Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_078716418.1 B5D49_RS03180 aspartate aminotransferase family protein
Query= BRENDA::Q6LFH8 (414 letters) >NCBI__GCF_900167125.1:WP_078716418.1 Length = 495 Score = 190 bits (483), Expect = 7e-53 Identities = 132/427 (30%), Positives = 223/427 (52%), Gaps = 45/427 (10%) Query: 31 VLKRGKGVFVYDIEDRRYYDFLSAYSSVNQGHCHPDILNAMINQAKKLTICSRAFFSD-- 88 ++ +G++++D ++Y D S N GH + ++ A+ Q+++ R F + Sbjct: 48 IIAGAEGIYMWDTRGKQYLDGCSGAVVNNIGHGNRRVIAAVERQSRQTFFAYRTQFENRP 107 Query: 89 SLGVCERYLTNLFGY-DKVLMMNTGAEASETAYKLCRKWGYEVKKIPENSAKIIVCNNNF 147 S + + + + + ++V ++ G+EA E+A K+CR++ + + + + K + + Sbjct: 108 SQELARQLVEHSAPHLNRVFFVSGGSEAVESAMKVCRQYFFNLGE--GSRYKFVSRVPAY 165 Query: 148 SGRTLGCVSASTDKKCKNNFGPFVPNFLKVP------------YDDLE-----ALEKEL- 189 G TLG +S ++ + F P V + K+P Y D E ALEK + Sbjct: 166 HGSTLGALSLTSYAPLEVAFKPLVRDNPKIPAPTCYRCVYHKQYPDCELECAWALEKTVL 225 Query: 190 -QDP-NVCAFIVEPVQGEA-GVIVPSDSYFPGVASLCKKYNVLFVADEVQTGLGRTGKLL 246 Q P N+ AF+VEPV G + G +VP D YF + +C+KY + V DEV TG GRTGKL Sbjct: 226 EQGPDNIAAFVVEPVGGASTGALVPPDEYFGIIQHICRKYGIFLVLDEVMTGFGRTGKLF 285 Query: 247 CTHHYGVKPDVILLGKALSGGHYPISAILANDDVM-LVLKPG--EHGSTYGGNPLAAAIC 303 H+GV+ DV+ L K ++ G+YP+ AIL D+++ +V++ G HG TY GNP+A A+ Sbjct: 286 AYEHWGVQADVVALSKGIASGYYPLGAILTTDEIVDVVVRRGGFAHGHTYAGNPMACAVG 345 Query: 304 VEALKVLINEKLCENADKLGAPFLQNLKEQLKDSKVVREVRGKGLLCAIEFKND------ 357 E L+V++ +KL ENAD++G L+ L + + + EVRG GLL A+E D Sbjct: 346 QEVLRVIMEDKLPENADRMGKILLKGLNRLGRKHRFIGEVRGLGLLTALELVRDPQTREP 405 Query: 358 LVNVWDICLKFKEN----GLI------TRSVHDKTVRLTPPLCITKEQLDECTEIIVKTV 407 W+ + +N GL+ ++ V + PPL + + Q+ E E + K + Sbjct: 406 FPPEWNAAMLLTDNAFADGLLIYPRRSINGLYGDHVLVAPPLIVREAQIAELLEKLDKAL 465 Query: 408 KFFDDNL 414 D+L Sbjct: 466 TRTADHL 472 Lambda K H 0.320 0.138 0.418 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: 490 Number of extensions: 30 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: 414 Length of database: 495 Length adjustment: 33 Effective length of query: 381 Effective length of database: 462 Effective search space: 176022 Effective search space used: 176022 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 Apr 10 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