GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS09620 CA265_RS09620 FAD-binding oxidoreductase

Query= SwissProt::P46681
         (530 letters)



>FitnessBrowser__Pedo557:CA265_RS09620
          Length = 467

 Score =  223 bits (569), Expect = 9e-63
 Identities = 147/475 (30%), Positives = 242/475 (50%), Gaps = 18/475 (3%)

Query: 58  FKKLTSDDLNYFKSILSEQEILRASESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLI 117
           F K+  + L   K+ +  +++   ++++ L  Y+ D     + Q ++V++P + E+VS +
Sbjct: 3   FTKINPEILAEIKAAVGAEKVF--TDADSLENYSHDETEDLRYQPEVVVKPTTPEEVSAL 60

Query: 118 LNYCNDEKIAVVPQGGNTGLVGGSVPIFDELILSLANLNKIRDFDPVSGILKCDAGVILE 177
           L  CN   + V P+GG TGL G ++PI+  + LS+     I D D  +     + GVI E
Sbjct: 61  LKICNAHHVPVTPRGGGTGLSGAALPIYGGISLSMEKFKAILDIDTENLQATVEPGVITE 120

Query: 178 NANNYVMEQNYMFPLDLGAKGSCHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQI 237
              N V E+  ++P+D  +KGSC +GG VA  +GG R+++YG++   +L LEVV+PNG I
Sbjct: 121 EFINAVAEKGLLYPVDPSSKGSCFIGGNVAHGSGGPRVVKYGTIREYILNLEVVLPNGDI 180

Query: 238 VNSMHSMRKDNTGYDLKQLFIGSEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKV 297
           + +  +  K  +GY+L QL IGSEGT+ ++T +    +PKP    +   S  + ED    
Sbjct: 181 IWTGANTLKYASGYNLTQLMIGSEGTLAVVTKIVTKLLPKPSQSVLMMGSFSTNEDACAA 240

Query: 298 FVRARQELSEILSAFEFMDAKSQVLAKSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSK 357
            V A        SA EFM+ K  V    +  D  F L+D+    ++IE  G + D     
Sbjct: 241 -VSAIFRAGVTPSALEFMERKG-VEWVIKFDDIKFDLKDDVAALLMIEFDGDDLDDIFKN 298

Query: 358 LETFLENVMEEGIVTDGVVAQDETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYS 417
            E     V+EE   T+ + A    + + LW+ R  + E+ ++N    + D  +P   L  
Sbjct: 299 CEK-TNIVLEEHNCTEVLFADTAAQKEELWRMRRTMAESVKSNSVYKEEDTVVPRAALPK 357

Query: 418 LVEATNARLSEAELVGDSPKPVVGAIGYGHVGDGNLHLNVAVREYNKNIEKTLEPF---- 473
           LV            +G   K    ++ YGH GDGNLH+N+     +    K    F    
Sbjct: 358 LVNGIKE-------IG--AKYGFESVCYGHAGDGNLHVNIIKAGMSDEDWKNKLKFGIAE 408

Query: 474 VYEFVSSKHGSVSAEHGLGFQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYK 528
           ++E  ++  G++S EHG+G  +K ++    S   + +M+ +K  +DP GILNP K
Sbjct: 409 IFELTTALGGTLSGEHGIGLVQKEFMPIKYSEIHLNLMRGIKNIFDPKGILNPGK 463


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: 610
Number of extensions: 30
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: 467
Length adjustment: 34
Effective length of query: 496
Effective length of database: 433
Effective search space:   214768
Effective search space used:   214768
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