Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_085771586.1 B1812_RS10730 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_002117405.1:WP_085771586.1 Length = 497 Score = 133 bits (335), Expect = 1e-35 Identities = 98/294 (33%), Positives = 142/294 (48%), Gaps = 27/294 (9%) Query: 72 LQYAASEGYAPLRQAIADFLPWDV----DADQILITTGSQQALDLIAKVLIDENSRVLVE 127 LQ + G+ PLRQAIAD L + + DA+Q+++ +QQ LDL A++L+D V VE Sbjct: 161 LQSGDARGFGPLRQAIADHLRYSMRVSCDAEQVMMLGSAQQGLDLCARLLLDPGDEVWVE 220 Query: 128 TPTYLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTG---ADKARFLYVLPNFQNPT 184 P Y+GA F VVAV D EG A V G A +AR YV P Q P Sbjct: 221 DPGYMGARDIFAAAGAKVVAVPVDAEG-------ADVSVGVQRAPRARLAYVTPAHQTPL 273 Query: 185 GRTMTEARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEG-CIYMGSFSKV 243 G +M RR AL++ + N ++ED+ G+ + P APL + + + IY G+FSK+ Sbjct: 274 GMSMALERRLALLRWSRAANAVVIEDDYDGEYRYTGRPLAPLKSLDEDDRVIYAGTFSKL 333 Query: 244 LAPGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYK 303 L P LRL ++V P + A + H Q ++ E + RH+ +R LY Sbjct: 334 LFPSLRLAYLVVPDRLADAFAAALSLSSRHQSLLPQIVLHEFIAEGHFARHLREMRILYG 393 Query: 304 QQCEAMLAALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLP-QAVERNVA 356 ++ M ++GL R+ G+ A LLP A +R VA Sbjct: 394 ERARQMEKFAASRLSGL-----------LTLPRIATGLDASALLPNDADDRRVA 436 Lambda K H 0.318 0.134 0.392 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: 416 Number of extensions: 17 Number of successful extensions: 4 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: 401 Length of database: 497 Length adjustment: 33 Effective length of query: 368 Effective length of database: 464 Effective search space: 170752 Effective search space used: 170752 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: 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