Align proline racemase (EC 5.1.1.4) (characterized)
to candidate HSERO_RS00875 HSERO_RS00875 hypothetical protein
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__HerbieS:HSERO_RS00875 Length = 336 Score = 259 bits (662), Expect = 7e-74 Identities = 132/335 (39%), Positives = 196/335 (58%) Query: 1 MKFSRSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHN 60 + ++R++Q ID+HT GE RIVV G+P I ++ E++ +L E+ D LR +M EPRGH Sbjct: 2 LSYTRTVQTIDAHTGGEPLRIVVSGLPKIPAGTILEQRAWLREHRDDLRCFLMNEPRGHA 61 Query: 61 DMFGSVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVME 120 DM+G+ + P ADFG+IF+ GY +MCGHG I +E G V P T + + Sbjct: 62 DMYGAYLLPPVTAGADFGVIFIHNEGYSDMCGHGIIALGKVLVEMGYVERTSPQTRICFD 121 Query: 121 APAGIIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHA 180 APAG I V +A +VSF NVPAF+Y+ VEVD PG G + DI FGG+F+ I+A Sbjct: 122 APAGFIEAFVEWDGERAGKVSFNNVPAFIYRRDVEVDTPGFGKITGDIVFGGAFYYYINA 181 Query: 181 SQLGLKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYK 240 +Q GL ++P+ +L +L + + + K+ I HP + T+ I P P A Sbjct: 182 TQAGLTVKPELVRQLIQLGAETKAAVMAKVAIAHPLEPGLNTLYGTIIDSAPNFPGADQS 241 Query: 241 NVVIFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVAD 300 NV IF +VDRSP GTGTS + A L +G+L + + +V SI+G+ F + T+V Sbjct: 242 NVCIFADREVDRSPTGTGTSGRAAQLFLRGQLALNQPYVNGSIVGSNFGVRVTAATQVGP 301 Query: 301 FNAVVPKITGSAYITGFNHFVIDEEDPLKHGFILK 335 F + +++G A+I N +V+++ DP GF L+ Sbjct: 302 FEGALTEVSGYAHIMSTNQWVLEQSDPFPTGFFLR 336 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: 327 Number of extensions: 11 Number of successful extensions: 1 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: 336 Length adjustment: 28 Effective length of query: 307 Effective length of database: 308 Effective search space: 94556 Effective search space used: 94556 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.
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