GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Pseudomonas putida KT2440

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 PP_5154 PP_5154 putative Oxidoreductase, FAD-binding

Query= SwissProt::P46681
         (530 letters)



>FitnessBrowser__Putida:PP_5154
          Length = 455

 Score =  293 bits (750), Expect = 9e-84
 Identities = 160/449 (35%), Positives = 256/449 (57%), Gaps = 21/449 (4%)

Query: 87  LSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIFD 146
           L  Y +DW + Y      ++ PK++E+V  I+++ N  K+A+VP GG TGL  G+V    
Sbjct: 16  LEAYGKDWTKHYPPAPSAIVFPKTIEQVQAIVHWANAHKVALVPSGGRTGLSAGAVAANG 75

Query: 147 ELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGVV 206
           E++++   +N+I  F+     + C  GV+      Y  EQ   +P+D  + GS  +GG +
Sbjct: 76  EVVVAFDYMNQILGFNAFDRTVVCQPGVVTRQLQTYAEEQGLYYPVDFASSGSSQIGGNI 135

Query: 207 ATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIGI 266
            TNAGG++++RYG     V GL+VV   G+++     + K+ TGYDL+QLFIG+EGT+G 
Sbjct: 136 GTNAGGIKVIRYGMTRNWVAGLKVVTGKGELLELNKDLIKNATGYDLRQLFIGAEGTLGF 195

Query: 267 ITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAK--SQVLAK 324
           +   ++     P+      L    F+ +  V    + +L   L+AFEF   K  +++LA+
Sbjct: 196 VVEATMRLDRAPRNLTAMVLGTPDFDSIMPVLHAFQGKLD--LTAFEFFSDKGLAKILAR 253

Query: 325 SQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETELQ 384
               D   P   + PFY L+E   S +D  +  L TF E+ +E+G V DGV++Q E++L+
Sbjct: 254 G---DVPAPFATDCPFYALLEFEASTEDVANEALATF-EHCVEQGWVLDGVMSQSESQLK 309

Query: 385 NLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIG 444
           NLWK RE + E + ++   YK D+S+ +  + + +   +A +SE         P    + 
Sbjct: 310 NLWKLREYLSE-TISHWTPYKNDISVTVSKVPAFLRDIDAIVSE-------HYPDYEVVW 361

Query: 445 YGHVGDGNLHLNVAVREYNKNIE-----KTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYI 499
           YGH+GDGNLHLN+   E+    +       +  +V+E V   +GS+SAEHG+G  K++Y+
Sbjct: 362 YGHIGDGNLHLNILKPEHMSKDDFFASCAKVNKWVFEIVERYNGSISAEHGVGMTKRDYL 421

Query: 500 GYSKSPEEVKMMKDLKVHYDPNGILNPYK 528
           GYS+SPEE+  MK +K  +DPNGI+NP K
Sbjct: 422 GYSRSPEEIACMKAIKAVFDPNGIMNPGK 450


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: 538
Number of extensions: 22
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: 455
Length adjustment: 34
Effective length of query: 496
Effective length of database: 421
Effective search space:   208816
Effective search space used:   208816
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