Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)
Query= SwissProt::P18335 (406 letters) >FitnessBrowser__PV4:5210744 Length = 426 Score = 226 bits (576), Expect = 1e-63 Identities = 144/393 (36%), Positives = 212/393 (53%), Gaps = 37/393 (9%) Query: 34 SRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISNVFTN--EPALRLGR 91 + +WD +GK Y+DF GIAV GH HP +V A+K Q + H V N E A+ L Sbjct: 32 AELWDVEGKRYIDFGTGIAVCNTGHSHPKVVAAVKAQLDNFSHTC-VMVNPYESAVALAE 90 Query: 92 KLIEATFA---ERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFT 148 +L ++ +F+ +G EA E K+AR + R +IAF+ FHGR+ T Sbjct: 91 QLNRIAPGGSDKKAIFVTTGAEAVENCVKIARAHTGRRG------VIAFNGGFHGRTNLT 144 Query: 149 VSVGGQ-PKYSDGFGPKPADIIHVPF----------NDLHAVKAV--MDDHTC---AVVV 192 +++ G+ Y FGP DI H P+ + L A++ + +D C A+VV Sbjct: 145 MALTGKITPYKHQFGPFAGDIFHAPYPVAFHGVSVKDSLKAIEHLFKVDIAPCDVAAIVV 204 Query: 193 EPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILT 252 EP+QGEGG AA PEFLQ LR LCDQH +LV DE+Q G GRTG +F+ H GV PD++T Sbjct: 205 EPVQGEGGFYAAPPEFLQALRALCDQHGIVLVMDEIQTGFGRTGKMFSCEHAGVEPDLMT 264 Query: 253 SAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGIQ 312 AK + GGFP++A++ +EI A PG G TYGG+P+ C A A +++ +++E Sbjct: 265 MAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSPVGCVAALAVLEVMQEEQLVERAV 324 Query: 313 AKRQRFVDHLQKIDQQY-DVFSDIRGMGLLIGAELK-----PQYKGRARDFLYAGAEA-G 365 F L + +QY + ++R G +I EL Q + A A A G Sbjct: 325 KIGDSFNQALSALKEQYPQLIGEVRNQGAMIAMELVIDGDIEQPNTALTQAIIANAAAHG 384 Query: 366 VMVLNAG--PDVMRFAPSLVVEDADIDEGMQRF 396 +++L G +V+RF P+L + D + EG+ +F Sbjct: 385 LVLLACGFYGNVIRFLPALTISDEIMAEGLAKF 417 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: 479 Number of extensions: 24 Number of successful extensions: 6 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: 426 Length adjustment: 31 Effective length of query: 375 Effective length of database: 395 Effective search space: 148125 Effective search space used: 148125 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