Align proline racemase (EC 5.1.1.4); 4-hydroxyproline epimerase (EC 5.1.1.8) (characterized)
to candidate Echvi_3951 Echvi_3951 Proline racemase
Query= BRENDA::H3ZMH5 (331 letters) >FitnessBrowser__Cola:Echvi_3951 Length = 332 Score = 236 bits (601), Expect = 8e-67 Identities = 131/326 (40%), Positives = 194/326 (59%), Gaps = 5/326 (1%) Query: 7 FHVVDTHTEGEPTRIVLSGVN-VKGEDIIEKREYFKEHYDWIRTALLHEPRGHSDQFGAV 65 F +D HT G P R+V G+ ++GE++ EKR++F +HYDWIR L+ EPRGH G++ Sbjct: 5 FSCIDAHTCGNPVRVVTGGLPFLEGENMFEKRQFFIKHYDWIRRGLMFEPRGHDMMSGSM 64 Query: 66 LVPSDIA--DFGVIYMDTSGYLDMCGHATMGVATVLVELGIIEKKEPYTTVKLETPAGLV 123 L P D V+Y++TSG L MCGH T+G TV +E G+I K P ++LETPAGLV Sbjct: 65 LYPPHDPENDVAVLYIETSGCLPMCGHGTIGTVTVAIEEGLITPKVP-GKLRLETPAGLV 123 Query: 124 EAKAKVKGGVVKEVTVVDVPSFYVGEFV-IEYPGRGKIKVDVAFGGNFYVIADARDLGLR 182 +G V V + +VPSF + + + I G++ DV++GGNFY I + ++ Sbjct: 124 LVSYTQEGEKVTSVKLTNVPSFVIAKDLNISCDVLGELIFDVSYGGNFYAIIEPQENFGG 183 Query: 183 VRREYIKELIPTALKLIKVANEQIKVQHPRKGVQNRINLAMLTDEPEREDSDGKNVVIWG 242 ++ ++LI + KL K NE HP N ++ E S G+N V +G Sbjct: 184 LQDFTAEQLITMSRKLRKAINEVYTFVHPENSRINGLSHIQWIGRTLDEHSHGRNAVFYG 243 Query: 243 EGSVDRSPCGTGSASRVATLYSKGILKEGDIFVHESILGTQFRIKIVGTTKIGEYTAIIP 302 + ++DRSPCGTG+++R+A LYS+G+LK + FV+ES +G+ F +I+G T +G+Y AIIP Sbjct: 244 DKAIDRSPCGTGTSARMAQLYSRGLLKANEPFVNESYIGSTFTGEIIGETNVGDYDAIIP 303 Query: 303 EITGSAYITKISQDIISKNDPLWKGF 328 I G A IT + + +DP GF Sbjct: 304 SIEGWAKITGYNTIFLDDDDPYVHGF 329 Lambda K H 0.319 0.139 0.406 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: 277 Number of extensions: 10 Number of successful extensions: 6 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: 331 Length of database: 332 Length adjustment: 28 Effective length of query: 303 Effective length of database: 304 Effective search space: 92112 Effective search space used: 92112 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