GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Dinoroseobacter shibae DFL-12

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 3608683 Dshi_2076 FAD linked oxidase domain protein (RefSeq)

Query= SwissProt::P46681
         (530 letters)



>FitnessBrowser__Dino:3608683
          Length = 472

 Score =  272 bits (695), Expect = 2e-77
 Identities = 157/446 (35%), Positives = 243/446 (54%), Gaps = 19/446 (4%)

Query: 90  YNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSV----PIF 145
           Y E+   +Y G   L++ P + E+V+ ++      K+ ++P GG TGLVGG +    P+ 
Sbjct: 29  YLEEPRGRYAGSGGLLVAPGATEEVATLVRLAQAHKVPIIPYGGGTGLVGGQIAPAGPV- 87

Query: 146 DELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGV 205
             +ILSL  +  IR   P   +L  DAG +L        +   +FPL L ++GS  +GGV
Sbjct: 88  -PVILSLRRMRSIRAVYPEENVLVADAGAVLAEVQQAARDVGRLFPLSLASEGSATIGGV 146

Query: 206 VATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIG 265
           +ATNAGG+ +LRYG+     LGLE VMP+G I + +  +RK+N GYDL+ L IG+EGT+G
Sbjct: 147 LATNAGGVNVLRYGNARDLCLGLEAVMPDGAIWHGLTRLRKNNMGYDLRHLLIGAEGTLG 206

Query: 266 IITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKSQVLAKS 325
           IITG ++   P P+   V  L V+S      +   A +   + +SAFE +  +       
Sbjct: 207 IITGAALRLSPLPQRHGVGLLVVDSPAAALDLLALAGEVAGDTISAFELISGRGFEFFAE 266

Query: 326 QLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETELQN 385
            + +   PL+    + +LI+ +G++    +  LET      E G+V+DGV+AQ E +   
Sbjct: 267 TMPEMRAPLDPVPAWSVLIDLAGASGFDPEGALETLFARAAEAGLVSDGVIAQSEAQADA 326

Query: 386 LWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIGY 445
           LW  RE IPEA++  G V  +D+S+PL ++ + +E   ARL+    +GD          +
Sbjct: 327 LWALRENIPEANRRIGSVSSHDISVPLSEIPNFIETATARLAG---IGD-----YRINCF 378

Query: 446 GHVGDGNLHLNV-----AVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYIG 500
           GHVGDGNLH NV       R  +++    ++  V++ V    GSVSAEHG+G  K   + 
Sbjct: 379 GHVGDGNLHYNVFPQPGRSRADHEDERPAIKTCVHDLVHELGGSVSAEHGVGRLKVEDLE 438

Query: 501 YSKSPEEVKMMKDLKVHYDPNGILNP 526
               P +   M+ +K   DP+G++NP
Sbjct: 439 RYGDPVKQAAMRAIKDALDPHGLMNP 464


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: 614
Number of extensions: 22
Number of successful extensions: 4
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: 472
Length adjustment: 34
Effective length of query: 496
Effective length of database: 438
Effective search space:   217248
Effective search space used:   217248
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