Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011799827.1 PNAP_RS01975 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000015505.1:WP_011799827.1 Length = 406 Score = 597 bits (1538), Expect = e-175 Identities = 307/386 (79%), Positives = 331/386 (85%), Gaps = 5/386 (1%) Query: 12 WTLARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPAA 71 WT ARRA++MNPSVIREILKVTEKPGIIS AGGLPSPKTFPVSAF+AA VL DG AA Sbjct: 3 WTQARRAQKMNPSVIREILKVTEKPGIISFAGGLPSPKTFPVSAFSAACEKVLREDGHAA 62 Query: 72 LQYAASEGYAPLRQAIADFLPWDVDADQILITTGSQQALDLIAKVLIDENSRVLVETPTY 131 LQYAASEGYAPLR+ +A LPW+VD +LITTGSQQ LDLIAKVLIDE SRVLVETPTY Sbjct: 63 LQYAASEGYAPLREMVASMLPWNVDPALVLITTGSQQGLDLIAKVLIDEGSRVLVETPTY 122 Query: 132 LGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEA 191 LGALQAFTPMEP +V+VASDD GV I DL AK A+ ARF YVLPNFQNPTGRTM E Sbjct: 123 LGALQAFTPMEPEIVSVASDDGGVDIADLAAK----AEGARFFYVLPNFQNPTGRTMPEE 178 Query: 192 RRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEGCIYMGSFSKVLAPGLRLG 251 RRAAL AA L LPLVEDNPYGDLWFD PPP PLTARNPEGC+Y+GSFSKVLAPGLRLG Sbjct: 179 RRAALSAEAARLGLPLVEDNPYGDLWFDTPPPLPLTARNPEGCVYLGSFSKVLAPGLRLG 238 Query: 252 FVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLA 311 F+VAP +++PKLLQAKQAADLH+PG+NQRLVAEVMK FLDRHVPTIRALYK Q +AMLA Sbjct: 239 FMVAPASIFPKLLQAKQAADLHSPGFNQRLVAEVMKDGFLDRHVPTIRALYKSQRDAMLA 298 Query: 312 ALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADPR 371 A+ +EM GVEWN P GGMFLWVRLPEGM+AIELLP+AVERNVAFVPG AFYAD D R Sbjct: 299 AMVREMPE-GVEWNTPAGGMFLWVRLPEGMNAIELLPRAVERNVAFVPGWAFYADQPDAR 357 Query: 372 TLRLSFVTSTVEQIATGIAALAAAIR 397 TLRLSFVTS+V QI GIAALA AIR Sbjct: 358 TLRLSFVTSSVAQIDIGIAALAGAIR 383 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: 612 Number of extensions: 22 Number of successful extensions: 3 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: 406 Length adjustment: 31 Effective length of query: 370 Effective length of database: 375 Effective search space: 138750 Effective search space used: 138750 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 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