Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_106709531.1 CU102_RS03165 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_003010955.1:WP_106709531.1 Length = 406 Score = 475 bits (1222), Expect = e-138 Identities = 233/396 (58%), Positives = 289/396 (72%) Query: 4 LSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTK 63 LS L VKPS TIA+T A EL G+D+I L GEPDFDTPD+IKAAAK+AID G TK Sbjct: 10 LSQRLKTVKPSPTIAITRLAAELRRNGKDIIALSQGEPDFDTPDHIKAAAKKAIDNGETK 69 Query: 64 YTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAP 123 YT VDG P+LKRAI +KF+ EN L Y + V+VGTGGKQ+++NA ATL+ GDEVIIPAP Sbjct: 70 YTDVDGTPDLKRAIVQKFKNENDLDYELSNVSVGTGGKQVIFNAFSATLDTGDEVIIPAP 129 Query: 124 YWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTR 183 YWVSYPDMVLL GG PV+VA G TGFKLT LE AIT RTKW + NSPSNPTG+ Y+ Sbjct: 130 YWVSYPDMVLLTGGVPVTVACGENTGFKLTASALEKAITERTKWLVLNSPSNPTGSGYSS 189 Query: 184 AELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCM 243 +EL + VL+RHP + +++DDMYEH+ +D ++F T A +EP + +R LTCNGVSKA+ M Sbjct: 190 SELKDIAAVLLRHPSILVLTDDMYEHIRYDGWEFATIAAVEPRMRERVLTCNGVSKAFAM 249 Query: 244 TGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRD 303 TGWRIGYA GP +LI+AM TIQSQST+N SI+Q AA+ AL+GP +FL FQ RRD Sbjct: 250 TGWRIGYAGGPADLIKAMATIQSQSTTNSSSISQAAAVAALTGPMDFLTERNAVFQERRD 309 Query: 304 LVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVV 363 L ++ N G++C P+GAFY++ +G IG+ G I +D FA+ LLE TGVAVV Sbjct: 310 LCLNAFNSTPGLSCRRPDGAFYLFSSCAGIIGRRQPNGETIENDVQFATYLLESTGVAVV 369 Query: 364 FGAAFGLSPNFRISYATADEVLREACARIQAFCAGL 399 G+AFGL FRIS+A++ E LR AC+RI C L Sbjct: 370 PGSAFGLGDYFRISFASSTERLRAACSRIGEACGAL 405 Lambda K H 0.318 0.134 0.399 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: 510 Number of extensions: 19 Number of successful extensions: 1 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: 400 Length of database: 406 Length adjustment: 31 Effective length of query: 369 Effective length of database: 375 Effective search space: 138375 Effective search space used: 138375 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: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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