GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Magnetospirillum magneticum AMB-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 WP_011386316.1 AMB_RS20045 dihydrolipoyllysine-residue succinyltransferase

Query= curated2:P37942
         (424 letters)



>NCBI__GCF_000009985.1:WP_011386316.1
          Length = 394

 Score =  276 bits (707), Expect = 6e-79
 Identities = 158/411 (38%), Positives = 231/411 (56%), Gaps = 29/411 (7%)

Query: 5   QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64
           ++ +P LGESVTE TI+KW    GD V   +P+ E+ TDKV  EV +   GT+T++V   
Sbjct: 4   EIKVPTLGESVTEATIAKWFKNVGDAVRADEPLVELETDKVTVEVNAPAAGTLTDIVAAA 63

Query: 65  GQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPAVLRL 124
           G T++VG ++  +   GA  A      PA   AA  P A  A A   P+ K+       +
Sbjct: 64  GATVEVGALLGVLGAAGAAAA------PAPKAAAPAPAAAPAAAGVMPSAKK-------I 110

Query: 125 AGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPEPKEE 184
           A + GID   ++GTG  GR+T+ D+                   AAPAP +A  P+P   
Sbjct: 111 AADAGIDTAAISGTGKDGRVTKGDVLAA---------------AAAPAP-AAPAPKPAAP 154

Query: 185 TSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKDSFKK 244
           +   A A  ++ + +T +RK IA  +K ++       T  EVD+T +   RN  KD F+K
Sbjct: 155 SGPRAKADQEERVKMTRLRKTIAGRLKEAQNTAAMLTTFNEVDMTALFDVRNQYKDQFEK 214

Query: 245 TEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVPVIKN 304
             G  L F +FFVKA   ALK++P +N+   GD ++ KK  +I +AV T   L VPV++ 
Sbjct: 215 RHGTKLGFMSFFVKACVAALKDWPAVNAEIDGDDLVYKKYYDIGVAVGTPQGLVVPVLRG 274

Query: 305 ADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQAAIL 364
           AD+ +  G+ + I  L KK RDGKL+ +D+ GGTFT++N G +GS+ S  I+N PQ+ IL
Sbjct: 275 ADQLSFAGVEQGIANLGKKARDGKLSMEDLMGGTFTISNGGVYGSLMSTPILNTPQSGIL 334

Query: 365 QVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
            +  + +RP+VM +G I  R M+ L LS DHR++DG     FL RVK+ +E
Sbjct: 335 GMHKVQQRPMVMPDGSIKARPMMYLALSYDHRIIDGREAVSFLVRVKECIE 385


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: 371
Number of extensions: 20
Number of successful extensions: 3
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: 394
Length adjustment: 31
Effective length of query: 393
Effective length of database: 363
Effective search space:   142659
Effective search space used:   142659
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