Align serine racemase (EC 5.1.1.18) (characterized)
to candidate AO353_25960 AO353_25960 threonine dehydratase
Query= BRENDA::Q2PGG3 (331 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25960 Length = 336 Score = 183 bits (465), Expect = 5e-51 Identities = 101/267 (37%), Positives = 158/267 (59%), Gaps = 2/267 (0%) Query: 28 RTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACNAVLSLDAEQAAKGVVTHSSGNH 87 RTP+ + +L+ + G + K E LQ +FK RGA N + L AEQ A+GV+T S+GNH Sbjct: 33 RTPLQVAPALSEVLGNQILLKREDLQPTFSFKIRGAYNKLAQLSAEQKARGVITASAGNH 92 Query: 88 AAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKVIWSEATMSSREEIASKVLQETG 147 A ++LAA+ GI A IV+P P+ KV V G + + E A + ++TG Sbjct: 93 AQGVALAARELGIEASIVMPTSTPELKVIGVRSRGANAVLHGESFPFALEYALNLARQTG 152 Query: 148 SVLIHPYNDGRIISGQGTIALELLEQIQ-EIDAIVVPISGGGLISGVALAAKSIKPSIRI 206 + P++D +I+GQGT+A+E+L Q Q +DAI VP+ GGGLI+G+A K ++P IRI Sbjct: 153 RTFVSPFDDPDVIAGQGTVAMEILRQHQGALDAIFVPVGGGGLIAGIAAYVKYLRPEIRI 212 Query: 207 IAAEPKGADDAAQSKVAGKIITLPVTNTIADGLR-ASLGDLTWPVVRDLVDDVVTLEECE 265 + E + + + +AG+ + LP T ADG+ A +G+ + + R VD+V+T+ E Sbjct: 213 VGVESEHSACLQAAMLAGERVVLPKVGTFADGVAVAQIGEYGFEICRHHVDEVLTVSNDE 272 Query: 266 IIEAMKMCYEILKVSVEPSGAIGLAAV 292 + A+K Y+ + EPSGA+ +A + Sbjct: 273 LCAAIKNIYDDTRSITEPSGALAVAGI 299 Lambda K H 0.316 0.133 0.380 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: 250 Number of extensions: 13 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: 336 Length adjustment: 28 Effective length of query: 303 Effective length of database: 308 Effective search space: 93324 Effective search space used: 93324 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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