Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_011885633.1 2-aminoadipate aminotransferase
Query= SwissProt::H3ZPL1 (417 letters) >NCBI__GCF_000016205.1:WP_011885633.1 Length = 393 Score = 343 bits (881), Expect = 4e-99 Identities = 184/393 (46%), Positives = 253/393 (64%), Gaps = 13/393 (3%) Query: 23 SEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQY 82 SE+A + +S IRE+LK+ E +VIS AGGLPAP TFP E + VL A ALQY Sbjct: 14 SERARKLTSSAIREILKVTERPEVISFAGGLPAPVTFPAERMRAAADLVLRDAPAAALQY 73 Query: 83 GTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPT 142 T+G+ PLR EW+ ERY + +S+V + T+GSQQALDL+G+ I+P ++VE PT Sbjct: 74 SATEGYLPLR----EWIAERYGVRVSQV--LITTGSQQALDLLGKALIDPDSPVLVETPT 127 Query: 143 YLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVT 202 YL ALQ+F YEP +VQ+P D++G LL E L +G +++Y P FQNP G Sbjct: 128 YLGALQSFSLYEPRYVQVPTDEQG----LLPEGLTPALTQG--ARLLYAQPNFQNPTGRR 181 Query: 203 MNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAP 262 + +RR+ L A F ++ED+PYG L Y GEP+ + + + V++LGTFSK+LAP Sbjct: 182 LPVERRRALAAFAQSSPFPVLEDDPYGALNYQGEPLPTMLSMAPD-HVVHLGTFSKVLAP 240 Query: 263 GFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFYKPRR 322 G R+G+I A KL AKQ+ DL T T +Q IA + ++ G+LD+HIP I + Y + Sbjct: 241 GLRLGYIIAPEELHFKLVQAKQATDLHTPTLTQRIAHEVIKDGFLDEHIPTIRKLYSAQC 300 Query: 323 DAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHR 382 DAML +L MP+GV W +PEGGMF+W LP ID+ +LE AVA VA+VPG FFA+ Sbjct: 301 DAMLASLARHMPEGVTWNRPEGGMFIWVNLPAQIDSMKLLEAAVADHVAFVPGAPFFAND 360 Query: 383 DVKNTMRLNFTYVPEEKIREGIKRLAETIKEEM 415 +NT+RL+F VP EKI EG+ RL + ++E + Sbjct: 361 AQRNTLRLSFVTVPPEKIEEGVARLGKLLRERL 393 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: 503 Number of extensions: 27 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: 393 Length adjustment: 31 Effective length of query: 386 Effective length of database: 362 Effective search space: 139732 Effective search space used: 139732 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 24 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