Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_013835162.1 THICY_RS03115 diaminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000214825.1:WP_013835162.1 Length = 428 Score = 156 bits (394), Expect = 1e-42 Identities = 122/403 (30%), Positives = 192/403 (47%), Gaps = 17/403 (4%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAI--QAQATRLTHYAFNA- 71 P +A + D +GKRYIDF GG G LN GH +P + +A+ Q +T+ A Sbjct: 21 PAVFDTATSATIVDVEGKRYIDFFGGAGSLNYGHNHPLINQALITYIQRNGITNALDKAT 80 Query: 72 -APHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFH 130 A H A + + + Y + + +GA E ALK+AR + +IAF +H Sbjct: 81 VAKHDFISAFQSIILKPRKMDYKIQ-FVGPTGANGVETALKLARKMKKRSNVIAFTNAYH 139 Query: 131 GRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSA-DTGVTCEQALKAMDRLFSVELAVE 189 G +L L + G Y ++P V +PY + D + L+ L E Sbjct: 140 GHSLGALAVTGNEF-YHGDYYDVPRNVNKMPYDNYFDHDMDSVDMLRHY--LGDGSSGYE 196 Query: 190 DVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLG 249 AA I E +QGEGG + Q L C E IL+I+DEIQ G GRTG F+F R G Sbjct: 197 LPAAVIVESIQGEGGINVASVGWLQKLSALCKEMDILLIMDEIQVGNGRTGDYFSFERAG 256 Query: 250 IEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDE 309 I PD++ L+KSI GMP+ V+ + + P G GT+ GN + A A+L ++ Sbjct: 257 IMPDIITLSKSIGTGMPMSIVLMKPSVDVWSP-GEHTGTFRGNSYAFIAGAAALELWRND 315 Query: 310 NLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVME 369 + + + + + + ++ ++A +I + G+G + G+E S +V + Sbjct: 316 DFSRSIRAKGKQVEAAFKDFQAR-FPGWITDVRGLGMIWGLE------SLVEGFCNEVSK 368 Query: 370 AARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 A RGL++ +G + +++ L PL I L EG +IL + Sbjct: 369 QAFQRGLMMETAGASDQVLKFLGPLVISETELNEGFEILTDAI 411 Lambda K H 0.320 0.137 0.402 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: 391 Number of extensions: 19 Number of successful extensions: 4 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: 416 Length of database: 428 Length adjustment: 32 Effective length of query: 384 Effective length of database: 396 Effective search space: 152064 Effective search space used: 152064 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 (21.8 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