAFLVETEAAAAGLLPGCETLGFGHLGDGNIHFSVHRGANDTERFAGTAEAIA 423

Query: 496 --VYEWTSKHRGSISAEHGLGVMKANEIFYSKSPETVALMASIKKLLDPKGILNPYKVL 552
             V     +  G+I AEHG+G      +  +     + L+ ++K+ LDP   +NP  V+
Sbjct: 424 AKVEAIALRLGGTICAEHGVGRRMRAAVADALDAAELDLIRAVKRALDPHNRMNPGAVI 482


Lambda     K      H
   0.317    0.136    0.390 

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: 557
Number of extensions: 28
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: 559
Length of database: 484
Length adjustment: 35
Effective length of query: 524
Effective length of database: 449
Effective search space:   235276
Effective search space used:   235276
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.

Links

Downloads

Related tools

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