Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_004302128.1 C665_RS05355 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000310185.1:WP_004302128.1 Length = 470 Score = 149 bits (375), Expect = 2e-40 Identities = 117/378 (30%), Positives = 181/378 (47%), Gaps = 11/378 (2%) Query: 26 IREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPAALQYAASEGYAPLRQ 85 I +IL P I+ L P + +P+ AA + P A G LR+ Sbjct: 95 IFQILDSVRDPAIVPLGSSFPDARLYPLDKLGRFLAAAARHLDPLATVTDLPPGNDELRR 154 Query: 86 AIA-DFLPW--DVDADQILITTGSQQALDLIAKVLIDENSRVLVETPTYLGALQAFTPME 142 +A +L V +I++T+G+ + L+L + L + VE+PT+ LQA + Sbjct: 155 QLALRYLAHGASVSPQEIVVTSGAMEGLNLCLQALTRPGDLIAVESPTFYAGLQASERLG 214 Query: 143 PSVVAVASDD-EGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEARRAALVKAAA 201 V+ + S EGV +D L + KA L++L NF NPTG + + + ALV+ Sbjct: 215 LEVIEIPSHPREGVSLDALADALRHHPIKA-CLFML-NFANPTGSRVPDDNKRALVELLH 272 Query: 202 ELNLPLVEDNPYGDLWFDNPPPAPLTARNPEGCI-YMGSFSKVLAPGLRLGFVVAPKAVY 260 + +PL+ED+ Y +L+F P A + EG + ++ SFSK LAPG RLG+V A + Y Sbjct: 273 QHQVPLIEDDVYAELYFGPEAPRCSKAMDTEGLVLHVSSFSKCLAPGYRLGWVAAGR--Y 330 Query: 261 PKLLQA-KQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLAALTQEMAG 319 K +Q K + L T Q + + +K D H+ +R +Q EA L A +E Sbjct: 331 AKEVQRQKYSTSLATAVPMQIALTDYLKHGGFDNHLRHLRRQLARQ-EAQLLAGIEEHFP 389 Query: 320 LGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADPRTLRLSFVT 379 G+ RPDGG FLW+ LP + + L +A+ + V+ PG F A LRL+F Sbjct: 390 PGIRLARPDGGYFLWLELPPRIDTLRLHEEALAQGVSIAPGPIFSAKREFSNYLRLNFGH 449 Query: 380 STVEQIATGIAALAAAIR 397 + +A L I+ Sbjct: 450 PATPRQDQALATLGRLIK 467 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: 461 Number of extensions: 40 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: 470 Length adjustment: 32 Effective length of query: 369 Effective length of database: 438 Effective search space: 161622 Effective search space used: 161622 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