Align proline racemase (EC 5.1.1.4); 4-hydroxyproline epimerase (EC 5.1.1.8) (characterized)
to candidate AO356_24910 AO356_24910 hypothetical protein
Query= BRENDA::H3ZMH5 (331 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24910 Length = 342 Score = 184 bits (468), Expect = 2e-51 Identities = 113/335 (33%), Positives = 183/335 (54%), Gaps = 5/335 (1%) Query: 1 MFADHVFHVVDTHTEGEPTRIVLSGVNVKGEDIIEKREYFKEHYDWIRTALLHEPRGHSD 60 M + + HVV H EGE +++ GV + ++ + +R +L+EPRG Sbjct: 1 MRSSKIIHVVSCHAEGEVGDVIVGGVAPPPGATVWEQSRWIAQDQTLRNFVLNEPRGGVF 60 Query: 61 QFGAVLVPSDI--ADFGVIYMDTSGYLDMCGHATMGVATVLVELGIIEKKEPYTTVKLET 118 + +LVP+ A I M+ + M G ++ VATVL++ GI+ EP T + LE Sbjct: 61 RHVNLLVPAKDPRAQMAWIIMEPADTPPMSGSNSLCVATVLLDSGILPMTEPQTRLVLEA 120 Query: 119 PAGLVEAKAKVKGGVVKEVTVVDVPSFYVG-EFVIEYPGRGKIKVDVAFGGNFYVIADAR 177 P GL+EA A + G V+ + + +VPSF + IE G G ++VD A+GG+ +VI DA+ Sbjct: 121 PGGLIEAVADCRDGKVRRIEIKNVPSFADRLDAWIEVEGLGSLQVDTAYGGDSFVIVDAQ 180 Query: 178 DLGLRVRREYIKELIPTALKLIKVANEQIKVQHPRKGVQNRINLAMLTDEPERED--SDG 235 LG +R + EL+ LK+ + ANEQ+ HP + I+ + +E+ + G Sbjct: 181 RLGFAIRPDEAAELVAVGLKITRAANEQLGFVHPLNPDWSHISFCQIAAPIVQENGIATG 240 Query: 236 KNVVIWGEGSVDRSPCGTGSASRVATLYSKGILKEGDIFVHESILGTQFRIKIVGTTKIG 295 N V+ G +DRSP GTG ++R+A L++KG+++ G+ F+ SI+G++F +I T + Sbjct: 241 ANAVVIQPGKIDRSPTGTGCSARMAVLHAKGLMQVGERFIGRSIIGSEFHCRIDSLTDVA 300 Query: 296 EYTAIIPEITGSAYITKISQDIISKNDPLWKGFLL 330 AI P I G A+IT Q ++ DP +G+ L Sbjct: 301 GRPAIYPCIAGRAWITGTHQLLLDPADPWPQGYRL 335 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: 267 Number of extensions: 20 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: 331 Length of database: 342 Length adjustment: 28 Effective length of query: 303 Effective length of database: 314 Effective search space: 95142 Effective search space used: 95142 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