Align proline racemase (EC 5.1.1.4) (characterized)
to candidate Pf6N2E2_671 2-methylaconitate racemase
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_671 Length = 342 Score = 190 bits (482), Expect = 5e-53 Identities = 110/337 (32%), Positives = 178/337 (52%), Gaps = 5/337 (1%) Query: 1 MKFSRSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHN 60 M+ S+ I + H GE ++VGG+ G ++ E+ ++ ++ LR ++ EPRG Sbjct: 1 MRSSKIIHVVSCHAEGEVGDVIVGGVAPPPGATVWEQSRWIAQD-QTLRNFVLNEPRGGV 59 Query: 61 DMFGSVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVME 120 +++ P A I M+ M G ++ T +++G++P EP T +V+E Sbjct: 60 FRHVNLLVPAKDPRAQMAWIIMEPADTPPMSGSNSLCVATVLLDSGILPMTEPQTRLVLE 119 Query: 121 APAGIIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHA 180 AP G+I DGK + V NVP+F + +++ G+G+++ D ++GG F I+ A Sbjct: 120 APGGLIEAVADCRDGKVQRVEIKNVPSFADRLDAWIEVEGLGSLQVDTAYGGDSFVIVDA 179 Query: 181 SQLGLKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPE---A 237 +LG I P A +L + +K+ NE++ HP + +I P E A Sbjct: 180 QRLGFAIRPDEAAELVAVGLKITRAANEQLGFVHPLNPDWSHISFCQI-AAPIVQENGIA 238 Query: 238 TYKNVVIFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETK 297 T N V+ G++DRSP GTG SA++A LHAKG ++VGE+F+ SI+G+ F I T Sbjct: 239 TGANAVVIQPGKIDRSPTGTGCSARMAVLHAKGLMQVGERFIGRSIIGSEFHCRIDSLTD 298 Query: 298 VADFNAVVPKITGSAYITGFNHFVIDEEDPLKHGFIL 334 VA A+ P I G A+ITG + ++D DP G+ L Sbjct: 299 VAGRPAIYPCIAGRAWITGTHQLLLDPADPWPQGYRL 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: 266 Number of extensions: 10 Number of successful extensions: 3 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: 342 Length adjustment: 28 Effective length of query: 307 Effective length of database: 314 Effective search space: 96398 Effective search space used: 96398 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