GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Leeuwenhoekiella blandensis MED217

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 WP_009781680.1 MED217_RS16440 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase

Query= curated2:P37942
         (424 letters)



>NCBI__GCF_000152985.1:WP_009781680.1
          Length = 411

 Score =  249 bits (637), Expect = 8e-71
 Identities = 161/434 (37%), Positives = 232/434 (53%), Gaps = 51/434 (11%)

Query: 1   MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60
           MA+E M +P  GES+TE  I++WLV  GD V K   IAEV +DK   E+P+  +G IT L
Sbjct: 1   MALE-MKVPSPGESITEVEIAQWLVEDGDYVEKDQAIAEVDSDKATLELPAEASGIIT-L 58

Query: 61  VGEEGQTLQVGEMICKIETEGANP---------------AEQKQEQPAASEAAENPVAKS 105
             EEG  + VGE++C I+T+ A P               AE K+E P+ S   E    K 
Sbjct: 59  KAEEGDAVAVGEVVCLIDTDAAKPEGDSSGDKEEQKEEKAEPKKEAPSKSSTPEQAQDKK 118

Query: 106 AGAADQPNKKRYSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEE 165
             A+  P     SPA  +   E GID   V GTG  GRIT++D      + G        
Sbjct: 119 TYASGSP-----SPAAKKTLDEKGIDAKDVKGTGRDGRITKEDAVNAQPSMGT------- 166

Query: 166 LKTAAPAPKSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMME 225
                  P + S+ E + + S               +R+ +A  +   K E     T  E
Sbjct: 167 -------PGTGSRGESRSKMSM--------------LRRKVAERLVSVKNETAMLTTFNE 205

Query: 226 VDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDI 285
           VD+T +   R+  K+ FK   G +L F +FF  A  +AL+ +P +NSM  G +++     
Sbjct: 206 VDMTPIFDLRSKYKEDFKAKHGVSLGFMSFFTLACVRALEMYPAVNSMIDGKEMVSYDFK 265

Query: 286 NISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTG 345
           +ISIAV+    L VPVI+NA+  + +G+  ++  LA + RDG++T D+M GGTFT+ N G
Sbjct: 266 DISIAVSGPKGLMVPVIRNAENLSFRGVESEVKRLALRARDGQITVDEMTGGTFTITNGG 325

Query: 346 SFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGR 405
            FGS+ S  IIN PQ+AIL + +IV+RP+V D G IA+  ++ + LS DHR++DG     
Sbjct: 326 VFGSMLSTPIINPPQSAILGMHNIVERPIVRDGG-IAIAPIMYVALSYDHRIIDGKESVG 384

Query: 406 FLGRVKQILESIDE 419
           FL  VK+ LE+ +E
Sbjct: 385 FLVAVKEALENPEE 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: 425
Number of extensions: 25
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: 411
Length adjustment: 32
Effective length of query: 392
Effective length of database: 379
Effective search space:   148568
Effective search space used:   148568
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 24 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