Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate PfGW456L13_1158 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1158 Length = 427 Score = 252 bits (643), Expect = 2e-71 Identities = 149/388 (38%), Positives = 217/388 (55%), Gaps = 6/388 (1%) Query: 16 YMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIW 75 Y++P+ + VRG+GS +WD R +DF+ G SLGH+ LV A+T QAQ + Sbjct: 33 YLMPSVERPKQVFVRGQGSWLWDSDDRAYLDFSQGGGANSLGHSPSVLVNAITAQAQSLI 92 Query: 76 HVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEII 135 + N L LA L +T +++ +L N+G+EA EAA KLAR++ G II Sbjct: 93 NPGFGLHNRGMLSLAEHLCASTGSDQAYLLNTGSEACEAAIKLARKWGQRHRGGAS-RII 151 Query: 136 AASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPI 195 A+N HGR+L T++ ++ F P+ G + VP+NDL AL AA+ ++T A++LEPI Sbjct: 152 VANNGCHGRSLATISASDSSTLANRFEPQLPGFSRVPFNDLPALHAAVDERTVAIMLEPI 211 Query: 196 QGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAK 255 Q E GV+PA YL+G +LC E LL+FDEVQ+G+GR G L A GV DI+ K Sbjct: 212 QSEAGVVPATVHYLKGVERLCRELGILLIFDEVQTGIGRCGSLLAEQSCGVTADIVVLGK 271 Query: 256 SLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKH 315 LGGG P+ A+L G+ A +G T+ GN L +A + LD + L V Sbjct: 272 GLGGGVPLAALLARGK-ACCFDIGELAGTHHGNALMTAAGLSVLDTVQDKAFLKHVAEAG 330 Query: 316 ERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDV 375 + + L ++ YG E+RG GLL G L+D+ A V+ AA E +++ D Sbjct: 331 QHLREGLGRLAHRYG-HGELRGQGLLWGLTLSDD---SADAVVKAALYEGLLLNAPQADC 386 Query: 376 VRFAPSLVIDDAEIDEGLERFERAVAKL 403 +RF P+L + +A IDE L R RA +++ Sbjct: 387 LRFTPALNVSNANIDEMLLRLARAFSRV 414 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: 460 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: 427 Length adjustment: 31 Effective length of query: 375 Effective length of database: 396 Effective search space: 148500 Effective search space used: 148500 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 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