Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate AZOBR_RS11880 AZOBR_RS11880 1-aminocyclopropane-1-carboxylate deaminase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__azobra:AZOBR_RS11880 Length = 384 Score = 180 bits (457), Expect = 5e-50 Identities = 126/373 (33%), Positives = 181/373 (48%), Gaps = 11/373 (2%) Query: 10 AMKPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAG 69 A+ P + V A E G++++ + G+P P+ V EAA R L Y G Sbjct: 12 AIPPFFVMEVMRAAAEREAAGLEVLHMEVGQPSTGAPKGVLEAAHRMLDADVLGYTGALG 71 Query: 70 IPELREALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYP 129 IP LR A+A +R G+ V +VT G A F A DPGD V + SP + +Y Sbjct: 72 IPALRAAIAGWYRDRYGIDVPERRVVVTTGSSGAFQLGFLAAFDPGDRVAMASPSYPAYR 131 Query: 130 EMVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEAL 189 + G VE+ T PE F P E + + + P + L+V SP NPTG + +E L AL Sbjct: 132 HTLTAIGVEPVELPTGPEHRFQPTIELLEQ-LDPPIQGLIVASPANPTGTMLSREELTAL 190 Query: 190 ARLAVEHDFYLVSDEIYEHLLYEGEHFSPGRVAPEHTLTVNGAAKAFAMTGWRIGYACGP 249 A LVSDEIY L Y E + V+ E L VN +K F+MTGWR+G+ P Sbjct: 191 AAWCDAKGVRLVSDEIYHGLTYGPEAVTAAEVS-ESALVVNSFSKYFSMTGWRLGWMIVP 249 Query: 250 KEVIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTA 309 ++I+++ ++ S +++Q A + A E V Y R R+LLL L Sbjct: 250 DDLIRSVECLAQNLFISAPSLSQAAAVAAFGCTEELDGHV----ARYARNRELLLRELPK 305 Query: 310 LGLKAVRPS-GAFYVLMDTSPIAPDEVRAAERLL-EAGVAVVPGTDF---AAFGHVRLSY 364 G + P+ GAFY+ D + + D +R+L E G+A PG DF VR S+ Sbjct: 306 AGFDKLAPADGAFYIYADVTEMTDDSEAFCKRILAETGIACTPGVDFDPARGLRFVRFSF 365 Query: 365 ATSEENLRKALER 377 A +EE + +A R Sbjct: 366 AGAEETIAEAARR 378 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: 352 Number of extensions: 20 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: 385 Length of database: 384 Length adjustment: 30 Effective length of query: 355 Effective length of database: 354 Effective search space: 125670 Effective search space used: 125670 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 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