Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_086511056.1 BZY95_RS16860 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_002151265.1:WP_086511056.1 Length = 455 Score = 132 bits (333), Expect = 2e-35 Identities = 92/311 (29%), Positives = 154/311 (49%), Gaps = 15/311 (4%) Query: 73 QYAASEGYAPLRQAIADFLPW---DVDADQILITTGSQQALDLIAKVLIDENSRVLVETP 129 +Y +G+ PLR AIA L +Q+L+T G+ A DLI + +D VLVETP Sbjct: 135 EYGMPQGFEPLRDAIARVLAGRSIHAAPEQVLLTFGANHAFDLIIRHFVDAGDSVLVETP 194 Query: 130 TYLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMT 189 Y +V V+ +G +++ + KV + R ++ PN NPTG +M+ Sbjct: 195 GYYPLFGKLRLARAKLVGVSRTAKGPDLEEFERKVRQY--RPRLFFLQPNAHNPTGTSMS 252 Query: 190 EARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNP-EGCIYMGSFSKVLAPGL 248 + L+K A + + LVED+ + DL A L A + E IY+G+FSK L+ GL Sbjct: 253 LSNMHQLLKIAEQYGVVLVEDDVFADLLPQGS--AHLAALDGLENVIYVGTFSKTLSTGL 310 Query: 249 RLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEA 308 R G++ +A+ L K +++ + + ++ E++ RH+ +R + + Sbjct: 311 RSGYIAGSRALIRSLTDIKMLTVVNSSTFIESVIHELIVKGRYRRHLVQLRERVAKASAS 370 Query: 309 MLAALTQEMAGLGVE-WNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAF--YA 365 AL + +G++ + P GG +LW RLP G++ +EL +A E + PGA F Sbjct: 371 AQRALRE----VGIDDVSGPGGGYYLWARLPAGLNTLELAKRATEEGIFIAPGAIFSLRP 426 Query: 366 DNADPRTLRLS 376 D D +R++ Sbjct: 427 DGIDGTAMRIN 437 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: 382 Number of extensions: 24 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: 401 Length of database: 455 Length adjustment: 32 Effective length of query: 369 Effective length of database: 423 Effective search space: 156087 Effective search space used: 156087 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 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