Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate AO353_24850 AO353_24850 aspartate aminotransferase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24850 Length = 396 Score = 252 bits (644), Expect = 1e-71 Identities = 143/368 (38%), Positives = 216/368 (58%), Gaps = 9/368 (2%) Query: 19 VNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALA 78 ++ +AL L+ QG D++ L+ G+PDFDTP + +AA +L G T YA G LRE++A Sbjct: 20 IHYRALALQEQGEDILLLSVGDPDFDTPVPIVQAAIDSLLSGNTHYAEVRGKRALRESIA 79 Query: 79 EKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGV 138 ++ ++ +G V+ ++ V G + ALF++ Q +L+PGDEVIV P +V+Y + G V Sbjct: 80 KRHQQRSGQPVSADQVTVLAGAQCALFSVAQCVLNPGDEVIVAEPMYVTYEAVFGACGAV 139 Query: 139 VVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDF 198 V+ V E GF PE V ITPRT+AL +NSP+NP+GA P+ +ALA L + HD Sbjct: 140 VIPVPVRSENGFRVLPEDVAARITPRTRALALNSPHNPSGASLPRTTWQALAELCIAHDL 199 Query: 199 YLVSDEIYEHLLYEGEHFSPGRV--APEHTLTVNGAAKAFAMTGWRIGYACGPKEVIKAM 256 +L+SDE+Y LL+EGEH SP + E T T+N +K+ AMTGWR+G+ P + + Sbjct: 200 WLISDEVYSELLFEGEHVSPASLPGMGERTATLNSLSKSHAMTGWRVGWVVAPPSLAAHL 259 Query: 257 ASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLT-ALGLKAV 315 +++ Q A + AL E++ + R+AYR+RRDL+ E L G++ + Sbjct: 260 ENLALCMLYGSPDFVQDAAVVAL---ESNLPELAAMRDAYRQRRDLVCESLADCPGVRPL 316 Query: 316 RPSGAFYVLMDTSPIAPDEVRAAERLLEA-GVAVVPGTDF--AAFGHVRLSYATSEENLR 372 +P G +V++D A+RLL+ GV+V+ G F +A GH+RL E LR Sbjct: 317 KPDGGMFVMVDIRETGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVVGAEPLR 376 Query: 373 KALERFAR 380 A +R AR Sbjct: 377 DACQRIAR 384 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: 14 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: 396 Length adjustment: 31 Effective length of query: 354 Effective length of database: 365 Effective search space: 129210 Effective search space used: 129210 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