Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate PfGW456L13_4910 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910 Length = 413 Score = 296 bits (759), Expect = 5e-85 Identities = 170/378 (44%), Positives = 230/378 (60%), Gaps = 6/378 (1%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +M TY + F +G G L+ GR +LD AGVAV +GH++P +V A+T QA L H Sbjct: 28 LMSTYQPLALSFNKGLGTRLWDQAGREYLDAVAGVAVTNVGHSHPKIVAAITEQAGLLLH 87 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 TSNL+ + Q+ LA++LT+ D FF NSGAEA E K+ R + + KG + + ++ Sbjct: 88 TSNLYSIDWQQRLAQKLTQLAGMDRAFFNNSGAEANETALKIARLHGWHKGIE-QPLVVV 146 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEA---VRNAVTDETAGICLE 181 E AFHGRTL +SA+ + GF L F VPFGDL A V+ A + +E Sbjct: 147 MENAFHGRTLGTLSASDGPAVRLGFNKLPGDFVKVPFGDLGALDKVQQAFGSRIVAVLME 206 Query: 182 PIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAV 241 PIQGE G++ +L +RE+C+ LL LDEIQ G+GRTG+ FA + GI PDVM + Sbjct: 207 PIQGESGVQLAPPGYLSAVRELCNRRSWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTL 266 Query: 242 AKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQR 301 AKG+G G P+GACLA KAA T G+HGST+GGNPLA VG VLD V E G L++ + Sbjct: 267 AKGLGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLDIVEEQGLLENARL 326 Query: 302 IGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDV-VVALRANGLLSVPAGDNV 360 G L +RL +A NP V + +RG+GLM+G+ + D+ ++A R +GLL N Sbjct: 327 QGARLLERLRTELAGNPNVSQ-IRGQGLMIGIELKQPIRDLSLIAARDHGLLINVTRGNT 385 Query: 361 VRLLPPLNIGEAEVEEAV 378 +RLLPPL + E EVE V Sbjct: 386 IRLLPPLTLDEREVEMIV 403 Lambda K H 0.321 0.139 0.414 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: 469 Number of extensions: 20 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: 389 Length of database: 413 Length adjustment: 31 Effective length of query: 358 Effective length of database: 382 Effective search space: 136756 Effective search space used: 136756 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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