Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_041361650.1 MCA_RS14695 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000008325.1:WP_041361650.1 Length = 390 Score = 248 bits (633), Expect = 2e-70 Identities = 150/391 (38%), Positives = 222/391 (56%), Gaps = 22/391 (5%) Query: 14 LARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPAALQ 73 L+RR ER+ S+IR+IL++T++PG+IS AGGLP+ + P F A +A + Q Sbjct: 5 LSRRTERLTSSLIRDILQITQRPGVISFAGGLPAEEMMPELDFGACAAD--------SRQ 56 Query: 74 YAASEGYAPLRQAIA---DFLPWDVDADQILITTGSQQALDLIAKVLIDENSRVLVETPT 130 Y SEG LR IA L +Q+L+TTGSQQ +DL+ K+ IDE + VL+E+PT Sbjct: 57 YGPSEGEPVLRDLIARGLSGLGLRCQTEQVLVTTGSQQGIDLVGKLFIDEGTPVLLESPT 116 Query: 131 YLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTE 190 YL ALQ F + G+ D LKA + + F+Y++P+FQNP+G + Sbjct: 117 YLAALQCFRVYGAEFHGLPLQVGGIDPDALKAAIVR--HRPAFVYLIPSFQNPSGCCYAD 174 Query: 191 ARRAALVKAAAELNLPLVEDNPYGDLWF---DNPPPAPLTARNPEGCIYMGSFSKVLAPG 247 A R A+ E PLVED+PY DL + D P R P +Y+GSFSK+ APG Sbjct: 175 AARRAVAAVLDETGTPLVEDDPYRDLVYTSCDRTPVCAYLERAP--WVYLGSFSKITAPG 232 Query: 248 LRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCE 307 LR+G++ + ++P L++ KQ++DLHT Q +A + +H+ + +Y + + Sbjct: 233 LRVGYLASSPGLFPWLVRLKQSSDLHTGRTGQAWLARFLSSGDFGKHLAHMNGVYAGRRD 292 Query: 308 AMLAALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFY--A 365 M AAL + +GL EW+ P GG+F W+RL + + L A+ R+VAF+PG F+ A Sbjct: 293 TMQAALERHFSGL-AEWSAPAGGLFFWLRLVGNIDTLAALKVALGRDVAFMPGEPFFPVA 351 Query: 366 DNADPRTLRLSFVTSTVEQIATGIAALAAAI 396 D P LRL+F +T E+I GI L+ + Sbjct: 352 DQRYP-ALRLNFSHATPEKIERGIGLLSEVL 381 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: 414 Number of extensions: 22 Number of successful extensions: 5 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: 390 Length adjustment: 31 Effective length of query: 370 Effective length of database: 359 Effective search space: 132830 Effective search space used: 132830 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 Jul 25 2024. The underlying query database was built on Jul 25 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