GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Dyella japonica UNC79MFTsu3.2

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate N515DRAFT_2310 N515DRAFT_2310 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component

Query= SwissProt::P85207
         (461 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2310
          Length = 456

 Score =  230 bits (586), Expect = 8e-65
 Identities = 148/454 (32%), Positives = 233/454 (51%), Gaps = 9/454 (1%)

Query: 4   YDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHHLK 63
           +D +VIG G  G P A R  + G +V  +E   VGG C+N GCIPTKA++ +A   H   
Sbjct: 5   FDAVVIGAGQAGPPLAERLGKAGRRVAVIERKLVGGTCVNTGCIPTKAMVASAYVAHMAG 64

Query: 64  GAEGFGLKAKPE--LDLKKLGAWRDGVVKKLTGGVAGLLKGN-KVELLRGFARFKGPREI 120
            A  +G++   +  +D++++     G+  K   GV   L G   V LLRG ARF+ P  +
Sbjct: 65  RAHEYGVRGSEDTRVDMQRVWERTQGISGKARSGVEQWLVGMPNVTLLRGHARFESPTTL 124

Query: 121 EVNGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVE-EGIPKRLLVIGGGAVGL 179
               +   A+SF I  G     +  FP   DV   T    +E   +P+ L+++GG  +GL
Sbjct: 125 RFGEDLIEAESFFINVGGRAS-VPDFPGIHDVPFLTNTGMMELRELPEHLMIVGGSYIGL 183

Query: 180 ELGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKKQDG 239
           E GQ++ R GS+VT++E     LP  D + A  +   L  EG+ V  G + +  E K   
Sbjct: 184 EFGQMFRRFGSKVTIVERSQRFLPREDADVADAVLAMLRDEGITVHLGAECIALEGKAGA 243

Query: 240 LHVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSAP 299
           + +     Q    E+ V   +L+AVGR+P T+ LGL++AGV +DERG I+V+    +S P
Sbjct: 244 IRIKARGNQ--LCEQAVGTHLLLAVGRQPNTDDLGLDRAGVALDERGNIKVDDHGRSSVP 301

Query: 300 GVYAIGDVARPPLLAHKAMKEGLVAAENAAGKNAL-FDFQVPSV-VYTGPEWAGVGLTEE 357
            ++A+GD        H +  +  + A+   G+       ++ +  ++T P  A +G++E+
Sbjct: 302 HIWAMGDCNGKGAFTHTSYNDFEIVADAVLGQGRRRISGRIQAYSLFTDPPLARIGMSEQ 361

Query: 358 EARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAEA 417
           EARK+G  V VG  P +  GRA+  G   G +KVV D  +  LLG  + G    E I   
Sbjct: 362 EARKSGREVLVGTRPMARVGRAVERGETVGFMKVVVDGASKELLGAAIFGVNGDEAIHCL 421

Query: 418 TLALEMGATVSDLGLTIHPHPTLSEGLMEAAEAL 451
              +   A  + +   +H HPT++E L    ++L
Sbjct: 422 LDTMYAKAPYTTVSEAVHIHPTVAELLPTTLQSL 455


Lambda     K      H
   0.316    0.138    0.395 

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: 24
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: 461
Length of database: 456
Length adjustment: 33
Effective length of query: 428
Effective length of database: 423
Effective search space:   181044
Effective search space used:   181044
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