GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Marino:GFF1560 HP15_1522 dihydrolipoamide
           acetyltransferase
          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 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