GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3682 Dihydrolipoamide succinyltransferase component (E2) of 2-oxoglutarate dehydrogenase complex (EC 2.3.1.61)

Query= curated2:P37942
         (424 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3682
          Length = 405

 Score =  253 bits (647), Expect = 6e-72
 Identities = 159/419 (37%), Positives = 237/419 (56%), Gaps = 27/419 (6%)

Query: 1   MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60
           MAIE +  P   ESV +GT++ W   PGD V + + I ++ TDKV  EV ++  G +  +
Sbjct: 1   MAIE-IKAPTFPESVADGTVATWHKKPGDAVKRDELIVDIETDKVVLEVLATADGVLGAI 59

Query: 61  VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120
           V  EG T+   E++  I  EG+  A       AA  AA  P A +A A    +    +PA
Sbjct: 60  VKNEGDTVLSDEVLGSIG-EGSAAA-------AAPAAAAAPAAAAAPAEAGEDDPVAAPA 111

Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180
             +LA E+GI++  V GTG GGR+T++D+   +             K AAPA   A    
Sbjct: 112 ARKLAEENGINIASVAGTGKGGRVTKEDVVAAVAA-----------KKAAPAAAPAKAAA 160

Query: 181 PKEETSYPASAAGD---KEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNS 237
           P    + P  AAGD   K +P+T VR  +A  +  +++ +    T  EVD+T ++A R+ 
Sbjct: 161 PA--AAAPVFAAGDRIEKRVPMTRVRATVAKRLVEAQSNMAMLTTFNEVDMTEVMALRSK 218

Query: 238 IKDSFKKTE-GFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDS 296
            KD F+K+  G  L F +FFVKA  +ALK FP +N+   G  I+     ++ +AV+++  
Sbjct: 219 YKDLFEKSHNGVRLGFMSFFVKAATEALKRFPAVNASIDGADIVYHGYADVGVAVSSDRG 278

Query: 297 LFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGII 356
           L VPV++NA+  ++  I   I    KK RDGKL+ D+M GGTFT+ N G+FGS+ S  I+
Sbjct: 279 LVVPVLRNAELMSLAEIEGGIATFGKKARDGKLSMDEMTGGTFTITNGGTFGSMMSTPIV 338

Query: 357 NYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
           N PQAAIL + +I++RP+ + NG + +R M+ L LS DHR++DG     FL  +K +LE
Sbjct: 339 NPPQAAILGMHNILQRPMAI-NGQVVIRPMMYLALSYDHRLIDGKEAVTFLVTIKNLLE 396


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: 442
Number of extensions: 21
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: 405
Length adjustment: 31
Effective length of query: 393
Effective length of database: 374
Effective search space:   146982
Effective search space used:   146982
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