Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_013818750.1 METME_RS10565 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000214665.1:WP_013818750.1 Length = 474 Score = 169 bits (428), Expect = 2e-46 Identities = 116/379 (30%), Positives = 177/379 (46%), Gaps = 9/379 (2%) Query: 25 VIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPAALQYAASEGYAPLR 84 ++ ++ P I L +P+P P A SA Y G LR Sbjct: 95 LVLRLVTAANNPRFIQLGAAVPAPSFLPTQKLAQLSAITARRYRQRIASYEFPPGAPELR 154 Query: 85 QAIADFLPWD---VDADQILITTGSQQALDLIAKVLIDENSRVLVETPTYLGALQAFTPM 141 + IA + VD + ILI+ G Q+AL L + + V +E+PT+ G LQ + Sbjct: 155 RQIAKRMSEQGCPVDPNDILISNGCQEALTLALRAITAPGDIVAIESPTFYGLLQVIESL 214 Query: 142 EPSVVAVASDD-EGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEARRAALVKAA 200 + + + EG+ +D L+ KA +PN+ NP G M++AR+ AL++ A Sbjct: 215 SLRAIEIPTHPREGIALDALQLACEQWPIKA--CIAVPNYSNPLGYCMSDARKQALIELA 272 Query: 201 AELNLPLVEDNPYGDLWFDNPPPAPLTARNPEG-CIYMGSFSKVLAPGLRLGFVVAPKAV 259 + L+ED+ YGDL F P+ L + + EG +Y SFSK L PGLR+G++V P A Sbjct: 273 KRYRIMLIEDDIYGDLGFGPQRPSTLKSWDKEGRVLYCSSFSKSLCPGLRVGWLV-PGAF 331 Query: 260 YPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLAALTQEMAG 319 K+ K +L TP Q VAEV++ DR++ R Y+Q E M AAL Sbjct: 332 QEKIEYLKYVTNLATPTLAQLTVAEVLEHGGYDRYLRQARQQYRQAVERMTAALGVYFP- 390 Query: 320 LGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADPRTLRLSFVT 379 G +P+GG LWV LP + AI L +A+ ++ PG F A +RL+ Sbjct: 391 TGTRITQPEGGFLLWVELPGTVDAIALTQEALTLGISIAPGPIFSATQKYQHFIRLNCAV 450 Query: 380 STVEQIATGIAALAAAIRS 398 E++ + L + + Sbjct: 451 DWDERLNKALVTLGQLVHA 469 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: 468 Number of extensions: 30 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: 474 Length adjustment: 32 Effective length of query: 369 Effective length of database: 442 Effective search space: 163098 Effective search space used: 163098 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