GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prdF in Pseudomonas litoralis 2SM5

Align proline racemase (EC 5.1.1.4) (characterized)
to candidate WP_090272723.1 BLU11_RS07275 hypothetical protein

Query= BRENDA::A8DEZ8
         (335 letters)



>NCBI__GCF_900105005.1:WP_090272723.1
          Length = 350

 Score =  256 bits (653), Expect = 8e-73
 Identities = 130/347 (37%), Positives = 207/347 (59%), Gaps = 15/347 (4%)

Query: 1   MKFSRSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHN 60
           M F R+I A+D+H AG   R++ GG+P+I GN++ EK ++LEEN D LR  ++ EPRG+ 
Sbjct: 1   MSFKRTIYAVDTH-AGTPMRVITGGVPHIPGNTVFEKMKWLEENDDQLRKLMLREPRGYP 59

Query: 61  DMFGSVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVME 120
               +++  PC P+AD G I M+   Y  M G  TI  +T  +E G++P  EPVT +V+E
Sbjct: 60  AHCCNIIVPPCHPEADAGYIIMEQIEYPVMSGGNTISVVTVLLEMGMLPMQEPVTELVLE 119

Query: 121 APAGIIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHA 180
           APAG+IR      +GK K V+F NVPAF       +++P +G V  D+ +GG F+ I   
Sbjct: 120 APAGLIRVKAECRNGKVKNVTFQNVPAFAAHLDAVIEVPHLGKVTVDVGWGGMFYVIADV 179

Query: 181 SQL-GLKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATY 239
            Q  GL+++P++  ++T ++  +R    E++ + HP    +  + + ++      P A +
Sbjct: 180 RQFKGLELKPEHGREITRVSSMIRQAAIEQLPVAHPDYPGV-GITISQLSGPTEDPNADW 238

Query: 240 KNVVIFGQGQ------------VDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTL 287
           KN V    G             +DR PCGTGTSAK+A LHAKGEL + + F ++ ++  +
Sbjct: 239 KNAVTMASGDFSWDDPATWTGALDRCPCGTGTSAKMAVLHAKGELPLHQDFRHQGLVNNI 298

Query: 288 FKGEIVEETKVADFNAVVPKITGSAYITGFNHFVIDEEDPLKHGFIL 334
           + G ++EET++ +  AV+P +TG+++I G N FV+D +DP   GF +
Sbjct: 299 YTGRLIEETRIGEHTAVIPTVTGTSWIYGLNTFVLDHDDPFTEGFTI 345


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: 325
Number of extensions: 18
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: 350
Length adjustment: 29
Effective length of query: 306
Effective length of database: 321
Effective search space:    98226
Effective search space used:    98226
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 24 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