Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_005453184.1 SACCYDRAFT_RS02235 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_000244975.1:WP_005453184.1 Length = 410 Score = 347 bits (891), Expect = e-100 Identities = 183/390 (46%), Positives = 242/390 (62%), Gaps = 3/390 (0%) Query: 4 LSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAI-DAGRT 62 +S +A + PS T+AV KA+ L A GR VIG GAG+PDF TP+ I AA A+ D G Sbjct: 15 VSARIAGITPSATLAVDAKAKALKAEGRPVIGFGAGQPDFPTPEYIVEAAAAAVRDRGNH 74 Query: 63 KYTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPA 122 YTA G+PEL+ AI K R++G +QV V GGKQ +Y+A L+PGDEV++ A Sbjct: 75 GYTAAAGLPELREAIAAKTLRDSGFSCDASQVLVTNGGKQAVYSAFATLLDPGDEVLLLA 134 Query: 123 PYWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYT 182 PYW +YP+ + LAGG PV V A TG+++T EQLEAA T RTK +FNSPSNPTGA YT Sbjct: 135 PYWTTYPESITLAGGVPVQVTADESTGYRVTVEQLEAARTERTKVLLFNSPSNPTGAVYT 194 Query: 183 RAELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYC 242 R ++ A+ H +W+++D++YEHLV+D + + P L DRTL NGV+K Y Sbjct: 195 REQVEAIGRWAAEH-DIWVITDEIYEHLVYDGVKAASLPTVVPELADRTLILNGVAKTYS 253 Query: 243 MTGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRR 302 MTGWR+G+ GP ++I+A + QS N +++Q AAL A+ GP + + R AF RR Sbjct: 254 MTGWRVGWIVGPQDVIKAASSFQSHLCGNVANVSQRAALAAVEGPLDVVHEMRAAFDSRR 313 Query: 303 DLVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAV 362 +VSML+E V CP PEGAFY YP + +GK G + D A +L E VAV Sbjct: 314 KKIVSMLSEIPNVECPTPEGAFYAYPSVKAVLGK-EIRGQRPADTVELADLILREVEVAV 372 Query: 363 VFGAAFGLSPNFRISYATADEVLREACARI 392 V G AFG FR SYA A++ L E R+ Sbjct: 373 VPGEAFGTPGYFRFSYALAEKDLVEGVTRV 402 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: 473 Number of extensions: 25 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: 400 Length of database: 410 Length adjustment: 31 Effective length of query: 369 Effective length of database: 379 Effective search space: 139851 Effective search space used: 139851 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