GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prdF in Pseudomonas simiae WCS417

Align proline racemase (EC 5.1.1.4) (characterized)
to candidate GFF2804 PS417_14305 hydroxyproline-2-epimerase

Query= BRENDA::A8DEZ8
         (335 letters)



>FitnessBrowser__WCS417:GFF2804
          Length = 308

 Score =  179 bits (454), Expect = 8e-50
 Identities = 116/327 (35%), Positives = 175/327 (53%), Gaps = 21/327 (6%)

Query: 5   RSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFG 64
           + +  IDSHT GE TR+V+ G P + G ++ ++   L    D  R A +LEPRG++ + G
Sbjct: 2   KRLHVIDSHTGGEPTRLVMSGFPALSGATIADQLHSLRTEHDQWRRACLLEPRGNDVLVG 61

Query: 65  SVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAG 124
           ++  +P  P A  G+IF +  GYL MCGHGTIG + +    G    ++P  H + + P G
Sbjct: 62  ALYCEPVTPGAICGVIFFNNAGYLGMCGHGTIGLVASLHHLG---RIQPGVHTI-DTPVG 117

Query: 125 IIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLG 184
            +   +   DG    V+  NVPA+   + V V++PG G V  DI++GG++F ++  S  G
Sbjct: 118 PVAATLH-EDG---AVTLRNVPAYRLHQQVPVEVPGHGVVYGDIAWGGNWFFLV--SDHG 171

Query: 185 LKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVI 244
            +++  N   LT+    +     + +E Q    A    +D +E++ +    ++  +N V+
Sbjct: 172 QRLQMDNVDALTDYTWAML----KALEDQGIHGADGALIDHIELFADDDRADS--RNFVM 225

Query: 245 FGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAV 304
                 DRSPCGTGTSAKLA L A G LK GE +   SI G+ F G         D   V
Sbjct: 226 CPGKAYDRSPCGTGTSAKLACLAADGTLKPGETWTQASITGSQFDGHY-----EWDGERV 280

Query: 305 VPKITGSAYITGFNHFVIDEEDPLKHG 331
            P ITG+AY+T  +  +IDE DP   G
Sbjct: 281 RPFITGNAYMTADSTLLIDERDPFAWG 307


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: 283
Number of extensions: 12
Number of successful extensions: 5
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: 308
Length adjustment: 28
Effective length of query: 307
Effective length of database: 280
Effective search space:    85960
Effective search space used:    85960
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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