GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Halioglobus japonicus S1-36

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 WP_084199888.1 C0029_RS05565 FAD-binding oxidoreductase

Query= SwissProt::P46681
         (530 letters)



>NCBI__GCF_002869505.1:WP_084199888.1
          Length = 456

 Score =  298 bits (764), Expect = 2e-85
 Identities = 161/440 (36%), Positives = 255/440 (57%), Gaps = 12/440 (2%)

Query: 91  NEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIFDELIL 150
           N  W R  +  +  ++RP++ E+VS I+  C+ ++  VVP GG TGLV G      +L+L
Sbjct: 27  NHSWGRG-ECPAMAIVRPRTTEEVSRIMALCHAQEQRVVPWGGLTGLVDGITCEAGDLVL 85

Query: 151 SLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGVVATNA 210
           S+  +  I   +P +G L+  AG +L++  +   E  + F +DLG +GS  +GG+VATNA
Sbjct: 86  SMERMQNIEHCEPDAGTLRVQAGAVLQSVQDAAAEAGWQFAVDLGGRGSAQIGGLVATNA 145

Query: 211 GGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIGIITGV 270
           GG  ++RYG +   VLGLEVV+ +G++++S++ + K+N GYD+KQLFIGSEGT+GI+T  
Sbjct: 146 GGNAVVRYGMMREQVLGLEVVLADGRVMSSLNEVLKNNAGYDMKQLFIGSEGTLGIVTRA 205

Query: 271 SILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKSQVLAKSQLKDA 330
            +   P   A   ++L + SF+DV  +    +  L   LS+FE M A        +L   
Sbjct: 206 VLRLRPAANARQTAFLGMNSFDDVAALLRHLQSHLEGKLSSFEVMWANHYRFMVEELATH 265

Query: 331 AFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETELQNLWKWR 390
              L  ++P+Y+L+E+ G   D +++   + L  +MEEG + D V+AQ   + + LW  R
Sbjct: 266 QTFLPVDYPYYVLVESEGQFPDREEALFTSVLGELMEEGTIADAVIAQSGQQAEQLWAMR 325

Query: 391 EMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIGYGHVGD 450
           + +    +A   +  +D+SLPL+D+ + V A    L++         P    + +GH+GD
Sbjct: 326 DDVASLIEAMAPMAAFDISLPLRDMQTYVAAMEQGLAKR-------LPEARVVVFGHLGD 378

Query: 451 GNLHLNVAVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYIGYSKSPEEVKM 510
           GN+HL V     N    K +E  VY  + +  GS+SAEHG+G +K++Y+ YSK   E+ +
Sbjct: 379 GNIHLVVG----NIPDHKAVEEVVYGELRNLGGSISAEHGIGLEKRDYLAYSKGEIEIDL 434

Query: 511 MKDLKVHYDPNGILNPYKYI 530
           M+ LK   DP GILNP K I
Sbjct: 435 MRTLKHALDPKGILNPGKVI 454


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: 540
Number of extensions: 21
Number of successful extensions: 3
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: 456
Length adjustment: 34
Effective length of query: 496
Effective length of database: 422
Effective search space:   209312
Effective search space used:   209312
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 24 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