Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase
Query= SwissProt::P40732 (405 letters) >FitnessBrowser__Marino:GFF3766 Length = 425 Score = 224 bits (572), Expect = 3e-63 Identities = 138/400 (34%), Positives = 207/400 (51%), Gaps = 34/400 (8%) Query: 34 SRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHT-SNVFTNEPALRLGRK 92 + +WD GK IDFAGGI V +GH HP +VEA+K+Q + L HT V E ++L K Sbjct: 32 AELWDADGKRMIDFAGGIGVLNIGHRHPKVVEAVKAQLDKLMHTCQTVMPYEGYVKLAEK 91 Query: 93 L---IDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTV 149 L + +V+ NSG EA E A K+AR + KT +I F +HGR+ +T+ Sbjct: 92 LSGVVPVRGHAKVMLANSGAEALENAMKIARA------ATGKTNVICFDGGYHGRTFYTM 145 Query: 150 SVGGQPK-YSDGFGPKPADIIHVPF----------NDLHAVKAVMD-----DHTCAVVVE 193 ++ G+ Y FGP P + P+ L +K M +T A+V+E Sbjct: 146 AMNGKAAPYQTDFGPMPGTVYRAPYPVPYHGVSEDEALRGLKMAMKADSPAHNTAAIVIE 205 Query: 194 PIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTS 253 P+ GEGG AA FLK +R +CDE+ L++ DEVQ G GRTG +FA H GV PD++T Sbjct: 206 PVLGEGGFYAAPTSFLKEIRKICDENDILMIADEVQSGFGRTGKMFAIEHSGVEPDLMTM 265 Query: 254 AKALGGGFPVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGAAFDIINTPEVLQGIHT 313 AK++ G P+SA++ T + A S G TY G+P ACA A A FD+ ++L Sbjct: 266 AKSMADGMPISAIVGTDKYMDASGPNSLGGTYTGSPTACAAALAVFDVFKEEDILGKSQA 325 Query: 314 KRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGA------EAGVM 367 ++ Q EQF ++R +G + EL + R A A E G++ Sbjct: 326 LGEKLKQRFSQWQEQFAHVDNVRNLGPMAAFELVESKESRTPKPELAAAVTKKAKEKGLI 385 Query: 368 VLNAG--ADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVA 405 +L+ G + +RF + +E+ + EG+ +++ +V A Sbjct: 386 LLSCGMYGNTLRFLMPVTIEDEVLEEGLAIVEESLKEVGA 425 Lambda K H 0.322 0.137 0.412 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: 456 Number of extensions: 24 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: 405 Length of database: 425 Length adjustment: 31 Effective length of query: 374 Effective length of database: 394 Effective search space: 147356 Effective search space used: 147356 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 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