GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Marinobacter adhaerens HP15

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 GFF1560 HP15_1522 dihydrolipoamide acetyltransferase

Query= curated2:P37942
         (424 letters)



>FitnessBrowser__Marino:GFF1560
          Length = 409

 Score =  234 bits (598), Expect = 3e-66
 Identities = 144/415 (34%), Positives = 231/415 (55%), Gaps = 22/415 (5%)

Query: 5   QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64
           ++  P   ESV EGT++ W   PG+  ++ + I ++ TDKV  EV +   G I E++  E
Sbjct: 4   EIKAPVFPESVAEGTVATWHKQPGEACSRDELIVDIETDKVVLEVVAPADGVIEEIIKNE 63

Query: 65  GQTLQVGEMICKIETEGAN----PAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120
           G T++ GE++ K + EGA     PAE K+E+  + E A    AKS  ++ +      SPA
Sbjct: 64  GDTVESGEVVGKFK-EGAKGESKPAEGKKEE--SKEEAPKEEAKSEASSGEAI---LSPA 117

Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180
             +LA E+ +D + + GTG  GR+T++D+Q  +++             AAP P +A  PE
Sbjct: 118 ARKLAEENNVDPNSIKGTGKDGRVTKEDVQNHVDSA------KSSGGAAAPQP-AAGMPE 170

Query: 181 PKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKD 240
                +       +K +P+T +R +IA  +  ++       T  EV++  ++  R   +D
Sbjct: 171 ----VNVSQGERPEKRVPMTRLRASIAKRLVNAQQSAAMLTTFNEVNMGPIMEMRKQYQD 226

Query: 241 SFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVP 300
           SF K  G  L F +FF KA  +ALK FP +N+   G+ ++     +I +AV+T+  L VP
Sbjct: 227 SFVKRHGIKLGFMSFFTKAATEALKRFPAVNASIDGNDMVYHGYQDIGVAVSTDRGLVVP 286

Query: 301 VIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQ 360
           V++++D   +  I K I     K ++GKL  +DM GGTFT+ N G FGS+ S  I+N PQ
Sbjct: 287 VLRDSDAMGLADIEKKIVEYGTKAKEGKLAIEDMTGGTFTITNGGIFGSLISTPILNPPQ 346

Query: 361 AAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
            AIL +  I +RP+ + NG + ++ M+ L LS DHR++DG    +FL  +K++LE
Sbjct: 347 TAILGMHKIQERPMAV-NGKVEIQPMMYLALSYDHRMIDGKEAVQFLVAIKEMLE 400


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: 421
Number of extensions: 26
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: 409
Length adjustment: 31
Effective length of query: 393
Effective length of database: 378
Effective search space:   148554
Effective search space used:   148554
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