Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate AO353_10500 AO353_10500 acetylornithine aminotransferase
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10500 Length = 390 Score = 288 bits (736), Expect = 2e-82 Identities = 157/388 (40%), Positives = 229/388 (59%), Gaps = 6/388 (1%) Query: 16 YMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIW 75 Y++ NYA RG+G+ +WD+ G E +D G+AVTSLGHA+P + A+ EQA ++ Sbjct: 7 YLMHNYARQPVSFSRGQGASLWDKHGVEYLDAIAGVAVTSLGHANPEIAAAIAEQAGQLL 66 Query: 76 HVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEII 135 H SN+F E +L+ +L + +R F NSGAEANEAA KLAR +AN + Q +++ Sbjct: 67 HTSNMFHIEWQEQLSERLCALSGMQRAFFCNSGAEANEAALKLARLHANARHVAQP-QVL 125 Query: 136 AASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALK--AAISDKTCAVVLE 193 NSFHGRTL T+ G P GF P G VPY+++E ++ AA S AV++E Sbjct: 126 VMENSFHGRTLATLAATGNPAVQRGFEPLMPGFLRVPYDNIEEIRKVAAQSPDIVAVLVE 185 Query: 194 PIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSS 253 P+QGEGGV A YL+ R+LCDEH+ L++ DEVQ+GMGR G F Y H G+VPD+++ Sbjct: 186 PVQGEGGVHAASAGYLQALRQLCDEHDWLMMVDEVQTGMGRTGAWFGYQHAGIVPDVITL 245 Query: 254 AKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKA 313 AK+LG GFPIGA L G+ A+ S G H +T+GGNPLA V LD++ + Sbjct: 246 AKALGNGFPIGACLARGKAAELFSPGHHASTFGGNPLACRVGCTVLDIMERDHIPQRAAT 305 Query: 314 KHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASP 373 R + LQ+ + IRG+GL++G L + A V A +++ +++ Sbjct: 306 SGRRLLAALQEALGNHSEVVSIRGLGLMVGIELNRQC---AELVGRALDEQRLLITVTRG 362 Query: 374 DVVRFAPSLVIDDAEIDEGLERFERAVA 401 +R P L+ +D++ID+ R R ++ Sbjct: 363 TTLRLLPPLICEDSQIDDIAARVSRLLS 390 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: 400 Number of extensions: 14 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: 406 Length of database: 390 Length adjustment: 31 Effective length of query: 375 Effective length of database: 359 Effective search space: 134625 Effective search space used: 134625 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