Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_108402496.1 B9Z44_RS11585 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_003063475.1:WP_108402496.1 Length = 396 Score = 276 bits (706), Expect = 8e-79 Identities = 159/396 (40%), Positives = 228/396 (57%), Gaps = 17/396 (4%) Query: 15 ARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPAALQY 74 A R + S IRE+ K+ KPGIIS AGG P F V AS L + AALQY Sbjct: 4 ADRLNNVETSAIRELFKLLGKPGIISFAGGFPDSAMFDVEGIREASNLALTQEPGAALQY 63 Query: 75 AASEGYAPLRQAIADFLP----WDVDADQILITTGSQQALDLIAKVLIDENSRVLVETPT 130 A+EGY PLR+ +A F+ + AD +++TTGSQQALDLIAK L++ N LVE PT Sbjct: 64 GATEGYQPLREQLAAFMASKGVKGLSADGLIVTTGSQQALDLIAKTLLNPNDVALVEGPT 123 Query: 131 YLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTE 190 +L +Q F P VV V D GV +D L+ + K + +Y++P F NP+G T++ Sbjct: 124 FLATIQCFRLYGPQVVGVPIDAHGVQVDKLEEMI--VQHKPKLVYLIPTFGNPSGATLSL 181 Query: 191 ARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNP------EGCIYMGSFSKVL 244 RR +++ A + +VED+PYGDL+F PP L A + E I+ GS SKVL Sbjct: 182 ERRLRVLELAVKYKTVVVEDDPYGDLYFGEAPPPSLLALSDQVPGSREWLIHCGSLSKVL 241 Query: 245 APGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQ 304 +PGLR+G+++AP + + KQ +D HT + Q A +K + + +R++Y + Sbjct: 242 SPGLRVGWMIAPPELLARATMCKQFSDAHTSTFAQATAAHYLKAGRMPATLAHVRSVYAE 301 Query: 305 QCEAMLAALTQEMAGLGVEWNRPDGGMFLWVRLP----EGMSAIELLPQAVERNVAFVPG 360 + +AM AL +E+ G + + +P GG+F W L + EL +A+E+ VAFVPG Sbjct: 302 RAQAMGDALKREL-GDALTFTQPKGGLFFWANLTGVGGKLNDGAELAKRAIEKGVAFVPG 360 Query: 361 AAFYADNADPRTLRLSFVTSTVEQIATGIAALAAAI 396 A F+A+N D +RLSF T+ VE+I GIA L A+ Sbjct: 361 APFFANNPDTTAIRLSFATADVEKIKEGIARLGQAL 396 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: 400 Number of extensions: 24 Number of successful extensions: 6 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: 396 Length adjustment: 31 Effective length of query: 370 Effective length of database: 365 Effective search space: 135050 Effective search space used: 135050 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: 50 (23.9 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