Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate AO353_07470 AO353_07470 acetylornithine aminotransferase
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07470 Length = 425 Score = 247 bits (630), Expect = 5e-70 Identities = 151/387 (39%), Positives = 218/387 (56%), Gaps = 8/387 (2%) Query: 17 MVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWH 76 ++P+ + VRG+GS +WD R +DF G A SLGH+ L+KA++ QAQ + + Sbjct: 34 LMPSVERPQQVFVRGQGSWLWDSDDRAYLDFTQGGAANSLGHSPSVLIKAISAQAQTLIN 93 Query: 77 VSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIA 136 + N L LA +L +T +++V+L NSG+EA EAA KLAR++ G II Sbjct: 94 PGSGLLNRGQLNLAERLCASTGSDKVYLLNSGSEACEAAIKLARKWGQLHRGGAS-RIIT 152 Query: 137 ASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPIQ 196 AS S HG ++ ++ F P+ G +HVP+NDL AL AA+ +T A++LEPIQ Sbjct: 153 ASGSCHGHGFAAMSASDCQ--NNRFEPQLPGFSHVPFNDLPALHAAVDAQTVAILLEPIQ 210 Query: 197 GEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKS 256 GV+PA YL+G +LC E LL+ DEVQ+G+GR G L A YGV DI+ K Sbjct: 211 CAAGVVPATGHYLKGVERLCRELGILLILDEVQTGIGRCGSLLAEQFYGVRADIVVLGKG 270 Query: 257 LGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHE 316 LGGG P+ A+L G+ A L G T+ GN L ++ A A LD + L+ V+ + Sbjct: 271 LGGGVPVAALLARGK-ACCLEPGELDGTHHGNALMASAALAVLDSVLDHGFLEQVRDSAQ 329 Query: 317 RFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDVV 376 + L ++ YG E+RG GLL G L+D+ A V+NAA E +++ PD + Sbjct: 330 HLREGLGRLANRYG-HGELRGQGLLWGLTLSDD---SADAVVNAALYEGLLLSAPKPDCL 385 Query: 377 RFAPSLVIDDAEIDEGLERFERAVAKL 403 RF P+L + IDE L R RA +++ Sbjct: 386 RFTPALTVSKTNIDEMLLRLARAFSRV 412 Lambda K H 0.318 0.135 0.394 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: 453 Number of extensions: 19 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: 406 Length of database: 425 Length adjustment: 31 Effective length of query: 375 Effective length of database: 394 Effective search space: 147750 Effective search space used: 147750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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