Align Aromatic-amino-acid aminotransferase; ARAT; AROAT; EC 2.6.1.57 (characterized)
to candidate 3606714 Dshi_0145 Aspartate transaminase (RefSeq)
Query= SwissProt::P95468 (394 letters) >FitnessBrowser__Dino:3606714 Length = 392 Score = 334 bits (857), Expect = 2e-96 Identities = 176/392 (44%), Positives = 242/392 (61%), Gaps = 3/392 (0%) Query: 1 MLGNLKPQAPDKILALMGEFRADPRQGKIDLGVGVYKDATGHTPIMRAVHAAEQRMLETE 60 M +L+PQA D IL LM F+ADPR GK+DLG+GV++DA G TP+ AV AE+R+ T+ Sbjct: 1 MFAHLRPQADDPILVLMRAFQADPRPGKVDLGIGVWRDAEGRTPVFGAVKTAEERLWRTQ 60 Query: 61 TTKTYAGLSGEPEFQKAMGELILGDGLKSETTATLATVGGTGALRQALELARMANPDLRV 120 TK+Y +G+P F A+G+L+LG + A AT GGT A++ L L+++A P +V Sbjct: 61 DTKSYVSFAGDPAFHAAVGDLLLGSVTRPR--AVTATTGGTSAVQTLLALSQVARPAAQV 118 Query: 121 FVSDPTWPNHVSIMNFMGLPVQTYRYFDAETRGVDFEGMKADLAAAKKGDMVLLHGCCHN 180 ++ TWPNH + +GL + + Y E G+D E + DLA A+ GD+V+LH CCHN Sbjct: 119 WIPAETWPNHRVLAEHLGLATRAFTYLAPEGTGIDREVLLRDLAQAQAGDVVILHACCHN 178 Query: 181 PTGANLTLDQWAEIASILEKTGALPLIDLAYQGFGDGLEEDAAGTRLIASRIPEVLIAAS 240 PTG + + AEI L +TGA+PL+D AY GFG E DAA R +AS +PE ++A S Sbjct: 179 PTGIDPDPELQAEIVDSLARTGAVPLVDCAYLGFGAVPEADAAFLRRLAS-LPEAMLAFS 237 Query: 241 CSKNFGIYRERTGCLLALCADAATRELAQGAMAFLNRQTYSFPPFHGAKIVSTVLTTPEL 300 SK+FG+YRER G L L E Q + LNR YSFPP HGA++V+ +L P L Sbjct: 238 GSKSFGLYRERVGLALVLLEQPGVVEAVQSQLTRLNRVNYSFPPDHGARVVTEILADPAL 297 Query: 301 RADWMAELEAVRSGMLRLREQLAGELRDLSGSDRFGFVAEHRGMFSRLGATPEQVKRIKE 360 R W AEL A+R+ + R+ LA LR SDRF +A GMF+ L E+V R++E Sbjct: 298 RTAWEAELAAIRTALSANRQALAKALRARLQSDRFDGLAAQSGMFAMLPLGKERVMRMRE 357 Query: 361 EFGIYMVGDSRINIAGLNDNTIPILARAIIEV 392 +F +Y VG R+N+AG+ T +A AI V Sbjct: 358 DFAVYAVGTGRVNLAGVTPRTTDRVAEAIAAV 389 Lambda K H 0.320 0.136 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: 406 Number of extensions: 19 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: 394 Length of database: 392 Length adjustment: 31 Effective length of query: 363 Effective length of database: 361 Effective search space: 131043 Effective search space used: 131043 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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