Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_039652243.1 PN53_RS05150 aspartate aminotransferase family protein
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000816635.1:WP_039652243.1 Length = 391 Score = 317 bits (813), Expect = 3e-91 Identities = 172/393 (43%), Positives = 251/393 (63%), Gaps = 15/393 (3%) Query: 34 YVMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVRAVSDQIQKLH 93 Y+MNTYG+F + G+G L+DTE K YLD +GI +LG+ + ++AV+DQ + L Sbjct: 10 YLMNTYGQFSVVFTHGKGCKLYDTEEKEYLDLTSGIGVSSLGYGNEEWIKAVTDQAKNLA 69 Query: 94 HVSNLYYIPEQGELAKWIVEHSCADRVFFCNSGAEANEAAIKLVRKYAHTVLDFLEQPVI 153 H+SN++ + LAK + E S +VFF NSGAEANE +IKL RKY++ + I Sbjct: 70 HISNIFLNIPELTLAKKLTEASGMSKVFFGNSGAEANEGSIKLARKYSYLKYG-KGRSTI 128 Query: 154 LTAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYNDIRSLENKVADLDEGNSRVA 213 LT SFHGRT+ T+ ATGQ K+ +YFDP GF Y D++SLE + + V Sbjct: 129 LTLNKSFHGRTITTLKATGQEKFHKYFDPFTEGFKYTDV-DVKSLEAAI------DPTVC 181 Query: 214 AIFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQVGVGRTGKLWGYEHLGVEP 273 AI +E +QGEGGV P + +V EI + DIL++FDEVQ G+GRTGKL+GY + GVEP Sbjct: 182 AIMMEAIQGEGGVYPLPKEFIDKVFEISKKKDILVIFDEVQCGMGRTGKLFGYMNYGVEP 241 Query: 274 DIFTSAKGLAGGVPIGAMMC-KKFCDVFEPGNHASTFGGNPLACAAGLAVLKTIEGDRLL 332 DI ++AKGLAGG+PIGA++C KK + F PG+H STFGGNP++ A V+ T++ L Sbjct: 242 DIVSTAKGLAGGLPIGAVLCNKKLENTFVPGDHGSTFGGNPISTAGANCVVDTLKKPGFL 301 Query: 333 DNVQARGEQLRSGLAEIKNQYPTLFTEVRGWGLINGLEISAESSLTSVEIVKAAMEQGLL 392 D+V +G +++ + ++ E+RG GL+ G+++++E S E+ K A+E G+L Sbjct: 302 DDVAKKGAFIKNFFKKASSKN---VLEIRGIGLMLGIQLNSEK---SSEVQKKALENGIL 355 Query: 393 LAPAGPKVLRFVPPLVVTEAEIAQAVEILRQAI 425 + AG V+R +PPLV++E E+ + L + I Sbjct: 356 VLTAGSSVVRLLPPLVISEQELESVLSSLVKII 388 Lambda K H 0.320 0.137 0.405 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: 419 Number of extensions: 32 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: 429 Length of database: 391 Length adjustment: 31 Effective length of query: 398 Effective length of database: 360 Effective search space: 143280 Effective search space used: 143280 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: 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