Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate N515DRAFT_0006 N515DRAFT_0006 aspartate aminotransferase
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__Dyella79:N515DRAFT_0006 Length = 399 Score = 276 bits (705), Expect = 1e-78 Identities = 150/397 (37%), Positives = 213/397 (53%), Gaps = 1/397 (0%) Query: 1 MAFLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRG 60 M LA + R KPSA + +++KAR+LKA GRD+I G P+F D++ +AA +A+ Sbjct: 1 MPQLAQRVGRAKPSAIMVIAEKARQLKAAGRDIISFSIGVPNFLPGDHVYEAAREALKHD 60 Query: 61 ETKYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVI 120 +Y G L +A + + Y +G G KQ+L+N A L+ GDE+ Sbjct: 61 SGQYGSNRGAEPLLDAFLRHIEALGFSGYGRMNLSIGIGAKQVLYNLAEAMLDEGDEICF 120 Query: 121 PAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAA 180 APYW +Y ++ + G + E N+KL L+ A+ K K F+FN+PSNP+G Sbjct: 121 AAPYWTTYHDIADIVGAKANVLHCGPEQNYKLVPAQLEAALQRKPKVFLFNNPSNPTGMV 180 Query: 181 YSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKA 240 Y+ EE+ AL DVL+K+P W++TDD+Y + + + V +P L ER + ++ VSK Sbjct: 181 YTREEIAALADVLVKYPDTWIVTDDIYNSMVFDGIGYHNFVFAQPELRERLVFVDSVSKT 240 Query: 241 YAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQG 300 Y M GWR+G AGP + KA+ + + + AAV A GPQD E F G Sbjct: 241 YGMPGWRVGLIAGPESVAKAVTTLNSNHITSVPEVITAAAVAAFGGPQDVPRAKCEEFAG 300 Query: 301 RRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGV 360 +RD+V L G+ CP P+GAFY +P + GK + G I D +F + LLE GV Sbjct: 301 KRDVVFEALTAIPGVVCPRPQGAFYAFPDISVAFGK-SHQGTKISNDVEFCAALLEATGV 359 Query: 361 AVVHGSAFGLGPNFRISYATSEALLEEACRRIQRFCA 397 A V GSAFG RISY A L+ RIQ F A Sbjct: 360 ACVPGSAFGEPRAMRISYTCPTAQLKPGLERIQAFFA 396 Lambda K H 0.318 0.134 0.402 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: 413 Number of extensions: 19 Number of successful extensions: 2 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: 400 Length of database: 399 Length adjustment: 31 Effective length of query: 369 Effective length of database: 368 Effective search space: 135792 Effective search space used: 135792 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