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

GapMind for catabolism of small carbon sources

Aligments 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 199617 SO0425 pyruvate dehydrogenase complex, E2 component, dihydrolipoamide acetyltransferase (NCBI ptt file)

Query= curated2:P09062
         (423 letters)



>FitnessBrowser__MR1:199617
          Length = 677

 Score =  215 bits (547), Expect = 4e-60
 Identities = 139/437 (31%), Positives = 236/437 (54%), Gaps = 36/437 (8%)

Query: 6   IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65
           I++PDIG+  + V+++E  V VGD+I+ DQ +  + TDKAT+E+P+P +GK+L+L  + G
Sbjct: 241 IQVPDIGDA-SNVDVIEVLVSVGDMISADQGLITLETDKATMEVPAPFAGKLLSLTVKVG 299

Query: 66  EVMAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKPAAYQASASHEAA 125
           + ++ GS +  IE       V    A  A  P A  AA     ++  PA   A+ S    
Sbjct: 300 DKVSQGSVIATIETTS----VATVSAGAATAPVAQAAAPAPVAQEAAPAPVAAAPSR--- 352

Query: 126 PIVPRQPG-DKPL------ASPAVRKRALDAGIELRYVHGSGPAGRILHEDLDAF----M 174
           P VP  P    P+      ASPAVR+ A + G++L  V GSG  GRI+ ED+ A+    +
Sbjct: 353 PPVPHHPSAGAPVSTGAVHASPAVRRLAREFGVDLTQVTGSGRKGRIMKEDVQAYVKYEL 412

Query: 175 SKPQSAAGQ---TPNG------------YARRTDSEQVPVIGLRRKIAQRMQDAKRRVAH 219
           S+P++ A     T NG            +++  + E++P+  +++     +      + H
Sbjct: 413 SRPKATAATSVATGNGGGLQVIAAPKVDFSKFGEVEEIPLSRIQKISGPNLHRNWVTIPH 472

Query: 220 FSYVEEIDVTALEALRQQLNSKHGDSRG--KLTLLPFLVRALVVALRDFPQINATYDDEA 277
            +  +E D+T +E  R+Q N      +   K+T L F+++A+   L+ FP  N++   + 
Sbjct: 473 VTQFDEADITEMEEFRKQQNDAAAKKKADYKITPLVFMMKAVAKTLQQFPVFNSSLSSDG 532

Query: 278 QIITRHGAVHVGIATQGDNGLMVPVLRHAEAGSLWANAGEISRLANAARNNKASREELSG 337
           + + +    H+G+A    NGL+VPV+R  +   +   + E++ ++  AR+ K    ++ G
Sbjct: 533 ESLIQKKYFHIGVAVDTPNGLVVPVVRDVDKKGIIELSRELADISIRARDGKLKSADMQG 592

Query: 338 STITLTSLGALGGIVSTPVVNTPEVAIVGVNRMVERPVVIDGQIVVRKMMNLSSSFDHRV 397
           S  T++SLG +GG   TP+VN P+VAI+GV++   +P     +   + M+ LS S+DHRV
Sbjct: 593 SCFTISSLGGIGGTAFTPIVNYPDVAILGVSKSEIKPKWNGKEFEPKLMLPLSLSYDHRV 652

Query: 398 VDGMDAALFIQAVRGLL 414
           +DG  AA F   + G+L
Sbjct: 653 IDGAMAARFSVTLSGIL 669



 Score = 60.8 bits (146), Expect = 1e-13
 Identities = 45/123 (36%), Positives = 61/123 (49%), Gaps = 12/123 (9%)

Query: 6   IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65
           I +PDIG G   V ++E  V  GD I  D  +  + TDKAT+++PSP +G V  +    G
Sbjct: 126 ISVPDIG-GDTDVSVIEVLVAAGDKIEVDAGLITLETDKATMDVPSPFAGVVKEVKVAVG 184

Query: 66  EVMAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKPAAYQASASHEAA 125
           + ++ GS +I +EV G         A PA  P A   A   P     PAA  A A   A 
Sbjct: 185 DKVSQGSLVIMLEVGG---------AAPAAAPQANAPAASAPVAQAAPAA--AVAPVAAV 233

Query: 126 PIV 128
           P+V
Sbjct: 234 PVV 236



 Score = 58.9 bits (141), Expect = 5e-13
 Identities = 33/100 (33%), Positives = 56/100 (56%), Gaps = 2/100 (2%)

Query: 8   MPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPGEV 67
           +PDIG    +V+++E    VGD +A ++ +  V +DKAT++IP+P +G +  L    G+ 
Sbjct: 9   VPDIGGD--EVQVIEICAAVGDTLAAEESILTVESDKATMDIPAPFAGVLAELKVAVGDK 66

Query: 68  MAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEP 107
           ++ G+ +  I+  G+      P A+ A    APV A P P
Sbjct: 67  VSEGTLIALIQAAGASAQAAAPVAQAAAPAPAPVQAAPAP 106


Lambda     K      H
   0.316    0.133    0.376 

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: 704
Number of extensions: 34
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 423
Length of database: 677
Length adjustment: 35
Effective length of query: 388
Effective length of database: 642
Effective search space:   249096
Effective search space used:   249096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources