GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Pseudomonas fluorescens FW300-N2C3

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 AO356_19700 AO356_19700 dihydrolipoamide succinyltransferase

Query= curated2:P37942
         (424 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_19700
          Length = 406

 Score =  262 bits (669), Expect = 2e-74
 Identities = 159/419 (37%), Positives = 239/419 (57%), Gaps = 26/419 (6%)

Query: 1   MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60
           MAIE +  P   ESV +GT++ W   PG+ V + D I ++ TDKV  EV +   G +  +
Sbjct: 1   MAIE-IKAPSFPESVADGTVATWHKKPGEAVKRDDLIVDIETDKVVLEVLAEADGVLGAI 59

Query: 61  VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120
           V EEG T+   +++  IE  GA  A      PAA++AA       A AAD  +    +PA
Sbjct: 60  VAEEGATVLSNQVLGSIEEGGAAAAAPAAAAPAAAQAA-------APAADGEDDPVAAPA 112

Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180
             ++A E+GI++  V GTG GGR+T++D+   +             K AAPA   A    
Sbjct: 113 ARKIAEENGINIASVAGTGKGGRVTKEDVVAAVAA-----------KKAAPAAAPAKPAA 161

Query: 181 PKEETSYPASAAGD---KEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNS 237
           P    + P  AAGD   K +P+T +R  +A  +  +++ +    T  EVD+T ++A R+ 
Sbjct: 162 PA--AAAPVFAAGDRVEKRVPMTRLRAKVAERLVEAQSNMAMLTTFNEVDMTEVMALRSK 219

Query: 238 IKDSFKKTE-GFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDS 296
            KD F+K+  G  L F +FFVKA  +ALK FP +N+   G  I+     +I +AV+++  
Sbjct: 220 YKDLFEKSHNGVRLGFMSFFVKAATEALKRFPAVNASIDGSDIVYHGYADIGVAVSSDRG 279

Query: 297 LFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGII 356
           L VPV++NA+  ++  I   I    KK RDGKL+ ++M GGTFT+ N G+FGS+ S  I+
Sbjct: 280 LVVPVLRNAELMSLAEIEGGIATFGKKARDGKLSIEEMTGGTFTITNGGTFGSMMSTPIV 339

Query: 357 NYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
           N PQAAIL + +I++RP+ + NG + +R M+ L LS DHR++DG     FL  +K +LE
Sbjct: 340 NPPQAAILGMHNILQRPMAI-NGQVVIRPMMYLALSYDHRLIDGKEAVTFLVTIKNLLE 397


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: 430
Number of extensions: 23
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: 406
Length adjustment: 31
Effective length of query: 393
Effective length of database: 375
Effective search space:   147375
Effective search space used:   147375
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