GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Paraburkholderia bryophila 376MFSha3.1

Align BadH (characterized)
to candidate H281DRAFT_00643 H281DRAFT_00643 3-oxoacyl-[acyl-carrier-protein] reductase

Query= metacyc::MONOMER-893
         (255 letters)



>FitnessBrowser__Burk376:H281DRAFT_00643
          Length = 246

 Score =  187 bits (474), Expect = 2e-52
 Identities = 101/251 (40%), Positives = 144/251 (57%), Gaps = 6/251 (2%)

Query: 3   RLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRC 62
           +L  K A+ITG G GIG AT  +FA EGA +   D+NLDA   VA   R+AGG A+A   
Sbjct: 2   KLNGKVAIITGAGQGIGAATALKFASEGAVVIACDMNLDAVATVAHLCREAGGKADAFAV 61

Query: 63  DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMH 122
           D+ +RT VD  +A    T G +D++VNNAG        K    +++ +I +NL G  H  
Sbjct: 62  DVTNRTQVDEMVAKVRGTYGRIDVVVNNAGITRDARLQKMTLQQFDDVIDVNLRGVFHTA 121

Query: 123 HAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNV 182
            AV+  M+E+  G I+N +S     G+ G+  YAA K G++ F+KT +RE    GI VN 
Sbjct: 122 QAVVDTMIEQGSGVILNASSVVGVYGNYGQTNYAAAKFGVIGFTKTWSRELGPKGIRVNA 181

Query: 183 VCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITG 242
           V PG  DT +L  +      PE ++      +PL RLGKP+++A   AF  SD+A ++ G
Sbjct: 182 VAPGFIDTPILKTI------PEDVLTKMRDQVPLRRLGKPEEIASIYAFLASDEASYVNG 235

Query: 243 QVLSVSGGLTM 253
            V+  +GGLT+
Sbjct: 236 AVIEATGGLTL 246


Lambda     K      H
   0.318    0.135    0.398 

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: 162
Number of extensions: 6
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: 255
Length of database: 246
Length adjustment: 24
Effective length of query: 231
Effective length of database: 222
Effective search space:    51282
Effective search space used:    51282
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 (21.7 bits)
S2: 46 (22.3 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