Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_041750777.1 BBTA_RS19685 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_000015165.1:WP_041750777.1 Length = 399 Score = 155 bits (391), Expect = 3e-42 Identities = 122/389 (31%), Positives = 174/389 (44%), Gaps = 23/389 (5%) Query: 9 ARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTKYTAVD 68 + V P + V A + A+G VI + G+P P AAA A+D R YT+ Sbjct: 24 SNVPPFMVMDVMAAAERIEASGGHVIHMEVGQPAAPAPRTALAAAHAALDQARIDYTSAL 83 Query: 69 GIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAPYWVSY 128 G+P L+ I + G P ++ + TG A +A PGD V + P + Y Sbjct: 84 GLPSLRGRIARHYRETYGCDIDPGRIVITTGSSAGFILAFLAMFEPGDRVAVTVPGYPPY 143 Query: 129 PDMVLLAGGTPVSVAAGMETGFKLTPEQLEAA--ITPRTKWFIFNSPSNPTGAAYTRAEL 186 ++ G PV + ET LT E L AA TP K + SP+NPTG +RA L Sbjct: 144 RHILTALGCEPVLIETTAETRHALTGEALLAAHRKTP-LKGVLVASPANPTGTMMSRAAL 202 Query: 187 AALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCMTGW 246 + R + +SD++Y L D+ PA L L N SK +CMTGW Sbjct: 203 GDVI-AAARDAGIRFISDEIYHGL-----DYAFPAVTAAQLTADALIINSFSKYFCMTGW 256 Query: 247 RIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRDLVV 306 R+G+ P L+R + +Q + +++Q AA A G E + + +Q R +++ Sbjct: 257 RVGWMVVPDALVRPIERLQQNLAISVPTLSQIAAEAAFDGRPE-MDGIKHGYQENRRILI 315 Query: 307 SMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVVFGA 366 +A +GAFY+Y D+S D FA +LEET VA G Sbjct: 316 EGFPKAGLSRFLPADGAFYLYADVSDF----------TKDSLDFAKRMLEETHVAATPGV 365 Query: 367 AFG--LSPNF-RISYATADEVLREACARI 392 F NF R SYA + E +REA ARI Sbjct: 366 DFDPIHGRNFVRFSYARSAEDMREAVARI 394 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: 340 Number of extensions: 19 Number of successful extensions: 5 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: 399 Length adjustment: 31 Effective length of query: 369 Effective length of database: 368 Effective search space: 135792 Effective search space used: 135792 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