Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_086510803.1 BZY95_RS15480 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P18335 (406 letters) >NCBI__GCF_002151265.1:WP_086510803.1 Length = 430 Score = 224 bits (571), Expect = 4e-63 Identities = 138/413 (33%), Positives = 209/413 (50%), Gaps = 34/413 (8%) Query: 22 APAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHI-SNV 80 +PA + + + IWD G +DFAGGI V +GH HP +V A+K Q + + H V Sbjct: 20 SPATQFADRAENALIWDADGNRIIDFAGGIGVLNIGHRHPKVVEAVKAQLDKVMHTCQTV 79 Query: 81 FTNEPALRLGRKLIEATFAE---RVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAF 137 E +++ KL + T +V+ NSG EA E A K+AR + K +I F Sbjct: 80 MPYEGYVKVAEKLSQVTPVRGHAKVMLANSGAEALENAVKIARA------ATGKNNVICF 133 Query: 138 HNAFHGRSLFTVSVGGQ-PKYSDGFGPKPADIIHVPFN-DLHAVK----------AVMDD 185 +HGR+ T+++ G+ Y+ FG P ++ P+ H V A+ D Sbjct: 134 DGGYHGRTFMTMAMNGKVAPYASDFGTMPGNVFRAPYPVPYHGVSEDEAIRGLKMAIKTD 193 Query: 186 ----HTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAY 241 T A+V+EP+ GEGG A FL+ +RE+CD+H L++ DEVQ G GRTG LFA Sbjct: 194 ANPRDTAAIVLEPVLGEGGFYPAPASFLKAIREICDEHGMLMIVDEVQSGFGRTGKLFAI 253 Query: 242 MHYGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDI 301 H GV PDI+T AK++ G PISA++ T ++ A P S G TY GNPL+CA A D+ Sbjct: 254 EHSGVEPDIITMAKSMADGMPISAVVGTDKVMDASGPNSLGGTYTGNPLSCAATLAVLDV 313 Query: 302 INTPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAG 361 +LE A + + + +D + R MG + +L D A Sbjct: 314 FEEENILEKSMALGDKLAKRFAQWQRDFDCVDNARNMGAMAALDLVTDKAKHTPDADLAA 373 Query: 362 A------EAGVMVLNAG--PDVMRFAPSLVVEDADIDEGMQRFAHAVAKVVGA 406 A E G+++L+ G + +RF + +ED ++EG+ A+ ++VG+ Sbjct: 374 ALCKKAREKGLILLSCGLYGNTIRFLMPVTIEDEILEEGLDIVEAALTELVGS 426 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: 449 Number of extensions: 25 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: 406 Length of database: 430 Length adjustment: 32 Effective length of query: 374 Effective length of database: 398 Effective search space: 148852 Effective search space used: 148852 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 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