Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_015927614.1 MNOD_RS04305 aspartate aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_000022085.1:WP_015927614.1 Length = 402 Score = 391 bits (1004), Expect = e-113 Identities = 192/385 (49%), Positives = 261/385 (67%) Query: 9 ARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTKYTAVD 68 A +KPS +IA +L A GR++I GE DFDTP +I AA +A +G T+YT+ + Sbjct: 11 ASIKPSPSIAARALVTQLRAEGREIIDFTLGESDFDTPPHIVEAAYQAARSGETRYTSSN 70 Query: 69 GIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAPYWVSY 128 G L+ AI KF RENG+ +T AQV VG G KQ+++ A ATL+ GDEVI+P PYWVSY Sbjct: 71 GTKALRAAIVGKFARENGIDFTEAQVVVGCGAKQLIHAAFAATLDEGDEVIVPTPYWVSY 130 Query: 129 PDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTRAELAA 188 PDM ++ GG PV V G ETGFKLTP L +AITPR KW + NSP+NP+GA YT E+A+ Sbjct: 131 PDMAVVNGGVPVIVPVGEETGFKLTPALLGSAITPRAKWLVLNSPNNPSGAVYTPEEIAS 190 Query: 189 LCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCMTGWRI 248 L VL +HPQV +M+D++YEH V+D ++ P L RTL NGVSKAY MTGWRI Sbjct: 191 LAAVLEQHPQVMLMTDEIYEHFVYDGQTAAAFTRVAPQLAGRTLVINGVSKAYAMTGWRI 250 Query: 249 GYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRDLVVSM 308 GYAAGP++LI + + SQST+ P S++Q AA+ AL+G Q F+ ++ RRD +V + Sbjct: 251 GYAAGPLKLIETITLLLSQSTTCPSSVSQAAAVAALNGDQSFVREANAIYETRRDRIVGL 310 Query: 309 LNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVVFGAAF 368 L+ G+TC P GAFYVYP++SG +GK ++ G + D + LL+E GVAV+ G+++ Sbjct: 311 LDAIPGITCARPAGAFYVYPNVSGLLGKRTSDGTTLNSDLDVSLFLLQEAGVAVIDGSSY 370 Query: 369 GLSPNFRISYATADEVLREACARIQ 393 GLSP RIS+AT+ + + CA+ + Sbjct: 371 GLSPYIRISFATSLDTIDAGCAQFR 395 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: 472 Number of extensions: 17 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: 402 Length adjustment: 31 Effective length of query: 369 Effective length of database: 371 Effective search space: 136899 Effective search space used: 136899 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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