GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Algoriphagus aquaeductus T4

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_111391064.1 CLV31_RS01310 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase

Query= curated2:P37942
         (424 letters)



>NCBI__GCF_003253485.1:WP_111391064.1
          Length = 551

 Score =  217 bits (552), Expect = 8e-61
 Identities = 145/435 (33%), Positives = 217/435 (49%), Gaps = 45/435 (10%)

Query: 6   MTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEG 65
           +TMP++ +++ EGTI+ WL   GD V   + IAEV TDK   E+ S   G +  +  E G
Sbjct: 130 ITMPKMSDTMQEGTIAAWLKKVGDTVKSGEIIAEVETDKATMELESYEDGVLLYIGVEAG 189

Query: 66  QTLQVGEMICKIETEGAN------------------------PAEQKQEQPAASEAAENP 101
            ++ V  +I  I  +GA+                        PA +K E PAA       
Sbjct: 190 NSVAVDGVIAVIGEKGADYETLLKAHQSGSKSSAPAETPTTPPAAEKTEAPAAPAPQTAA 249

Query: 102 VAKSAGAADQPNKKRYSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQ 161
            A +A  A    + + SP   ++A E G+D+ QV G+G GGRI +KD++  +        
Sbjct: 250 PATTAVPATSGERVKASPLAKKIAAEKGLDIRQVPGSGEGGRIVKKDVETFV-------- 301

Query: 162 NPEELKTAAPAP-KSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHA 220
            P     AA AP  SA+ P P             +E  V+ +RK IA  +  SK   PH 
Sbjct: 302 -PAVSPMAAAAPVSSAAAPAPM------IGQESFREEKVSQMRKTIAKRLAESKYSAPHF 354

Query: 221 WTMMEVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKII 280
           +  ME+++   +  R S+ +       FN       +KA A AL++ P++NS W GDKI 
Sbjct: 355 YLTMEINMDKAIEARKSMNEFSPVKISFN----DMVIKAAAAALRQHPKVNSSWLGDKIR 410

Query: 281 QKKDINISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFT 340
               I+I +AVA E+ L VPVI+ AD  ++  I+     L  K ++ +L   D +G TFT
Sbjct: 411 YNDHIHIGMAVAVEEGLLVPVIRFADSLSLSQISNQAKTLGGKAKNKELQPKDWEGNTFT 470

Query: 341 VNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDG 400
           ++N G FG  +   IIN P A IL V  I K  V++ +G + + +++ + LS DHRV+DG
Sbjct: 471 ISNLGMFGIEEFTAIINPPDACILAVGGI-KETVIVKDGQMRIGNIMKVTLSCDHRVVDG 529

Query: 401 LVCGRFLGRVKQILE 415
            V   FL  +K +LE
Sbjct: 530 AVGSAFLQTLKGLLE 544



 Score = 53.5 bits (127), Expect = 2e-11
 Identities = 34/106 (32%), Positives = 54/106 (50%), Gaps = 10/106 (9%)

Query: 4   EQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGE 63
           E + MP++ +++ EG I+ WL   GD V   D +AEV TDK   E+ S   G +  +  +
Sbjct: 3   EIIRMPKMSDTMEEGVIASWLKKVGDTVKPGDILAEVETDKATMELESYEEGVLLYIGVK 62

Query: 64  EGQTLQVGEMICKIETEG----------ANPAEQKQEQPAASEAAE 99
           E  ++ V  +I  I  +G          A    +KQE+PAA ++ E
Sbjct: 63  EKDSVPVNGIIAIIGEKGEEFQHLLNGSAEAPAKKQEEPAAPKSEE 108


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: 549
Number of extensions: 31
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 424
Length of database: 551
Length adjustment: 34
Effective length of query: 390
Effective length of database: 517
Effective search space:   201630
Effective search space used:   201630
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: 52 (24.6 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