Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate BPHYT_RS27000 BPHYT_RS27000 aspartate aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS27000 Length = 392 Score = 216 bits (550), Expect = 9e-61 Identities = 137/399 (34%), Positives = 203/399 (50%), Gaps = 17/399 (4%) Query: 5 SDTLARVKPSQTIA--VTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRT 62 S+ + R++ +T A + A++ A G DVI L G+PDF TP I A A+ G T Sbjct: 4 SNLVERLQGRRTSAWEIHRVAQQAEARGEDVIVLSVGDPDFATPAPIVERAIEALRGGDT 63 Query: 63 KYTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPA 122 Y+AV G ++ AI + R G + A V + G + ++ A + L GDEVI+P Sbjct: 64 HYSAVSGREPVRAAIAAEHTRMTGCAASAANVILTAGAQNGVFAASLCLLEAGDEVIVPE 123 Query: 123 PYWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYT 182 P +++Y V AG T V+V F + + LEAA+T RTK F +P NPTG Sbjct: 124 PMYLTYEACVRAAGATLVTVPVDAARAFHVDCDALEAAVTSRTKAIFFATPCNPTGVVMQ 183 Query: 183 RAELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYC 242 RA+L + + RH +W++SD++Y L F+ + A PG+ +RT+T +SK++ Sbjct: 184 RADLERIARLACRH-DLWVLSDEVYAELTFEREHVSIAAL--PGMAERTVTLGSLSKSHA 240 Query: 243 MTGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRR 302 M GWR+G+A GP ELI MG + Q AAL A+ A RE ++RRR Sbjct: 241 MAGWRVGWAIGPTELIEHMGRLALAMLYGLPGFIQQAALTAVQHKARIAAEMREIYRRRR 300 Query: 303 DLVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAV 362 D+V L+ G+ C PE ++ D+SG G D F L GV++ Sbjct: 301 DVVFERLHRVPGLRCLLPEAGMFMMVDVSGT-------GLDTVD---FTWQLFRARGVSL 350 Query: 363 VFGAAFGLSPN--FRISYATADEVLREACARIQAFCAGL 399 + +AFG + N R+ + + L +AC RI AF GL Sbjct: 351 LDASAFGETANGFVRLGFVVDEARLIDACERIAAFVGGL 389 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: 375 Number of extensions: 11 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: 392 Length adjustment: 31 Effective length of query: 369 Effective length of database: 361 Effective search space: 133209 Effective search space used: 133209 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