Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011840441.1 RSPH17029_RS02910 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000015985.1:WP_011840441.1 Length = 470 Score = 172 bits (437), Expect = 1e-47 Identities = 120/362 (33%), Positives = 185/362 (51%), Gaps = 10/362 (2%) Query: 39 ISLAGGLPSPKTFPVSAFAAA-SAAVLANDGPAALQYAASEGYAPLRQAIADFLPWD--- 94 ++ + G P P+ P A A A A+L+ A Y + G + LR+A+A +L D Sbjct: 107 LAFSDGAPDPELVPDKALARAFRRALLSPAFRAGADYGDARGTSSLREALAAYLASDRGV 166 Query: 95 -VDADQILITTGSQQALDLIAKVLIDENSRVLVETPTYLGALQAFTPMEPSVVAVASDDE 153 D ++LI GSQ AL L A+ + + VE P Y A +AF V V D Sbjct: 167 VADPARLLIARGSQMALFLAARAALAPGEAIAVEEPGYPLAWEAFRAAGAEVRGVPVDGG 226 Query: 154 GVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEARRAALVKAAAELNLPLVEDNPY 213 G+ ID L+A + + R +YV P+ Q PT TM ARR L++ A L L+ED+ Sbjct: 227 GLRIDALEAALARDP-RLRAVYVTPHHQYPTTVTMGAARRLQLLELAERHGLALIEDDYD 285 Query: 214 GDLWFDNPPPAPLTARNPEGC--IYMGSFSKVLAPGLRLGFVVAPKAVYPKLLQAKQAAD 271 + F+ P PL AR PEG IY+GS SK+L+PG+RLG+ +AP+ + ++ A+ A D Sbjct: 286 HEYRFEGRPVLPLAARAPEGLPLIYVGSLSKLLSPGIRLGYALAPEPLLTRMAAARAAID 345 Query: 272 LHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLAALTQEMAGLGVEWNRPDGGM 331 + +AE+++ L RH R +Y+ + + + LT ++AG ++ P GG+ Sbjct: 346 RQGDAPLEAALAELIRDGDLGRHARKARRVYRARRDLLAERLTAQLAGRAA-FDLPAGGL 404 Query: 332 FLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADPRTLRLSFVTSTVEQIATGIAA 391 LW+R G+SA A + +A +PG F ++ P+ RL + QIA + Sbjct: 405 ALWLRC-AGVSAETWAEAAGQAGLALLPGTRFALESPAPQAFRLGYAALDEGQIARAVEI 463 Query: 392 LA 393 LA Sbjct: 464 LA 465 Score = 24.3 bits (51), Expect = 0.008 Identities = 21/59 (35%), Positives = 24/59 (40%), Gaps = 1/59 (1%) Query: 312 ALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADP 370 A QE+ G P G F+ LP+GM P VE VA G AF DP Sbjct: 59 AAYQELLTQGWLQAEPARGTFVAQDLPQGMLVRRPAPAPVE-PVAMRAGLAFSDGAPDP 116 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: 450 Number of extensions: 30 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 16 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