GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Pedobacter sp. GW460-11-11-14-LB5

Align Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; EC 2.3.1.168; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCKAD-E2; BCKADE2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (uncharacterized)
to candidate CA265_RS17525 CA265_RS17525 dihydrolipoamide succinyltransferase

Query= curated2:P37942
         (424 letters)



>FitnessBrowser__Pedo557:CA265_RS17525
          Length = 413

 Score =  257 bits (657), Expect = 4e-73
 Identities = 157/419 (37%), Positives = 235/419 (56%), Gaps = 26/419 (6%)

Query: 5   QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64
           ++ +P +GES+TE  +S+W+   GD V   + IAE+ +DK   E+ +   GT+ + +  E
Sbjct: 4   EIKVPPVGESITEVVLSRWIKNDGDVVEMDEVIAELESDKATFELTAEQAGTL-KTIAAE 62

Query: 65  GQTLQVGEMICKIETEGANPAEQKQEQPAASEA------AENPVAKSAGAA--DQPNKKR 116
           G TL +G ++CKIE  GA  + + + +   S+A      AE P  + +G A  D      
Sbjct: 63  GDTLAIGAVVCKIEDGGAAASPKPEAESPKSDAQAPAAVAEAPKTQDSGLATKDSYATGT 122

Query: 117 YSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSA 176
            SPA  ++  E GI+   V GTG  GRIT+ D  +  E G    + PE  K +AP   +A
Sbjct: 123 PSPAAGKILAEKGIEASAVKGTGVDGRITKDDAVKA-EAG----KKPEAPKASAPVVAAA 177

Query: 177 SKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRN 236
                      PA + G++   ++ +R+ +A  +   K E     T  EV++  ++  R 
Sbjct: 178 -----------PAGSRGERREKMSPLRRTVAKRLVAVKNETAMLTTFNEVNMKPIMDLRG 226

Query: 237 SIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDS 296
             KD FK+  G  L F +FF KAV +ALK+FP +N    G++++     +ISIAV+    
Sbjct: 227 KYKDQFKEKFGVGLGFMSFFTKAVTEALKDFPAVNGRIEGEELVYNDFADISIAVSAPKG 286

Query: 297 LFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGII 356
           L VPVI+NA+  T+  I K +  LA K RD KLT ++M GGTFT+ N G FGS+ S  II
Sbjct: 287 LVVPVIRNAESMTLAQIEKSVLELALKARDSKLTIEEMTGGTFTITNGGVFGSMMSTPII 346

Query: 357 NYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
           N PQ+AIL + +IV+RPV  + G + +R M+ + LS DHR++DG     FL RVKQ+LE
Sbjct: 347 NAPQSAILGMHNIVERPVA-EKGEVVIRPMMYVALSYDHRIIDGRESVGFLVRVKQLLE 404


Lambda     K      H
   0.312    0.129    0.359 

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: 411
Number of extensions: 18
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: 424
Length of database: 413
Length adjustment: 32
Effective length of query: 392
Effective length of database: 381
Effective search space:   149352
Effective search space used:   149352
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 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