GapMind for catabolism of small carbon sources

 

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

Align proline racemase (EC 5.1.1.4) (characterized)
to candidate H281DRAFT_01193 H281DRAFT_01193 4-hydroxyproline epimerase

Query= BRENDA::A8DEZ8
         (335 letters)



>FitnessBrowser__Burk376:H281DRAFT_01193
          Length = 323

 Score =  178 bits (452), Expect = 1e-49
 Identities = 114/332 (34%), Positives = 178/332 (53%), Gaps = 20/332 (6%)

Query: 6   SIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFGS 65
           SI  IDSHT GE TR+VV G P++    + E+ +    + D++R  ++ EPRG + M G+
Sbjct: 3   SITVIDSHTGGEPTRLVVEGGPDLGRGPLAERLDIFRRDFDHVRAGVVNEPRGSDVMVGA 62

Query: 66  VMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAGI 125
           ++ +P       G+IF +  GYL MCGHGTIG + +    G    ++P  H + E P G+
Sbjct: 63  LLCEPHDTRCSAGVIFFNNVGYLGMCGHGTIGLIVSLAHMG---RIKPGVHRI-ETPVGV 118

Query: 126 IRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLGL 185
           +  ++   DG    VS  NVPA+ Y+  V++D+PG+G V  DI++GG++F ++  +  G 
Sbjct: 119 VEAELH-GDG---SVSVRNVPAYRYRTEVQLDVPGLGRVHGDIAWGGNWFFLV--ADHGQ 172

Query: 186 KIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVIF 245
            +E  N   LT +   +R      +E    T      +D +E++ + T P    +N V+ 
Sbjct: 173 TLEFANVESLTNVTWAIR----AALEANGITGEGGALIDHIELFADSTTPGVDSRNFVLC 228

Query: 246 GQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKG--EIVEETKVADFNA 303
                DRSPCGTGTSAK+A L A   L  G  +  ESI+G++F+   E  E+T     NA
Sbjct: 229 PGKAYDRSPCGTGTSAKIACLAADAHLAPGATWRQESIIGSIFEASYEPHEDTSHNVDNA 288

Query: 304 ----VVPKITGSAYITGFNHFVIDEEDPLKHG 331
               V P I G+A+++     +   +DP   G
Sbjct: 289 SRRYVRPSIRGTAHVSAEAKLIFSADDPFAWG 320


Lambda     K      H
   0.319    0.139    0.403 

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: 287
Number of extensions: 13
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: 335
Length of database: 323
Length adjustment: 28
Effective length of query: 307
Effective length of database: 295
Effective search space:    90565
Effective search space used:    90565
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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