GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Desulfovibrio vulgaris Miyazaki F

Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes (uncharacterized)
to candidate 8499450 DvMF_0222 FAD-dependent pyridine nucleotide-disulphide oxidoreductase (RefSeq)

Query= curated2:Q8KCW2
         (469 letters)



>FitnessBrowser__Miya:8499450
          Length = 473

 Score =  279 bits (714), Expect = 1e-79
 Identities = 181/481 (37%), Positives = 259/481 (53%), Gaps = 28/481 (5%)

Query: 6   TLAAQFDVAVIGSGPGGYEAAIHAARYGLKTCIVEKAVLGGVCVNWGCIPTKALLRSAEV 65
           T + ++D+ ++G GPGG  AA  AA  GL   +V++  LGG C+N GCIPTK LL +   
Sbjct: 2   TPSTRYDMIILGGGPGGSRAAFDAAARGLSVALVDRDGLGGTCLNRGCIPTKLLLGATAA 61

Query: 66  FDLAKNPETFGVNVGNVSFDLAQAVKRSRNVALKSSKGVAYLLKKAAVEVLAGEAVLTGG 125
             L +  +      G+++FDL    +R       + + +   LK A + V AGE  +TG 
Sbjct: 62  LPLLETQKKLKGADGHIAFDLPALQQRKDRYVKGTRQALEKRLKAAGIAVYAGEGRVTGE 121

Query: 126 A--------GVMVTMPDGSVR--MLGAKNIIVATGSTPRVIPGLEPDGKKIITSREALIL 175
                     V+    DG+ +   LG   +IVATGSTP   PGL  DG  ++ S   L +
Sbjct: 122 RQGDADGELAVVAAQADGTTQETRLGWGTLIVATGSTPASFPGLAADGAAVLDSTALLDV 181

Query: 176 KEVPKSMIVVGGGAIGVEMAWFYAKAGSKVTIVELMPRMLPAEEAEVSEALKRSFEKAGI 235
            E P+S+IVVGGGAIG+EMA F+++ G+++TIVE M R+ P E+AEV + L++ + + G 
Sbjct: 182 TEAPESLIVVGGGAIGLEMADFFSRFGTRITIVEGMGRLAPTEDAEVGDTLRKVYAREGW 241

Query: 236 TVHCGAKLDNVAVSESGVSAELVVEGSAPQTLNASCLLVAVGVTGAIDGLGLDAVGVETE 295
           T+H G K+ ++A     V    V+     + L AS  L+AVG   A  G+GL+A+G    
Sbjct: 242 TIHNGRKVASLAT----VDGHAVLRFEDGEELTASKALLAVGRRPASVGIGLEALGTTLR 297

Query: 296 -RGFIRTDGQCRTSAPGIYAIGDVRGGMLLAHKASAEAAIAVEAIAGKSPEPLSEPLIPR 354
             G+++TD   R +AP +YAIGDV G  LLAH A  +A  AV    G +  P    ++P 
Sbjct: 298 GPGWMQTDEWLR-AAPHVYAIGDVNGRTLLAHAADHQARYAVRHACGDTAAPYDAGVMPA 356

Query: 355 CVYAQPSVASVGLTEEAAVNAGYQVAVGRSQFAASGKANAYGQLEGFVKLVFDAATGKML 414
           C+Y       VG T E   NAG+   V RS   A+  A AYG  +GF+K+V+    G++ 
Sbjct: 357 CIYGHLEAMRVGPTAEELKNAGFSPRVSRSMLIANPIAQAYGTTQGFIKIVW--VDGRIR 414

Query: 415 GGHLIGHD-------AVELIGELGLACRYGVTAGGLVNTVHAHPTLSETVREAAFDALQS 467
           G   +GH        A  L G  G A   G TA    N + AHPTL E + EAA +A Q 
Sbjct: 415 GVTAVGHGVSHLVTLAAVLAGGSGTAT--GWTAHDAGNVIFAHPTLDEAL-EAAIEAPQE 471

Query: 468 M 468
           +
Sbjct: 472 L 472



 Score = 24.6 bits (52), Expect = 0.007
 Identities = 13/36 (36%), Positives = 18/36 (50%)

Query: 5   DTLAAQFDVAVIGSGPGGYEAAIHAARYGLKTCIVE 40
           D   A   + V+G G  G E A   +R+G +  IVE
Sbjct: 180 DVTEAPESLIVVGGGAIGLEMADFFSRFGTRITIVE 215


Lambda     K      H
   0.316    0.133    0.377 

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: 635
Number of extensions: 31
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 469
Length of database: 473
Length adjustment: 33
Effective length of query: 436
Effective length of database: 440
Effective search space:   191840
Effective search space used:   191840
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: 51 (24.3 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