Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_002968535.1 BIBO1_RS18510 aspartate aminotransferase family protein
Query= BRENDA::B1A0U3 (469 letters) >NCBI__GCF_000182725.1:WP_002968535.1 Length = 484 Score = 180 bits (457), Expect = 8e-50 Identities = 126/412 (30%), Positives = 205/412 (49%), Gaps = 45/412 (10%) Query: 58 AKGSSVWDPEGNKYIDFLSGYSAVNQGHCHPKILKALHDQADRLTVSSRAFYNDRFPVFA 117 A+G +D G + +DF G+ ++ GH HP+I+ A + L + ++ Sbjct: 68 AEGMYYYDQNGRRILDFFGGFGSLAFGHNHPRIIAARRKFQEELRHEIAIAFMSQYAAAL 127 Query: 118 EYLTALFG---YDMVLPMNTGAEGVETALKLARKWGYEKKKIPNDEALIVSCCGCFNGRT 174 Y A DMV ++G+E +E A+K+A + KK IV F+G+T Sbjct: 128 AYDLAACSPGDLDMVFLGSSGSEAMEAAIKVAERAAGPKKP------KIVYAENSFHGKT 181 Query: 175 LGVISMSCDNEATRGFGPLMPGHLKVDFGDAEAIERIFKEKGDRVAAFILEPIQGEAGVV 234 GV+S++ D RG L+ ++V FGD AIE F+ + + +LE +QG G++ Sbjct: 182 KGVLSIT-DGGLYRGEFKLVDNTVRVPFGDITAIENAFRSDPE-IGTIVLETVQGGGGII 239 Query: 235 IPPDGYLKAVRDLCSKYNVLMIADEIQTGLARTGKMLACDWEDVRPDVVILGKALGGGIL 294 + + +R LC +Y V+ +ADE+Q G RTGK A + V PDV L K+LGGG Sbjct: 240 QADAEFWQKLRQLCDRYGVIWVADEVQCGFGRTGKFYAFEHYGVIPDVTALAKSLGGGKA 299 Query: 295 PVSAVLADKDVMLCIKPGQHG----------STFGGNPLASAVAIAALEVIKEERLTERS 344 ++A++A +D+ + +G +TFGG A AI A+ ++ +E+L + S Sbjct: 300 AMAAMIARRDIYM----KAYGTPKTAMIHAMATFGGIGEACITAIEAVNILYDEQLIDNS 355 Query: 345 TKLGGELLGLLHKIQKKHPEHVKEVRGKGLFIGVE------------------LNSESLS 386 ++G LL L ++Q ++P +K+VRGKG+ +G+E L+ + Sbjct: 356 AEVGDYLLERLKELQVRYPGLLKDVRGKGMMVGLEFHDFSQAMPMVLRPMLAMLDDKLKG 415 Query: 387 PVSGFELSEKLKERGVLAKST--HDTIIRFTPPLCISADEIQQGSKALAEVL 436 + GF S L++ GVL T + +IR PPL + + KAL EVL Sbjct: 416 SLPGFIGSHLLRDHGVLVAFTEYNRNVIRLEPPLICQRAHVDEFIKALDEVL 467 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: 501 Number of extensions: 34 Number of successful extensions: 6 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: 484 Length adjustment: 33 Effective length of query: 436 Effective length of database: 451 Effective search space: 196636 Effective search space used: 196636 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 24 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