GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdC in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_0772 Echvi_0772 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component)

Query= curated2:P37942
         (424 letters)



>lcl|FitnessBrowser__Cola:Echvi_0772 Echvi_0772 2-oxoglutarate
           dehydrogenase complex dihydrolipoamide
           succinyltransferase (E2 component)
          Length = 524

 Score =  263 bits (672), Expect = 9e-75
 Identities = 159/419 (37%), Positives = 237/419 (56%), Gaps = 25/419 (5%)

Query: 3   IEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVG 62
           +++M +P +GES+TE T++ WL   GD V   + IAEV +DK   E+P+   G I + V 
Sbjct: 116 VKEMVVPTVGESITEVTLASWLKEDGDFVEMDEIIAEVDSDKATFELPAEAQG-ILKRVA 174

Query: 63  EEGQTLQVGEMICKIET-EGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRY---- 117
           EEG TL++G +ICKIE  EG        + P A + A+    +S  +A       Y    
Sbjct: 175 EEGDTLEIGGLICKIEVVEG--------DAPEADDTADTSKEESTSSASSSGSGSYAEGH 226

Query: 118 -SPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSA 176
            SPA  ++  E GID  +V GTG  GR+T++D ++       Q+Q P   K AA    S+
Sbjct: 227 ASPAAAKILAEKGIDAKEVKGTGKDGRVTKEDAEK------AQKQAP---KPAASKSSSS 277

Query: 177 SKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRN 236
           +  E   E    A     K   ++ +RK I+  +  +K E     T  EV++  ++  R 
Sbjct: 278 AAKETAPEAPKVAGERNMKREKMSSLRKTISKRLVAAKNETAMLTTFNEVNMKPIMDLRK 337

Query: 237 SIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDS 296
             K+ FK+    NL F +FF KAV  AL+E+P +N+   G++II     ++SIAV+    
Sbjct: 338 QYKEMFKEKHNVNLGFMSFFTKAVCVALQEWPAVNAQIDGNEIIYHDFCDVSIAVSAPKG 397

Query: 297 LFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGII 356
           L VPVI+NA+  +   + K++  LA K RDGKLT ++M GGTFT+ N G FGS+ S  II
Sbjct: 398 LVVPVIRNAESLSFDQVEKEVVRLATKARDGKLTIEEMTGGTFTITNGGIFGSMMSTPII 457

Query: 357 NYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
           N PQ+AIL + +IV+RP+ + NG + +  M+ + LS DHR++DG     FL R+KQ+LE
Sbjct: 458 NQPQSAILGMHNIVERPMAV-NGEVKILPMMYIALSYDHRIIDGRESVSFLVRLKQLLE 515



 Score = 64.7 bits (156), Expect = 6e-15
 Identities = 40/122 (32%), Positives = 67/122 (54%), Gaps = 6/122 (4%)

Query: 5   QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64
           ++ +P +GES+TE TI +W    G+ V   + I E+ +DK   E+ +   G +T +  E 
Sbjct: 4   EIKVPAVGESITEVTIGQWFKNSGEYVEMDEVICELESDKATFELTAEADGILT-VKAEA 62

Query: 65  GQTLQVGEMICKIET----EGANPA-EQKQEQPAASEAAENPVAKSAGAADQPNKKRYSP 119
           G TL++G +IC+I+T    + A PA E+K+E PA S+ ++   + S        K+   P
Sbjct: 63  GDTLEIGAVICEIDTKASADDAAPAKEEKKEAPADSKESKGSSSDSKSGKTGEVKEMVVP 122

Query: 120 AV 121
            V
Sbjct: 123 TV 124


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: 518
Number of extensions: 27
Number of successful extensions: 7
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: 524
Length adjustment: 33
Effective length of query: 391
Effective length of database: 491
Effective search space:   191981
Effective search space used:   191981
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 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