Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__SynE:Synpcc7942_0943 Length = 422 Score = 303 bits (775), Expect = 8e-87 Identities = 175/386 (45%), Positives = 233/386 (60%), Gaps = 11/386 (2%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 VM TY R + ERGEG ++ T GR +LDF AG+A LGHA+P LV+A++ Q KL H Sbjct: 27 VMQTYGRFPLALERGEGCRVWDTQGRSYLDFVAGIATCTLGHAHPELVDAISDQIRKLHH 86 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 SNL+ + Q LA LT + AD VFF NSGAEA E KL RK+ + I+T Sbjct: 87 VSNLYYIPEQGQLAAWLTANSCADRVFFCNSGAEANEAAIKLARKHGNTVLEAENPIILT 146 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVR------NAVTDETAGI 178 + +FHGRTLAAV+A Q K KGF PL+ GF VP+ DL A+ +A + A I Sbjct: 147 AQASFHGRTLAAVTATGQPKYHKGFQPLVQGFRYVPYNDLAALEATLAELDAAGETVAAI 206 Query: 179 CLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDV 238 LEP+QGEGG+ G + + +R++CD+ +LL LDE+Q GMGR+G+L+ +E GI PD Sbjct: 207 LLEPLQGEGGVNPGDRAYFQAVRQLCDQRRMLLILDEVQVGMGRSGQLWGYENLGIEPDA 266 Query: 239 MAVAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDH 298 VAKG+GGG P+GA L + + + + AG H ST+GGNPLA G A+ + L + Sbjct: 267 FTVAKGLGGGVPIGA-LLVKASCNILQAGEHASTFGGNPLACRAGLAIAQVMERDQLLAN 325 Query: 299 VQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLAC--GPAVGDVVVALRA--NGLLSV 354 VQ G L+ L LV P + GVRG GL+ GL P V + + A GLL V Sbjct: 326 VQARGEQLRAGLQELVDRYPNLLAGVRGWGLINGLVLRNDPNVTPIALVKAAIEQGLLLV 385 Query: 355 PAGDNVVRLLPPLNIGEAEVEEAVAI 380 PAG VVR +PPL + AE++EA+A+ Sbjct: 386 PAGAEVVRFVPPLIVSAAEIDEALAM 411 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: 456 Number of extensions: 27 Number of successful extensions: 4 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: 422 Length adjustment: 31 Effective length of query: 358 Effective length of database: 391 Effective search space: 139978 Effective search space used: 139978 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 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