Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_041306183.1 MVAN_RS10450 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000015305.1:WP_041306183.1 Length = 480 Score = 135 bits (341), Expect = 2e-36 Identities = 115/371 (30%), Positives = 170/371 (45%), Gaps = 27/371 (7%) Query: 42 AGGLPSPKTFPVSAFAAASAAVLANDGPAALQYAASEGYAPLRQAIADF-----LPWDVD 96 A L +P AFA A+ V ++ G PLR AIA+ LP D Sbjct: 115 AATLAAPAAIAARAFAEAAEEVTPYLHQIGVELT---GVLPLRTAIAEKYCARGLP--TD 169 Query: 97 ADQILITTGSQQALDLIAKVLIDENSRVLVETPTYLGALQAFTPMEPSVVAVASDDEGVL 156 D+I++TTG+ A+ LI + RVLVE PTY GAL A V VA +G Sbjct: 170 PDEIMVTTGALHAIGLILATYTQPDDRVLVEQPTYHGALAAMASRGLRTVPVAMAPDGWE 229 Query: 157 IDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEARRAALVKAAAELNLPLVEDNPYGDL 216 +D ++A + A Y++P+ NPTG T+ R L ++ + D D+ Sbjct: 230 LDAVEAAIRQLA--PNLAYLVPDNHNPTGMTLPVPERKRLAHIISDTRTRTIVDETITDM 287 Query: 217 WFDNPPPAPLTAR---NPEGCIYMGSFSKVLAPGLRLGFVVAPKAVYPKLLQAKQAADLH 273 W D P PAPL A + + +GS SK GLR+G++ A ++ + + A D+ Sbjct: 288 WLDEPVPAPLAASMTGRRDLVLTVGSMSKSFWGGLRIGWIRAERSTLATVAVQRPAVDMG 347 Query: 274 TPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLAALTQEMAGLGVEWNRP---DGG 330 TP + Q A+++ D +P R + + + +LA L + + +W RP GG Sbjct: 348 TPIFEQLAAAKLLASE--DEVLPERREILRSRRALLLALLAEHLP----DW-RPAPGKGG 400 Query: 331 MFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADPRTLRLSFVTSTVEQIATGIA 390 + LWVRLP MS+ L A + PG F D + R +R+ + T Q+ I Sbjct: 401 LSLWVRLPAPMSS-ALSAAASRMGLEIPPGPRFGVDGSLERFIRVPY-TLPDGQLVEAIE 458 Query: 391 ALAAAIRSHKG 401 LA A RS G Sbjct: 459 LLARAWRSVTG 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: 464 Number of extensions: 29 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: 480 Length adjustment: 32 Effective length of query: 369 Effective length of database: 448 Effective search space: 165312 Effective search space used: 165312 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