Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_012281785.1 HM1_RS02935 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_000019165.1:WP_012281785.1 Length = 397 Score = 370 bits (949), Expect = e-107 Identities = 190/390 (48%), Positives = 258/390 (66%), Gaps = 2/390 (0%) Query: 11 VKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTKYTAVDGI 70 + PS T+++ KA+++ + G DVIG GAGEPDFDTPD++K AA AI+AG TKYT G Sbjct: 10 IHPSPTLSIDAKAKKMRSEGVDVIGFGAGEPDFDTPDHVKQAAIAAIEAGFTKYTPASGT 69 Query: 71 PELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAPYWVSYPD 130 ELK+AIC+K + ENG+ Y PA + V G K L NA A NPGDEVIIPAPYWVSYP+ Sbjct: 70 LELKQAICDKLKAENGVDYAPANIIVSNGAKHSLVNAFEAICNPGDEVIIPAPYWVSYPE 129 Query: 131 MVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTRAELAALC 190 MV L PV V E+ FK T EQ++ A+T +TK + NSPSNPTG Y++ ELA + Sbjct: 130 MVKLVDAVPVFVYTTEESRFKFTVEQIKQALTSKTKALVLNSPSNPTGMVYSKEELAEIA 189 Query: 191 EVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCMTGWRIGY 250 ++ + + ++++SD++YE L++DDF+ + A I + ++T+ NGVSKAY MTGWRIGY Sbjct: 190 DLAVEY-GIFVISDEIYEKLIYDDFEHVSIASINDKIKEQTIIVNGVSKAYSMTGWRIGY 248 Query: 251 AAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRDLVVSMLN 310 A + + M IQS +TSNP SIAQ AAL A++GPQ+ + T F RRRD +V +N Sbjct: 249 TASNAPIAKIMANIQSHATSNPNSIAQKAALAAITGPQDIVGTMVGEFVRRRDYMVERIN 308 Query: 311 EAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVVFGAAFGL 370 G++C P GAFYV +IS IG T A G +I + FA LLE+ VA+V G+ FG+ Sbjct: 309 AIPGLSCLKPNGAFYVMMNISKIIGSTFA-GRRINGSDDFADLLLEQAQVALVPGSGFGI 367 Query: 371 SPNFRISYATADEVLREACARIQAFCAGLS 400 + R+SYAT+ E + E RI+ F L+ Sbjct: 368 DTHVRLSYATSMENITEGLNRIENFLLSLT 397 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: 434 Number of extensions: 19 Number of successful extensions: 3 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: 397 Length adjustment: 31 Effective length of query: 369 Effective length of database: 366 Effective search space: 135054 Effective search space used: 135054 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 Apr 10 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