Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_078429378.1 BK574_RS16655 LL-diaminopimelate aminotransferase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_002019605.1:WP_078429378.1 Length = 390 Score = 166 bits (421), Expect = 8e-46 Identities = 112/368 (30%), Positives = 179/368 (48%), Gaps = 10/368 (2%) Query: 21 AKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKT-KYAPPAGIPELREALAE 79 AK L ++G D++ L G PD TP+H+ ++ + A K KY P G L+EA+AE Sbjct: 23 AKVGALVKEGADIINLGQGNPDQPTPDHIVKSLKEAADLPKYHKYPPFRGYRFLKEAVAE 82 Query: 80 KFRRENGLSVTPE-ETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGV 138 ++RE G+ + PE E V GGK L + Q +L+PGD +V P + Y V AGG Sbjct: 83 FYQREYGVDIDPEKEVCVLFGGKGGLVEISQCMLNPGDVTLVPDPGYPDYWSGVALAGGQ 142 Query: 139 VVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDF 198 + + F+PD + + + K + +N PNNPTGA K + A +HD Sbjct: 143 MEMMPLQENNNFLPDYQVISEDAKKKAKLMFLNYPNNPTGATASKAFYDETVTFARQHDL 202 Query: 199 YLVSDEIYEHLLYEGE---HFSPGRVAPEHTLTVNGAAKAFAMTGWRIGYACGPKEVIKA 255 +V D Y + ++G+ F A E + + +K + M GWR+ +A G VI+ Sbjct: 203 CVVHDFAYGGIGFDGQKPVSFLQSEGAKEVGIEIYTLSKTYNMAGWRVAFAVGNASVIEM 262 Query: 256 MASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAV 315 + S Q A AL + + V+ + Y RR++L+EGL ++G Sbjct: 263 LNLYQDHMYVSLFGAIQKAAATALLSPQTC---VDELVKKYEGRRNVLIEGLQSIGWDVK 319 Query: 316 RPSGAFYVLMDTSPIAPDEVRAAERLLEAGVAVVPGTDF--AAFGHVRLSYATSEENLRK 373 P+G+F+ + E A L +A +AV PG F + G+VR+ E+ L++ Sbjct: 320 APNGSFFAWLPCPEGMSSEEFADILLYKAHIAVAPGRGFGESGEGYVRVGLLEEEDRLKE 379 Query: 374 ALERFARV 381 A+ER ++ Sbjct: 380 AVERIRKL 387 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: 378 Number of extensions: 17 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: 390 Length adjustment: 30 Effective length of query: 355 Effective length of database: 360 Effective search space: 127800 Effective search space used: 127800 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