GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_3582 N515DRAFT_3582 FAD/FMN-containing dehydrogenase

Query= SwissProt::P46681
         (530 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3582
          Length = 467

 Score =  281 bits (720), Expect = 3e-80
 Identities = 162/450 (36%), Positives = 248/450 (55%), Gaps = 22/450 (4%)

Query: 86  DLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIF 145
           DL  Y  DW R++      +  P +VE+   +L + N+  +AVVP GG TGL GG+V   
Sbjct: 31  DLEHYGRDWTRRWTPAPLAIALPATVEEAQAVLRWANEHGVAVVPSGGRTGLSGGAVAAQ 90

Query: 146 DELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGV 205
            EL+LSL  +N++  FDP+   L   AG+ L+  ++       ++P+D  A+GSC +GG 
Sbjct: 91  GELVLSLERMNRVLGFDPIDRTLTVQAGIALQAVHDAARSHGLIYPVDFAARGSCSIGGN 150

Query: 206 VATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIG 265
           +ATNAGG+R++RYG+    + GL+V+  NG+++     + K+++GYDL+ L IGSEGT+G
Sbjct: 151 IATNAGGIRVIRYGNTREWIAGLKVIAGNGELLELNRGLIKNSSGYDLRHLTIGSEGTLG 210

Query: 266 IITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMD--AKSQVLA 323
           I+   ++     P    V  L++     + +VF   R  L   L AFEF    A   VLA
Sbjct: 211 IVVEATLRLAEPPPPSQVMLLALPDMAALMQVFALFRARLK--LQAFEFFTDIALRHVLA 268

Query: 324 KSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETEL 383
                 A   L+ EHPFY++ E   +++   D+ L  F E+ + EG + DG +AQ E + 
Sbjct: 269 HG----AQRALDGEHPFYVVTEFDAADEAAQDAALAAF-EHGVNEGWIADGAIAQSEAQA 323

Query: 384 QNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAI 443
             LW+ RE I E S A    YK D+SL +  L + ++   A L +A        P    +
Sbjct: 324 AALWRLREGITE-SLAPHKPYKNDISLRIGALPAFLDEIQALLGDA-------YPHFEVV 375

Query: 444 GYGHVGDGNLHLNVAVREYNKNIE-----KTLEPFVYEFVSSKHGSVSAEHGLGFQKKNY 498
            +GH+GDGNLH+NV   E   + E     + +   +   +    GS+SAEHG+G  KK Y
Sbjct: 376 WFGHIGDGNLHINVLKPEGLADAEFIAQCEQVTKLLAAALQRHGGSISAEHGIGLVKKPY 435

Query: 499 IGYSKSPEEVKMMKDLKVHYDPNGILNPYK 528
           +  ++S  E+ +M+ +K  +DPNGILNP K
Sbjct: 436 LESTRSAAEIALMRGVKQVFDPNGILNPGK 465


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: 523
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: 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