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 Ac3H11_1770 Threonine dehydratase (EC 4.3.1.19)
Query= SwissProt::Q8R238 (329 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1770 Length = 313 Score = 124 bits (310), Expect = 4e-33 Identities = 101/314 (32%), Positives = 160/314 (50%), Gaps = 21/314 (6%) Query: 4 ALAERVGAEP-FHRVTPLLE-SWALSQVAGMPVFLKYENVQIAGSFKIRGIGH--FCQQM 59 A ++ +P F R TPL+ S V V+LK E++Q+ GSFK RG+ + + Sbjct: 9 AARRQLATQPDFLRTTPLMRVSGKTLGVDCAEVWLKLEHLQVGGSFKARGMLYRLLANPV 68 Query: 60 AKRGCRHLVCSSGGNAGIAAAYSARKLGIPVTIVLPEGTSVQVVRRLEGEGAEVQLTGKV 119 + G ++ +SGGNAGIA A +A+ LG+ + +PE + RL GAEV +TG Sbjct: 69 PESG---VIIASGGNAGIAVAAAAQALGVRCEVFVPEVSPEAKRARLRALGAEVIVTGAA 125 Query: 120 WDEANVKAQELATRDGWVNVSPFDHPLIWEGHASLVRELKESLGTPPGAVVLAVGGGGLL 179 + +A G + +D P + G +L EL+E G P V+++VGGGGL+ Sbjct: 126 YSQAFEACVARQKTTGALQAHAYDQPEVVAGAGTLALELEEQGGRLPDTVLVSVGGGGLI 185 Query: 180 AGVTAGLLEVGWQHVPIVAMETRGAHSFNSALQAGRPVTLPDITSVAKSLGAKTVAARTL 239 GV A + +VA+E A + ++A AG+PV + A SLGAK + A Sbjct: 186 GGVAAWV----ESRAHVVALEPERAPTLHAARAAGQPVDVEVGGVAADSLGAKRIGAIGW 241 Query: 240 ECAKECEVLSEVVEDREAVSAVQRFLDDE-RMLVEPACGAALAAIYSGILWRLQAEGRLS 298 E ++ V ++ +A+ A Q +L E ++ VEPA LAA+ +G ++ Q + Sbjct: 242 EVSQR-HVHDALLLPDDAIRAAQLWLWKELKLAVEPAAALGLAALQTG-AYKPQPQ---- 295 Query: 299 SALASVVVIVCGGN 312 +V +I+CG N Sbjct: 296 ---ETVALILCGAN 306 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: 250 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: 313 Length adjustment: 28 Effective length of query: 301 Effective length of database: 285 Effective search space: 85785 Effective search space used: 85785 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