GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdC in Pseudomonas simiae WCS417

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 GFF1750 PS417_08900 dihydrolipoamide succinyltransferase

Query= curated2:P37942
         (424 letters)



>lcl|FitnessBrowser__WCS417:GFF1750 PS417_08900 dihydrolipoamide
           succinyltransferase
          Length = 408

 Score =  261 bits (667), Expect = 3e-74
 Identities = 160/419 (38%), Positives = 237/419 (56%), Gaps = 24/419 (5%)

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

Query: 61  VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120
           V EEG T+   +++  IE   A  A       AA  AA  P A  A   + P     +PA
Sbjct: 60  VAEEGATVLSNQVLGSIEEGSA--AAAAPAAAAAPAAASAPAAAPAAGGEDPIA---APA 114

Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180
             +LA E+GI+L  + GTG  GR+T++D+   +E    ++  P      A AP +A+   
Sbjct: 115 ARQLAEENGINLASIKGTGKDGRVTKEDVVAAVEA---KKNAPAAAPAKAAAPAAAA--- 168

Query: 181 PKEETSYPASAAGD---KEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNS 237
                  P  AAGD   K +P+T VR  +A  +  +++ +    T  EVD+T ++A R+ 
Sbjct: 169 -------PVFAAGDRTEKRVPMTRVRATVAKRLVEAQSNMAMLTTFNEVDMTEVMALRSK 221

Query: 238 IKDSFKKTE-GFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDS 296
            KD F+K+  G  L F +FFVKA  +ALK FP +N+   G+ I+     +I +AV+++  
Sbjct: 222 YKDLFEKSHNGVRLGFMSFFVKAATEALKRFPAVNASIDGNDIVYHGYADIGVAVSSDRG 281

Query: 297 LFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGII 356
           L VPV++NA+  ++  I   I    KK RDGKLT D+M GGTFT+ N G+FGS+ S  I+
Sbjct: 282 LVVPVLRNAELMSLAEIEGGIATFGKKARDGKLTIDEMTGGTFTITNGGTFGSMMSTPIV 341

Query: 357 NYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
           N PQAAIL + +I++RP+ + NG + +R M+ L LS DHR++DG     FL  +K +LE
Sbjct: 342 NPPQAAILGMHNIIQRPMAI-NGQVVIRPMMYLALSYDHRLIDGKEAVTFLVTIKNLLE 399


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: 424
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: 408
Length adjustment: 31
Effective length of query: 393
Effective length of database: 377
Effective search space:   148161
Effective search space used:   148161
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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