GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ydiJ 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)



>lcl|FitnessBrowser__Dino:3608683 Dshi_2076 FAD linked oxidase
           domain protein (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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