Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate GFF2092 PGA1_c21250 aspartate aminotransferase AatA
Query= SwissProt::A3PMF8 (400 letters) >FitnessBrowser__Phaeo:GFF2092 Length = 400 Score = 624 bits (1610), Expect = 0.0 Identities = 303/399 (75%), Positives = 343/399 (85%) Query: 1 MAFLSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAG 60 M FLSD+LARVKPS +IA+T A EL AAGRDVIGL AGEPDFDTPDNIK AA RAI AG Sbjct: 1 MQFLSDSLARVKPSPSIAITTLAGELRAAGRDVIGLSAGEPDFDTPDNIKEAAIRAIQAG 60 Query: 61 RTKYTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVII 120 +TKYTA DGI ELK+A+C+KF R+NGL+YTPAQV+VGTGGKQILYNAL+ATLNPGDEV+I Sbjct: 61 KTKYTAPDGIAELKQAVCDKFARDNGLEYTPAQVSVGTGGKQILYNALMATLNPGDEVVI 120 Query: 121 PAPYWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAA 180 PAPYWVSYPDMV LAGGTP+ V + +ETGFK+TP+QLEAAITP+TKWF+FNSPSNPTGA Sbjct: 121 PAPYWVSYPDMVRLAGGTPICVESSLETGFKITPDQLEAAITPKTKWFVFNSPSNPTGAG 180 Query: 181 YTRAELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKA 240 Y EL AL +VL+RHP VW+M+DDMYEHLVFDDF F TPAQIEP LYDRTLTCNGVSKA Sbjct: 181 YHPNELKALTDVLLRHPHVWVMTDDMYEHLVFDDFTFCTPAQIEPKLYDRTLTCNGVSKA 240 Query: 241 YCMTGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQR 300 Y MTGWRIGYAAGP LI AM IQSQSTSNPC+I+Q+AA+EAL+G Q+++ N F+R Sbjct: 241 YAMTGWRIGYAAGPKPLIDAMRKIQSQSTSNPCTISQWAAVEALNGTQDYILPNTAVFRR 300 Query: 301 RRDLVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGV 360 RRDLV+SML++ +GV CP P+GAFYVYP I+G IG+TSAGG ITDDEAFA ALLEE V Sbjct: 301 RRDLVISMLSQIEGVACPVPDGAFYVYPSIAGLIGRTSAGGVAITDDEAFAKALLEEADV 360 Query: 361 AVVFGAAFGLSPNFRISYATADEVLREACARIQAFCAGL 399 AVV GAA+GLSPNFRISYA ADE L EAC RIQ FCA L Sbjct: 361 AVVHGAAYGLSPNFRISYAAADETLTEACRRIQVFCAAL 399 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: 652 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: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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 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