Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate H281DRAFT_05099 H281DRAFT_05099 Aspartate/methionine/tyrosine aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >FitnessBrowser__Burk376:H281DRAFT_05099 Length = 408 Score = 157 bits (398), Expect = 4e-43 Identities = 116/392 (29%), Positives = 183/392 (46%), Gaps = 28/392 (7%) Query: 6 DTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTKYT 65 D + ++PSQ V N +A DV+ GE D TP I+ AA A+ AG T YT Sbjct: 16 DAVRALRPSQIREVANAGFGVA----DVLPFWFGESDRVTPAFIRDAASAALSAGATFYT 71 Query: 66 AVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAPYW 125 GI L+ A+ + +G K TP + V + G L A + GD V+ P W Sbjct: 72 HNLGIAPLRSALADYVSELHG-KTTPDHIAVTSAGVNALMLAAQLVVGAGDRVVAVTPLW 130 Query: 126 VSYPDMVLLAGGTPVSVAAGM-ETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTRA 184 + ++ + G +V+ E G++L EQL AA+TP T+ + NSP+NPTG TR Sbjct: 131 PNLVEIPKILGAHVETVSLDYGEHGWQLDVEQLLAALTPDTRMLLVNSPNNPTGWVMTRE 190 Query: 185 ELAALCEVLMRHPQVWIMSDDMYEHLVF----DDFDFTTPAQIEPGLYD------RTLTC 234 + A+ +H +WI++D++YE L + DD + A+ P D R + Sbjct: 191 QQQAVLAHCRQHG-IWIVADEVYERLYYPDHSDDGESAVGARTAPSFLDLATRDERVICV 249 Query: 235 NGVSKAYCMTGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATN 294 N SKA+ MTGWR+G+ PV L+ +G + +TS + Q A + A+ + F Sbjct: 250 NSFSKAWLMTGWRLGWIVAPVSLMDDLGKLVEYNTSCAPAFVQQAGIAAVEQGERFTQEL 309 Query: 295 REAFQRRRDLVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASAL 354 + RD +V L+ G+ P GA Y++ ++G + A+ Sbjct: 310 VRELKASRDHLVRALSAVPGIDVKAPAGAMYLFFSMTGA-----------SRSLELCKAM 358 Query: 355 LEETGVAVVFGAAFGLSPNFRISYATADEVLR 386 + E G+ + G+AFG + + A +V R Sbjct: 359 VLEVGLGLAPGSAFGPQGEGFLRWCYACDVAR 390 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: 389 Number of extensions: 26 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: 408 Length adjustment: 31 Effective length of query: 369 Effective length of database: 377 Effective search space: 139113 Effective search space used: 139113 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