Align proline racemase (EC 5.1.1.4) (characterized)
to candidate BPHYT_RS28265 BPHYT_RS28265 hypothetical protein
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__BFirm:BPHYT_RS28265 Length = 335 Score = 283 bits (723), Expect = 6e-81 Identities = 136/335 (40%), Positives = 207/335 (61%) Query: 1 MKFSRSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHN 60 MK SR+IQ ++ HT GEA RIV G+P + G+++ +++ +L+EN D +R A+M EPRGH Sbjct: 1 MKISRTIQTVEVHTGGEAFRIVTSGLPRLPGDTIVKRRAWLKENADDIRRALMFEPRGHA 60 Query: 61 DMFGSVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVME 120 DM+G +T+P P+ADFGIIF+ GY + CGHG I TAA+E G V P T + ++ Sbjct: 61 DMYGGYLTEPVSPNADFGIIFLHNEGYSDHCGHGVIALSTAAVELGWVQREIPETRIGID 120 Query: 121 APAGIIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHA 180 AP G I V A V F+NVP+F++K V V+ P G+V DI+FGG+F+ Sbjct: 121 APCGFIEAFVEWDGEHAGNVRFVNVPSFIWKRDVTVETPSFGSVTGDIAFGGAFYFYTDG 180 Query: 181 SQLGLKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYK 240 GL + + +L +++ N+ ++HP + I + I + P H +T Sbjct: 181 EPHGLAVRESSVEELIRFGAEVKQAANQAFPVEHPYIPEINHIYGTIIANAPRHAGSTQA 240 Query: 241 NVVIFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVAD 300 N +F +VDRSP G+GT ++A L+ +G+L + V ESI+GT+FKG ++ ET V D Sbjct: 241 NCCVFADREVDRSPTGSGTGGRVAQLYLRGKLGKDDTLVNESIIGTVFKGRVLSETTVGD 300 Query: 301 FNAVVPKITGSAYITGFNHFVIDEEDPLKHGFILK 335 F AVVP++ G+A++ GF ++IDE DPL +GF+++ Sbjct: 301 FKAVVPEVEGNAFVCGFATWIIDERDPLAYGFLVR 335 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: 343 Number of extensions: 14 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: 335 Length adjustment: 28 Effective length of query: 307 Effective length of database: 307 Effective search space: 94249 Effective search space used: 94249 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