GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Chryseobacterium arthrosphaerae CC-VM-7

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_065398074.1 BBI00_RS06900 2-oxo acid dehydrogenase subunit E2

Query= curated2:P37942
         (424 letters)



>NCBI__GCF_001684965.1:WP_065398074.1
          Length = 435

 Score =  283 bits (724), Expect = 7e-81
 Identities = 177/443 (39%), Positives = 264/443 (59%), Gaps = 28/443 (6%)

Query: 1   MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60
           MA  ++ +P +GE V E TI  WL   GD V + D + E+ TDKV+++VP+  +G I ++
Sbjct: 1   MAEYKLLLPSMGEGVMEATIITWLFNEGDNVKEDDSVVEIATDKVDSDVPTPVSGKIVKI 60

Query: 61  VGEEGQTLQVGEMICKIETEGANPA--EQKQEQPAASEAAEN------PVAKSAGAADQP 112
           + ++ +  +VGE I  +E EG   A  E + E PAA+  AE       P+ ++  A  + 
Sbjct: 61  LKQKDEVAKVGEAIAILEIEGEGTASEEVQAETPAAAPDAETLKTIEQPLQQTIAANVEF 120

Query: 113 NKKRY-SPAVLRLAGEHGI---DLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKT 168
           +   Y SP V  +A +  I   +L  + G+G  GRIT++DI   +   G Q   P+    
Sbjct: 121 SGDLYLSPLVKSIAQQENISEAELKSIKGSGLEGRITKEDILAYVANRGTQP-TPQ---- 175

Query: 169 AAPAPKSASKPEPKEETSYPAS----AAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMM 224
           AAP  ++AS P+P    S PA+    +AGD+ IP+  +RK IA NM ++K   PH  + +
Sbjct: 176 AAPV-QAASTPQPA--VSAPAATIPVSAGDEIIPMDRMRKIIAENMVKAKQIAPHVTSFI 232

Query: 225 EVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKD 284
           E DVTN+V +RN  K  F+K EG  LTF   FVKAV +A+++FP +N    G+ II+KK+
Sbjct: 233 ETDVTNVVKWRNKNKAVFEKREGEKLTFMPIFVKAVVKAIQDFPMINVSVNGENIIKKKN 292

Query: 285 INISIAVATED-SLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNN 343
           INI +A A  D +L VPVIKNAD+ ++ G+AK I  LA + R+ KL  +D QG T+T++N
Sbjct: 293 INIGMATALPDGNLIVPVIKNADQLSLSGLAKAINDLAYRARNKKLRPEDTQGATYTISN 352

Query: 344 TGSFGSVQSMGIINYPQAAILQVESIVKRPVVM---DNGMIAVRDMVNLCLSLDHRVLDG 400
            GSFG++    II  PQ AIL + +IVK+P V+   D  +IA+R+++ +  S DHRV+DG
Sbjct: 353 VGSFGNLMGTPIIPQPQVAILAIGAIVKKPAVLETADGDVIAIRNLMFMSHSYDHRVVDG 412

Query: 401 LVCGRFLGRVKQILESIDEKTSV 423
            + G  L  V   LE+ D  T +
Sbjct: 413 SLGGMMLKHVHDYLENWDLNTEI 435


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: 414
Number of extensions: 23
Number of successful extensions: 6
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: 435
Length adjustment: 32
Effective length of query: 392
Effective length of database: 403
Effective search space:   157976
Effective search space used:   157976
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: 51 (24.3 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