GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Pseudomonas putida KT2440

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 PP_4188 PP_4188 2-oxoglutarate dehydrogenase dihydrolipoyltranssuccinylase subunit

Query= curated2:P37942
         (424 letters)



>FitnessBrowser__Putida:PP_4188
          Length = 407

 Score =  258 bits (659), Expect = 2e-73
 Identities = 159/419 (37%), Positives = 238/419 (56%), Gaps = 25/419 (5%)

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

Query: 61  VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120
           V  EG T+   E++  I   GA  A      PAA+ AA    A +    D P     +PA
Sbjct: 60  VKGEGDTVLSDELLGSIVEGGAAAAPAAAAAPAAAPAA----AAADAGEDDPIA---APA 112

Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180
             +LA E+GIDL  V GTG GGR+T++D+   +             K +APA   A+KP 
Sbjct: 113 ARKLAEENGIDLATVAGTGKGGRVTKEDVVAAVAK-----------KKSAPAAAPAAKPA 161

Query: 181 PKEETSYPASAAGD---KEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNS 237
                     AAGD   K +P+T +R  IA  +  +++ +    T  EVD+T ++A R+ 
Sbjct: 162 AAAAAPVVV-AAGDRTEKRVPMTRLRAKIAERLVEAQSNMAMLTTFNEVDMTEVMALRSK 220

Query: 238 IKDSFKKTE-GFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDS 296
            KD F+KT  G  L F +FFVKA  +ALK FP +N+   G+ I+     ++ +AV+++  
Sbjct: 221 YKDLFEKTHNGVRLGFMSFFVKAATEALKRFPAVNASIDGNDIVYHGFADVGVAVSSDRG 280

Query: 297 LFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGII 356
           L VPV++NA+  ++  I   I    KK RDGKL+ ++M GGTFT+ N G+FGS+ S  I+
Sbjct: 281 LVVPVLRNAESMSLAEIENGIATFGKKARDGKLSIEEMTGGTFTITNGGTFGSMMSTPIV 340

Query: 357 NYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
           N PQAAIL + +I++RP+ + NG + +R M+ L LS DHR++DG     FL  +K +LE
Sbjct: 341 NPPQAAILGMHNIIQRPMAI-NGQVVIRPMMYLALSYDHRLIDGKEAVTFLVTIKNLLE 398


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: 433
Number of extensions: 27
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: 407
Length adjustment: 31
Effective length of query: 393
Effective length of database: 376
Effective search space:   147768
Effective search space used:   147768
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