Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate GFF1577 PS417_08025 acetylornithine aminotransferase
Query= BRENDA::B1A0U3 (469 letters) >FitnessBrowser__WCS417:GFF1577 Length = 389 Score = 266 bits (679), Expect = 1e-75 Identities = 157/390 (40%), Positives = 221/390 (56%), Gaps = 12/390 (3%) Query: 48 YHPLPIVFAHAKGSSVWDPEGNKYIDFLSGYSAVNQGHCHPKILKALHDQADRLTVSSRA 107 Y PL + F G+ +WD +G +Y+D ++G + N GH HP+++ A+ +QA L +S Sbjct: 10 YQPLALSFTRGLGTRLWDQQGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLHTSNL 69 Query: 108 FYNDRFPVFAEYLTALFGYDMVLPMNTGAEGVETALKLARKWGYEKKKIPNDEALIVSCC 167 + D A+ LT L G D N+GAE ETALKLAR G++K + L+V Sbjct: 70 YSIDWQQRLAQRLTQLSGLDRAFFNNSGAEANETALKLARLHGWKKGI---EAPLVVVME 126 Query: 168 GCFNGRTLGVISMSCDNEATRGFGPLMPGHLKVDFGDAEAIERIFKEKGDRVAAFILEPI 227 F+GRTLG ++ S GF L LKV FGD A+E I K G R+ A +LEPI Sbjct: 127 NAFHGRTLGTLAASDGPSVRLGFQQLPGDFLKVRFGDLAALEAITKAFGPRITAVLLEPI 186 Query: 228 QGEAGVVIPPDGYLKAVRDLCSKYNVLMIADEIQTGLARTGKMLACDWEDVRPDVVILGK 287 QGE+GV+ P GYL+A+RD C++ LM+ DEIQTG+ RTG A E + PDV+ L K Sbjct: 187 QGESGVLPAPSGYLQALRDHCTRQGWLMMLDEIQTGIGRTGTWFAFQHEGIVPDVMTLAK 246 Query: 288 ALGGGILPVSAVLADKDVMLCIKPGQHGSTFGGNPLASAVAIAALEVIKEERLTERSTKL 347 LG G+ P+ A LA V PG HGSTFGGNPLA V L++I+E+ L + + + Sbjct: 247 GLGNGV-PIGACLARAAVAQLFTPGSHGSTFGGNPLACRVGCTVLDIIEEQGLLQNAAQQ 305 Query: 348 GGELLGLLHKIQKKHPEHVKEVRGKGLFIGVELNSESLSPVSGFELSEK-LKERGVLAKS 406 G LL L +H + V +RG+GL IG+EL S +L+++ +E G+L Sbjct: 306 GERLLARLRVELNEHAQ-VVAIRGQGLMIGIELASPCR------DLAQRAAQEHGLLINV 358 Query: 407 THDTIIRFTPPLCISADEIQQGSKALAEVL 436 T IIR PPL + E++ +A+ +L Sbjct: 359 TRGKIIRLLPPLTLDTQEVEMIVRAITRLL 388 Lambda K H 0.319 0.137 0.409 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: 409 Number of extensions: 20 Number of successful extensions: 5 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: 469 Length of database: 389 Length adjustment: 32 Effective length of query: 437 Effective length of database: 357 Effective search space: 156009 Effective search space used: 156009 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: 51 (24.3 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