Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_012974929.1 AZL_RS12610 1-aminocyclopropane-1-carboxylate deaminase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_000010725.1:WP_012974929.1 Length = 387 Score = 174 bits (440), Expect = 5e-48 Identities = 124/374 (33%), Positives = 185/374 (49%), Gaps = 12/374 (3%) Query: 10 AMKPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALA-QGKTKYAPPA 68 A+ P + V A E G++++ + G+P P+ V +AA A+ Y Sbjct: 12 AIPPFFVMEVMRAAAEREAAGLEVLHMEVGQPSSGAPKGVVQAAATAVVGSDPLGYTGAL 71 Query: 69 GIPELREALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSY 128 GIP LR A+A+ ++ G+ V +VT G A F A DPGD V + SP + +Y Sbjct: 72 GIPPLRAAIAKWYKDRYGVEVPERRVVVTTGSSGAFQLGFLAAFDPGDRVAMASPSYPAY 131 Query: 129 PEMVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEA 188 + AG + VE+ T PE F P + A+ + L+V SP NPTG + +E L A Sbjct: 132 RHTLTAAGVIPVELPTGPEHRFQP-TVALLEALDEPVQGLIVASPANPTGTMLSREELTA 190 Query: 189 LARLAVEHDFYLVSDEIYEHLLYEGEHFSPGRVAPEHTLTVNGAAKAFAMTGWRIGYACG 248 L+ + +VSDEIY L Y + + V + L VN +K F+MTGWR+G+ Sbjct: 191 LSDWCRANGVRMVSDEIYHGLTYGTDAVTAAEV-NDQALVVNSFSKYFSMTGWRLGWMIV 249 Query: 249 PKEVIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLT 308 P ++++++ ++ S T++Q + + A E V Y R R LLLE L Sbjct: 250 PDDLLRSVECLAQNLFISAPTLSQVSAVAAFDCTEELDGHV----ARYARNRALLLEELP 305 Query: 309 ALGLKAVRPS-GAFYVLMDTSPIAPDEVRAAERLL-EAGVAVVPGTDF-AAFGH--VRLS 363 G + P+ GAFY+ D S + D A+RLL E G+A PG DF A G +R S Sbjct: 306 KAGFAKLAPADGAFYIYADVSDLTDDSEALAKRLLEETGIACTPGIDFDTARGRRFLRFS 365 Query: 364 YATSEENLRKALER 377 +A SEE + +A R Sbjct: 366 FAGSEETIAEAARR 379 Lambda K H 0.317 0.133 0.379 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: 349 Number of extensions: 22 Number of successful extensions: 6 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: 385 Length of database: 387 Length adjustment: 30 Effective length of query: 355 Effective length of database: 357 Effective search space: 126735 Effective search space used: 126735 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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