GapMind for catabolism of small carbon sources

 

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

Align Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial; Branched-chain alpha-keto acid dehydrogenase complex component E2; Dihydrolipoamide branched-chain transacylase E2; EC 2.3.1.168 (characterized)
to candidate N515DRAFT_0354 N515DRAFT_0354 pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase)

Query= SwissProt::Q23571
         (448 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0354
          Length = 461

 Score =  132 bits (333), Expect = 2e-35
 Identities = 130/463 (28%), Positives = 179/463 (38%), Gaps = 86/463 (18%)

Query: 33  FKLSDIGEGIAEVQVKEWYVKEGDTISQFDKVCEVQSDKAAVTISCRYDGIVKKLYHEVD 92
           F L D+GEG+ +  + EW+VKEGD I     +C +++ KA V +   Y G V+KLY    
Sbjct: 7   FHLPDLGEGLPDATIVEWHVKEGDYIKLDAPLCSMETAKAVVDVPSPYTGTVQKLYGAPG 66

Query: 93  GMARVGQALIDVEIEGNVEEPEQ---------PKKEAASSSPE----------------- 126
            +   G AL D   + N ++  +         PKK   S +P+                 
Sbjct: 67  DIIETGAALADFAPDPNAKQRAEAEATGHHHGPKKSVGSPAPDNAAKVVASDEGGEVEAK 126

Query: 127 -----------APKSSAPKAPESAHSEGKVLATPAVRRIAIENKIKLAEVRGTGKDGRVL 175
                      A  S      E   S G V A PAVR +A + K+ L  VR TG DG V 
Sbjct: 127 GEREDEGTVVGAMVSGNTVHVEQVSSAGGVKAVPAVRALAKKLKVDLTRVRPTGADGVVT 186

Query: 176 KEDVLKF-------LGQVPADHTSGSTNIRTTHQAPQPSSKSYEPLKEDVAVPIR----- 223
            +DV          LG  PA     S       + P+P +            P+R     
Sbjct: 187 LQDVKTAAANGSAPLGAAPARAVPASAGRHLAPELPEPGAAPSRTAVSLAGKPVRTAPPS 246

Query: 224 -----------GYTRAMVKTMTEALKIPHFGYNDEINVDSLVKYRAELKEFAKERHIKLS 272
                      G  R M + M EA    H        VD      A+L  +  ++ I   
Sbjct: 247 VQASGQPEQLKGVRRNMARVMAEA----HANVVPTTLVDD-----ADLHGWIGKQDITAR 297

Query: 273 YMPFFIKAASLALLEYPSLNSTTDEKMENVIHKASHNICLAMDTPGGLVVPNIKNCEQRS 332
                I+A   A    P+LN+  D K          +I +A+DT  GL VP ++N +   
Sbjct: 298 ----LIRAIVAACKAVPALNAWFDGKNLTRTLHPHVDIGIAVDTEDGLFVPALRNADVLD 353

Query: 333 IFEIAQELNRLLEAGKKQQIKREDLIDGTFSLSNIGNIGGTYASPVVFPPQVAIGAIGKI 392
              +   + RL    + + I   +L   T SLSN G   G YA+PVV PP VAI   GK+
Sbjct: 354 GAGVRAAIKRLRAQVEDRSIPASELSGYTISLSNFGMFAGRYATPVVVPPTVAIIGAGKL 413

Query: 393 EKLPRFDKHDNVIPV------NIMKVSWCADHRVVDGATMARF 429
                   HD V  +        M +S   DHR   G   ARF
Sbjct: 414 -------CHDVVAVMGGIEVHRRMPISLTFDHRAATGGEAARF 449


Lambda     K      H
   0.316    0.132    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: 439
Number of extensions: 23
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: 448
Length of database: 461
Length adjustment: 33
Effective length of query: 415
Effective length of database: 428
Effective search space:   177620
Effective search space used:   177620
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