Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate RR42_RS14595 RR42_RS14595 2-aminoadipate aminotransferase
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >FitnessBrowser__Cup4G11:RR42_RS14595 Length = 395 Score = 426 bits (1094), Expect = e-124 Identities = 223/386 (57%), Positives = 277/386 (71%), Gaps = 6/386 (1%) Query: 12 WTLARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPAA 71 W ++RRA+++ S IREILKVTE+P +IS AGGLPSP TFPV+A A A + A++ AA Sbjct: 3 WAISRRAQQLTSSAIREILKVTERPEVISFAGGLPSPATFPVAAMEQAVARIFADNPQAA 62 Query: 72 LQYAASEGYAPLRQAIADFLPWDVDADQILITTGSQQALDLIAKVLIDENSRVLVETPTY 131 LQYAA+EGY PLR+ IA VD +++LITTGSQQALDLIAKV+ID S VLVETP+Y Sbjct: 63 LQYAATEGYMPLREFIAK--RHAVDVERVLITTGSQQALDLIAKVMIDPGSPVLVETPSY 120 Query: 132 LGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEA 191 LGALQAF+ EP V+V DD+ +L + L ++ GA RFLY LPNFQNPTGR M Sbjct: 121 LGALQAFSLFEPEFVSVPGDDKSLLPESLTPELTAGA---RFLYALPNFQNPTGRRMPLE 177 Query: 192 RRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEGCIYMGSFSKVLAPGLRLG 251 RR ALV A EL L LVED+PYG+L + L + NP+G IYMGSFSK+LAPGLRLG Sbjct: 178 RRQALVARARELGLLLVEDDPYGELSYSGDQLPSLLSMNPDGVIYMGSFSKILAPGLRLG 237 Query: 252 FVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLA 311 FV+AP ++ KL QAKQA+DLHTP + QRL EV++ LD H+PTIR LY QC+AML Sbjct: 238 FVIAPPELHFKLCQAKQASDLHTPSFTQRLAYEVVRDGLLDSHIPTIRTLYAAQCQAMLD 297 Query: 312 ALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADPR 371 +L + M GV WN P+GGMF+W+ LPEG+ ++E+L +AV RNVA+VPGA FYA N Sbjct: 298 SLARHMPE-GVTWNAPEGGMFIWMELPEGLDSMEILQEAVNRNVAYVPGAPFYASNPRRN 356 Query: 372 TLRLSFVTSTVEQIATGIAALAAAIR 397 LRL+FVT E+I G+A L R Sbjct: 357 ALRLAFVTVAPERIEQGVAILGTLFR 382 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: 540 Number of extensions: 17 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: 395 Length adjustment: 31 Effective length of query: 370 Effective length of database: 364 Effective search space: 134680 Effective search space used: 134680 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 Aug 03 2021. The underlying query database was built on Aug 03 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