Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate AO353_26890 AO353_26890 aspartate aminotransferase
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26890 Length = 395 Score = 213 bits (543), Expect = 6e-60 Identities = 129/376 (34%), Positives = 202/376 (53%), Gaps = 15/376 (3%) Query: 19 VSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPELREAIA 78 + +A EL+ +G DV+ L G+PDFDTP I +AAID++ G+T Y+ V G LR +IA Sbjct: 20 IHYRALELREQGVDVLLLSVGDPDFDTPKPIVQAAIDSLLAGDTHYSEVRGTRSLRTSIA 79 Query: 79 KKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALCGGT 138 ++ R + A +V G + +++ L+PGDEV++ P +V+Y + CG Sbjct: 80 RRHTRRSGQVVDADHVLVLPGAQCAVYSVVQCLLDPGDEVLVAEPMYVTYEGVFGACGAK 139 Query: 139 PVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMKHPH 198 V + R EN F++ D+ ITP+T+ + NSP+NPSGA+ S +AL + +KH Sbjct: 140 VVPIAVRPENGFRVDPTDIAARITPRTRAILLNSPNNPSGASLSLAIWQALARLCVKH-D 198 Query: 199 VWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAGPLHLI 258 +W+++D++Y L Y + +P + PG+ ERT T+N +SK++AMTGWR+G+ GP L Sbjct: 199 LWLISDEVYSELLY-EGEHISPASL-PGMAERTATVNSLSKSHAMTGWRVGWVIGPKRLT 256 Query: 259 KAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVSMLNQAKGISCP 318 + ++ + G Q AA AL + + ++ RRDLV + L GIS Sbjct: 257 EHLENLSLCMLFGIPDFVQNAARVALEADLPELALMRNEYRARRDLVCARLGDCPGISPV 316 Query: 319 TPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAFG--LGPNFRI 376 P+G +V + +T + F +LLE V+V+ G AFG + RI Sbjct: 317 IPDGGMFVMVD----VRQTGVGAQA------FAEKLLEGYAVSVLAGEAFGPSAAGHIRI 366 Query: 377 SYATSEALLEEACRRI 392 + L EACRRI Sbjct: 367 GLVLDQQRLAEACRRI 382 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: 371 Number of extensions: 16 Number of successful extensions: 4 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: 395 Length adjustment: 31 Effective length of query: 369 Effective length of database: 364 Effective search space: 134316 Effective search space used: 134316 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