Align Serine dehydratase-like; L-serine deaminase; L-serine dehydratase/L-threonine deaminase; L-threonine dehydratase; TDH; SDH; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate RR42_RS33880 RR42_RS33880 serine dehydratase
Query= SwissProt::Q8R238 (329 letters) >FitnessBrowser__Cup4G11:RR42_RS33880 Length = 314 Score = 288 bits (736), Expect = 2e-82 Identities = 158/306 (51%), Positives = 203/306 (66%), Gaps = 10/306 (3%) Query: 15 HRVTPLLESWALSQVAGMPVFLKYENVQIAGSFKIRGIGHFCQQMAKRGCRHLVCSSGGN 74 H VTPLL S + S G V+ K E +Q GSFK RGIGH CQ + G + LVCSSGGN Sbjct: 13 HIVTPLLRSTSFSARLGRSVWFKMEALQPPGSFKARGIGHACQTYKEWGAKRLVCSSGGN 72 Query: 75 AGIAAAYSARKLGIPVTIVLPEGTSVQVVRRLEGEGAEVQLTGKVWDEANVKAQELATRD 134 AGIA AYS R LG+PVT+V+PE TS R+ EGAE+ + G+ W EAN A L R Sbjct: 73 AGIAVAYSGRLLGVPVTVVVPETTSAAARERIAAEGAELVVYGRAWSEANDHALSLM-RP 131 Query: 135 GWVNVSPFDHPLIWEGHASLVRELKESLGTPPGAVVLAVGGGGLLAGVTAGLLEVGWQHV 194 + + PFD PL+WEGHA+++ E+ + G PGAVVL+VGGGGLL GV AGL GW V Sbjct: 132 EYAFIHPFDDPLLWEGHATMIDEVAAA-GVKPGAVVLSVGGGGLLCGVLAGLERNGWHDV 190 Query: 195 PIVAMETRGAHSFNSALQAGRPVTLPDITSVAKSLGAKTVAARTLECAKECEVLSEVVED 254 P++A ET GA S+ ++L AG V LP ITS+A SLGA++ A+ LE +K ++SEVV D Sbjct: 191 PVIAAETVGADSYAASLAAGAQVELPAITSIATSLGARSPCAKALEWSKVHSIVSEVVTD 250 Query: 255 REAVSAVQRFLDDERMLVEPACGAALAAIYSGILWRLQAEGRLSSALASVVVIVCGGNNI 314 +EAV A RFL + R++VEPACGAALAA L+ + +A + V+VIVCGG Sbjct: 251 KEAVGACLRFLAEHRIVVEPACGAALAA--------LERKPAAVTAASDVLVIVCGGAGA 302 Query: 315 SSQQLQ 320 +++QLQ Sbjct: 303 TAEQLQ 308 Lambda K H 0.318 0.134 0.395 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: 285 Number of extensions: 11 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: 329 Length of database: 314 Length adjustment: 28 Effective length of query: 301 Effective length of database: 286 Effective search space: 86086 Effective search space used: 86086 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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