Align Alanine--glyoxylate aminotransferase; AGT; Serine--pyruvate aminotransferase; SPT; EC 2.6.1.44; EC 2.6.1.51 (characterized)
to candidate 203421 SO4343 aminotransferase, class V (NCBI ptt file)
Query= SwissProt::P31030 (392 letters) >FitnessBrowser__MR1:203421 Length = 378 Score = 266 bits (680), Expect = 7e-76 Identities = 149/365 (40%), Positives = 210/365 (57%), Gaps = 2/365 (0%) Query: 21 PHRLLLGPGPSNLPPRVLAAGGLQMIGHMHEEMYQVMDEIKQGIQYAFQTRNALTLAVSG 80 P R+L+GPGPS++ P VLAA +GH+ +MDE+K IQYAFQT+N +T+AVS Sbjct: 14 PRRILMGPGPSDVYPEVLAAQARPTVGHLDPLFVSMMDELKSLIQYAFQTKNEMTMAVSA 73 Query: 81 SGHCALETALFNLLEPGDAFLVGANGIWGQRAAEVGERIGARVHPMIKDPGSHYTLQEVE 140 G +ET NL+EPG+ +V NG++G+R + ER+GA + + G+ VE Sbjct: 74 PGSAGMETCFVNLVEPGEKVIVCRNGVFGERMRQNVERVGAIAVLVDNEWGTPVDPVAVE 133 Query: 141 ECLAQHKPV-LLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVASLGGAPIYMDQQG 199 L H L H E+STG L L +Y CL +VD+V SLGG + +D+ G Sbjct: 134 AALKAHPDAKFLAFVHAETSTGALSDAKTLCALAKQYGCLSIVDAVTSLGGVELRVDEWG 193 Query: 200 IDVLYSGSQKALNAPPGTSLISFSDKAKSKIYARKTKPFSFYMDVQLLANIWGCDGKPRM 259 ID +YSGSQK L+ PG S +SFS A K+ RKT S+++D L+ W G R Sbjct: 194 IDAIYSGSQKCLSCVPGLSPVSFSPAAVEKLKNRKTPVQSWFLDQSLVMAYWTSAGGKRS 253 Query: 260 YHHTTPVIGIFALRESLALLVEQGLEKSWQRHREVAQHLYRRLQELGLQLFVKDPALRLP 319 YHHT PV ++A+ ESL +L +GLE +W+RH+++ L L++LGL+ FV A RLP Sbjct: 254 YHHTAPVNALYAMHESLRILAAEGLENAWKRHQDMHLVLRAGLEKLGLK-FVVAEASRLP 312 Query: 320 TVTTVIVPASYRWRDIVSYVMHHFGIEITGGLGPSADKVLRIGLLGCNATRENVDRLATA 379 + + +P + + ++ + +EI GLG A K RIGL+G A RENV A Sbjct: 313 QLNAIYIPEGVDDAAVRARLLKDYNLEIGAGLGALAGKAWRIGLMGFGARRENVALCLRA 372 Query: 380 LREAL 384 L E L Sbjct: 373 LEEVL 377 Lambda K H 0.322 0.138 0.420 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: 377 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: 392 Length of database: 378 Length adjustment: 30 Effective length of query: 362 Effective length of database: 348 Effective search space: 125976 Effective search space used: 125976 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 (21.9 bits) S2: 50 (23.9 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