GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Shewanella oneidensis MR-1

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 201092 SO1931 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase (NCBI ptt file)

Query= curated2:P37942
         (424 letters)



>FitnessBrowser__MR1:201092
          Length = 395

 Score =  242 bits (618), Expect = 1e-68
 Identities = 152/415 (36%), Positives = 227/415 (54%), Gaps = 29/415 (6%)

Query: 1   MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60
           M+IE + +P L ESV + TI+ W V  G +V++   + ++ TDKV  EV +   G I E 
Sbjct: 1   MSIE-IKVPVLPESVADATIATWHVKVGQQVSRDQNLVDIETDKVVLEVVAPEDGHIGEF 59

Query: 61  VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120
           +  EG T+   ++I K      +  E  + Q  A        A  A A+D+ N    SP+
Sbjct: 60  LFHEGDTVLGEQVIAKFIAGAVSGQEVTKAQAEA--------AAPAVASDESNDA-LSPS 110

Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180
           V RL  EH +D  +V GTG GGRIT++D++  I++                APK+A+   
Sbjct: 111 VRRLLAEHNVDASKVKGTGVGGRITKEDVEAFIKS----------------APKAAASAA 154

Query: 181 PKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKD 240
           P  +    A+   +K +P+T +RK IA+ +  +K       T  EV++  ++  R   +D
Sbjct: 155 PVVQPL--AAGRSEKRVPMTRLRKTIANRLLEAKNSTAMLTTFNEVNMKPIMDIRKQYQD 212

Query: 241 SFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVP 300
            F+K  G  L F +F+VKAV +ALK FP++N+   GD I+     ++SIAV+T   L  P
Sbjct: 213 IFEKRHGIRLGFMSFYVKAVTEALKRFPEVNASIDGDDIVYHNYFDVSIAVSTPRGLVTP 272

Query: 301 VIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQ 360
           V+++ D  ++  I K +  LA K RDGKLT  DM GG FTV N G FGS+ S  I+N PQ
Sbjct: 273 VLRDTDTMSLADIEKAVRDLAIKGRDGKLTVADMTGGNFTVTNGGVFGSLMSTPILNLPQ 332

Query: 361 AAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
           +AIL + +I  RP+ + NG + +  M+ L LS DHR++DG     FL  +K  LE
Sbjct: 333 SAILGMHAIKDRPMAV-NGQVEILPMMYLALSYDHRIIDGRESVGFLVAIKDFLE 386


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: 354
Number of extensions: 19
Number of successful extensions: 4
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: 395
Length adjustment: 31
Effective length of query: 393
Effective length of database: 364
Effective search space:   143052
Effective search space used:   143052
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:

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