Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_012050345.1 SWIT_RS21085 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P18335 (406 letters) >NCBI__GCF_000016765.1:WP_012050345.1 Length = 434 Score = 239 bits (610), Expect = 1e-67 Identities = 142/411 (34%), Positives = 217/411 (52%), Gaps = 35/411 (8%) Query: 24 AEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFT 82 A + + + IWD +G+ Y+DFA GIAV +GH HP ++ A++ Q H + V Sbjct: 28 APIFAARAENAEIWDVEGRRYIDFASGIAVLNVGHRHPRIIAAVEEQLGRFTHTAFQVVG 87 Query: 83 NEPALRLGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHN 139 EP +RL +L + +F +G EA E A K+AR+ + ++ +IAF N Sbjct: 88 YEPYVRLAERLNALAPVVGPAKTIFFTTGAEATENAVKIARY------ASGRSAVIAFVN 141 Query: 140 AFHGRSLFTVSVGGQP-KYSDGFGPKPADIIHVPF----------NDLHAVKAVMDD--- 185 FHGR+L ++ G+ Y GFGP P DI H+PF + L A+ V+ Sbjct: 142 GFHGRTLLASAMTGKVLPYKKGFGPLPGDIYHIPFPSEAHGITVEHSLAALANVLSSDVE 201 Query: 186 --HTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMH 243 + A+++EP+QGEGG A EFL+ LR LCD+H L+ DEVQ G+GRTG LFA H Sbjct: 202 AANVAAIILEPVQGEGGFHVAPFEFLRALRSLCDEHGIALIADEVQTGIGRTGKLFAVEH 261 Query: 244 YGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIIN 303 GV PD++T AK+LGGGFP+SA++ A + PG G TY G+P+ACA A D+I Sbjct: 262 AGVRPDLITVAKSLGGGFPLSAVVGNAALIDRVPPGGLGGTYAGSPIACAAGLAVLDVIE 321 Query: 304 TPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDI-RGMGLLIGAELKPQYK------GRARD 356 + + + +R + L + + ++ + RG+G +I +++ A+ Sbjct: 322 QDRLCDRAERMGRRITERLSAVAARRELPIGLPRGLGAMIAFDIRAGLDDLRPDGAAAKR 381 Query: 357 FLYAGAEAGVMVLNAGP--DVMRFAPSLVVEDADIDEGMQRFAHAVAKVVG 405 E G+++L G + +R L DA +DEG+ A A+A +G Sbjct: 382 VCVRALELGLILLTCGQHGEAIRLLAPLTASDAVLDEGLDILAQALADTLG 432 Lambda K H 0.322 0.138 0.415 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: 476 Number of extensions: 19 Number of successful extensions: 7 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: 406 Length of database: 434 Length adjustment: 32 Effective length of query: 374 Effective length of database: 402 Effective search space: 150348 Effective search space used: 150348 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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