Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate NP_661271.1 CT0367 acetylornithine aminotransferase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000006985.1:NP_661271.1 Length = 400 Score = 269 bits (687), Expect = 1e-76 Identities = 143/367 (38%), Positives = 209/367 (56%), Gaps = 1/367 (0%) Query: 9 YARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNL 68 YAR + G+G +LY G R+LD AGV VN +G+ + L +A+T QA K H SNL Sbjct: 19 YARLPLDIASGKGSFLYTASGERYLDMIAGVGVNAIGYGDKRLEQAITEQASKYIHVSNL 78 Query: 69 FRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQA 128 F Q LA +L E + VFF NSG EA E KL R++ GD +T++++ Sbjct: 79 FMQKPQFDLAAKLLEISRMSKVFFCNSGTEAIEAAIKLARRFAARNGDTDKTQVLSLTNC 138 Query: 129 FHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGEGG 188 FHGRT A+S + K + GF PL+ ++ F D+E + V++ TA + +E +QGEGG Sbjct: 139 FHGRTYGALSLTAKPKYVDGFEPLVPETGMIDFNDVEDLERKVSNRTAAVFVEFVQGEGG 198 Query: 189 IRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIGGG 248 I S F+ L+E+ EH L+ DEIQ G GRTG F++ I PD++ VAK +GGG Sbjct: 199 IHKVSEAFIAKLKELAKEHDFLIVADEIQAGCGRTGAFFSYMPFDIQPDLVCVAKPLGGG 258 Query: 249 FPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGLLQD 308 PLGA + +EK A T G+HG+T+GGNP+A A G A+++ +L G + + +G +++ Sbjct: 259 LPLGAIIGSEKVAEVFTPGSHGTTFGGNPVACAAGLAMIEAILADGLMQNALEVGSMMRT 318 Query: 309 RLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLLPPLN 368 + AE A +R GLM+G+ V G+L +NV+RLLPPL+ Sbjct: 319 AFEKM-AEKHAQILEIRQYGLMIGVTVHREAKYYVEEALKRGVLVNATSNNVIRLLPPLS 377 Query: 369 IGEAEVE 375 I + E + Sbjct: 378 ISKEEAQ 384 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: 403 Number of extensions: 19 Number of successful extensions: 3 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: 400 Length adjustment: 31 Effective length of query: 358 Effective length of database: 369 Effective search space: 132102 Effective search space used: 132102 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 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