Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate Ac3H11_1358 Valine--pyruvate aminotransferase (EC 2.6.1.66)
Query= SwissProt::H3ZPL1 (417 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1358 Length = 401 Score = 305 bits (780), Expect = 2e-87 Identities = 168/391 (42%), Positives = 243/391 (62%), Gaps = 9/391 (2%) Query: 23 SEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQY 82 + +A M S IRE+LK+ E +ISLAGGLP+P+TFPV + VL ALQY Sbjct: 15 ARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPAALQY 74 Query: 83 GTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPT 142 ++G+ PLR A+A+++ +D+ + I+ T+GSQQALDLI +V I+ ++VE PT Sbjct: 75 AASEGYAPLRQAIADFLP--WDVDADQ--ILITTGSQQALDLIAKVLIDENSRVLVETPT 130 Query: 143 YLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVT 202 YL ALQAF EP V + DDEG+ +D L+ K+ K + +Y +P FQNP G T Sbjct: 131 YLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGT---GADKARFLYVLPNFQNPTGRT 187 Query: 203 MNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAP 262 M E RR L++ A++ + +VEDNPYG+L + P P+ A + EG IY+G+FSK+LAP Sbjct: 188 MTEARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEG-CIYMGSFSKVLAP 246 Query: 263 GFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFYKPRR 322 G R+G++ A KL AKQ+ DL T ++Q + + ++G +LD+H+P I YK + Sbjct: 247 GLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQC 306 Query: 323 DAMLKALEEFMPD-GVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAH 381 +AML AL + M GV+W +P+GGMF+W LPEG+ +L +AV + VA+VPG AF+A Sbjct: 307 EAMLAALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYAD 366 Query: 382 RDVKNTMRLNFTYVPEEKIREGIKRLAETIK 412 T+RL+F E+I GI LA I+ Sbjct: 367 NADPRTLRLSFVTSTVEQIATGIAALAAAIR 397 Lambda K H 0.318 0.137 0.398 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: 401 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: 417 Length of database: 401 Length adjustment: 31 Effective length of query: 386 Effective length of database: 370 Effective search space: 142820 Effective search space used: 142820 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 17 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