GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Marinobacter adhaerens HP15

Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex (uncharacterized)
to candidate GFF3909 HP15_3849 pyridine nucleotide-disulfide oxidoreductase dimerization region

Query= curated2:O84561
         (465 letters)



>FitnessBrowser__Marino:GFF3909
          Length = 729

 Score =  253 bits (646), Expect = 2e-71
 Identities = 160/467 (34%), Positives = 253/467 (54%), Gaps = 32/467 (6%)

Query: 5   FDCVVIGAGPGGYVAAITAAQAGLKTALIEKREAGGTCLNRGCIPSKALLAGAEVVTQIR 64
           ++ +VIG G  G V+A  AA    K ALIEK + GG CLN GC+PSKAL+  A+    +R
Sbjct: 238 YNLLVIGGGSAGLVSAYIAAAVKAKVALIEKHKMGGDCLNTGCVPSKALIRSAKAADTLR 297

Query: 65  HADQFGIHVEGFSINYPAMVQRKDSVVRSIRDGLNGLIRSNKITV--FSGRGSLISSTEV 122
           HA+++G+       ++  ++ R  +V+  +    +   R  K+ V   +G  S +S  E+
Sbjct: 298 HANRYGLESVPVKGSFKNIMNRVKNVIAKVEPH-DSPERYRKLGVDCIAGEASFVSPWEL 356

Query: 123 KILGENPSV--IKAHSIILATGSEPRAFPGIPFSAESPRILCSTGVLNLKEIPQKMAIIG 180
           ++   +     + A SI++ATG +P A P IP   +    L S  +  L+E P+++ ++G
Sbjct: 357 EVRHNDGRTERLTARSIVVATGGKP-AVPPIP-GLKDMEPLTSDNLWELQEQPERLLVLG 414

Query: 181 GGVIGCEFASLFHTLGSEVSVIEASSQILALNNPDISKTMFDKFTRQGLRFVLEAS---- 236
           GG IG E A  F  LGS+V+ +E   ++LA  + D+S+ +  +F   G+   L+ +    
Sbjct: 415 GGPIGSELAHAFARLGSKVTQVEMGERLLAKEDEDVSELVLKQFQADGVDVRLKHAAAEF 474

Query: 237 -------VSNIEDIGDRVRLTINGNVEEYDYVLVSIGRRLNTENIGLDKAGVICDERGVI 289
                  V+  E  G+RVR+        +D VLV++GR  NT  + L++ GV     G +
Sbjct: 475 RMEEGEKVAYCEHEGERVRIP-------FDQVLVAVGRAANTAGLNLERIGVDTLPNGTV 527

Query: 290 PTDATMRTNVPNIYAIGDITGKWQLAHVASHQGIIAARN-IAGH--KEEIDYSAVPSVIF 346
           P +  M    PN++A GD+ G +Q  H A+HQ   AA N + G   + ++DY  +P V F
Sbjct: 528 PVEEDMSLRYPNVFACGDVAGPYQFTHAAAHQAWYAAVNGLFGQFKRFKVDYRVMPWVTF 587

Query: 347 TFPEVASVGLSPTAAQQQKIPVKVTKFPFRAIGKAVAMGEADGFAAIISHETTQQILGAY 406
           T PEVA VGLS   A  Q +  +VT++    + +A+A  E  GF  +++     +ILGA 
Sbjct: 588 TSPEVARVGLSEAEATAQGVAYEVTRYGLDDLDRAIAESEDHGFIKVLTPPGKDKILGAV 647

Query: 407 VIGPHASSLISEITLAVRNELTLPCIYETIHAHPTLAEVWAESALLA 453
           V+G HA  +++E TLA+++ L L  I  TIH +PT    W ESA  A
Sbjct: 648 VVGSHAGEILAEFTLAMKHGLGLNKILGTIHPYPT----WNESAKYA 690


Lambda     K      H
   0.319    0.135    0.388 

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: 710
Number of extensions: 31
Number of successful extensions: 6
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: 465
Length of database: 729
Length adjustment: 36
Effective length of query: 429
Effective length of database: 693
Effective search space:   297297
Effective search space used:   297297
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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