GapMind for catabolism of small carbon sources

 

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

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate H281DRAFT_03491 H281DRAFT_03491 short chain enoyl-CoA hydratase (EC 4.2.1.17)/Enoyl-CoA hydratase (EC 4.2.1.17)

Query= BRENDA::Q5SLK3
         (254 letters)



>FitnessBrowser__Burk376:H281DRAFT_03491
          Length = 266

 Score =  179 bits (454), Expect = 5e-50
 Identities = 106/261 (40%), Positives = 148/261 (56%), Gaps = 9/261 (3%)

Query: 2   VLKERQDGVLVLTLNRPEKLNAITG-ELLDALYAALKEGEEDREVRALLLTGAGRAFSAG 60
           VL E   GV  +TLNRPE  NA+T  E++DAL  +L+  + D  VRA++LTGAG AFS+G
Sbjct: 5   VLYELDGGVATITLNRPETRNALTEMEVVDALVESLERAQADLNVRAIVLTGAGPAFSSG 64

Query: 61  QDLTEFGDRKPDY--------EAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALW 112
            ++    D    +        E + R   R+  A   L+ P + AVNG A GAG  LAL 
Sbjct: 65  GNIKHMRDEVGTFGGNSAQIRENYRRGIQRIPRAFHELDLPCIAAVNGPAHGAGCDLALM 124

Query: 113 GDLRLAAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGL 172
            D+R+AA  A F  +F +IG++P  G ++LLPR VGL++A E++     + A+ AL  GL
Sbjct: 125 CDIRIAAHSALFAESFAKIGIIPGDGGAWLLPRAVGLSRAAEMIFTGTPIDAQCALDWGL 184

Query: 173 VHRVVPAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQ 232
           V RVVP  +L+  A  LA  +A  P     ++K+L+ E  R+ L   L L A  QG   +
Sbjct: 185 VSRVVPDAELLSTARELAARIASNPPNVLRMSKRLIREGQRMDLPSLLELSAAFQGIVHR 244

Query: 233 TQDHEEGVRAFREKRPPRFQG 253
           T DH E + A  EKR P + G
Sbjct: 245 TADHREALAATFEKRTPNYTG 265


Lambda     K      H
   0.318    0.135    0.371 

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: 160
Number of extensions: 12
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: 254
Length of database: 266
Length adjustment: 24
Effective length of query: 230
Effective length of database: 242
Effective search space:    55660
Effective search space used:    55660
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: 47 (22.7 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