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.
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:
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