Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate RR42_RS14595 RR42_RS14595 2-aminoadipate aminotransferase
Query= SwissProt::H3ZPL1 (417 letters) >FitnessBrowser__Cup4G11:RR42_RS14595 Length = 395 Score = 322 bits (826), Expect = 1e-92 Identities = 174/395 (44%), Positives = 249/395 (63%), Gaps = 13/395 (3%) Query: 23 SEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQY 82 S +A + +S IRE+LK+ E +VIS AGGLP+P TFPV + + + + ALQY Sbjct: 6 SRRAQQLTSSAIREILKVTERPEVISFAGGLPSPATFPVAAMEQAVARIFADNPQAALQY 65 Query: 83 GTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPT 142 T+G+ PLR E++ +R+ + + +V + T+GSQQALDLI +V I+PG ++VE P+ Sbjct: 66 AATEGYMPLR----EFIAKRHAVDVERV--LITTGSQQALDLIAKVMIDPGSPVLVETPS 119 Query: 143 YLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVT 202 YL ALQAF +EPEFV +P DD+ LL E L G + +Y +P FQNP G Sbjct: 120 YLGALQAFSLFEPEFVSVPGDDKS----LLPESLTPELTAG--ARFLYALPNFQNPTGRR 173 Query: 203 MNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAP 262 M +RR+ L+ A + ++VED+PYGEL YSG+ + + + + +G VIY+G+FSKILAP Sbjct: 174 MPLERRQALVARARELGLLLVEDDPYGELSYSGDQLPSLLSMNPDG-VIYMGSFSKILAP 232 Query: 263 GFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFYKPRR 322 G R+G++ A P KL AKQ+ DL T +F+Q +A++ V G LD HIP I Y + Sbjct: 233 GLRLGFVIAPPELHFKLCQAKQASDLHTPSFTQRLAYEVVRDGLLDSHIPTIRTLYAAQC 292 Query: 323 DAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHR 382 AML +L MP+GV W PEGGMF+W LPEG+D+ +L++AV + VAYVPG F+A Sbjct: 293 QAMLDSLARHMPEGVTWNAPEGGMFIWMELPEGLDSMEILQEAVNRNVAYVPGAPFYASN 352 Query: 383 DVKNTMRLNFTYVPEEKIREGIKRLAETIKEEMKK 417 +N +RL F V E+I +G+ L +E + K Sbjct: 353 PRRNALRLAFVTVAPERIEQGVAILGTLFREAIAK 387 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: 481 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 417 Length of database: 395 Length adjustment: 31 Effective length of query: 386 Effective length of database: 364 Effective search space: 140504 Effective search space used: 140504 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