Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Pf6N2E2_462 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_462 Length = 394 Score = 213 bits (541), Expect = 1e-59 Identities = 128/387 (33%), Positives = 206/387 (53%), Gaps = 16/387 (4%) Query: 14 SATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPEL 73 +A + +A ++ +G DV+ L G+PDFDTP I AA+ ++ GET Y+ + G+ L Sbjct: 15 AAAWQIHDRALAMREQGMDVLLLSVGDPDFDTPRAIVDAAVGSLRAGETHYSDIRGLHTL 74 Query: 74 REAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVA 133 R +IA++ + A Q +V G + ++ LNPGDEV++ P +V+Y + Sbjct: 75 RTSIARRHRLRCGQPAGAEQVVVLPGAQCAVYAVAQCLLNPGDEVIVAEPMYVTYEAVFG 134 Query: 134 LCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVL 193 CG T V V R EN F+++ D+ R +TP+T+ + NSP+NPSGA+ +AL + Sbjct: 135 ACGATVVPVAVRPENGFRVEPADVARLVTPRTRAMLLNSPNNPSGASLPMPTWQALARLC 194 Query: 194 MKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAG 253 ++H +W+++D++Y L Y D +P + PG+ ERT T+N +SK++AMTGWRIG+ G Sbjct: 195 IEH-DLWLISDEVYSDLLY-DGEHISPASL-PGMAERTATINSLSKSHAMTGWRIGWVIG 251 Query: 254 PLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVSMLNQAK 313 P L + + G Q AA AL + + + ++ RRDLV +ML+ Sbjct: 252 PESLADHLANLSLCMLFGLPDFVQRAAQVALEQALPEVAQMHDEYRQRRDLVCAMLDDCP 311 Query: 314 GISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAFG--LG 371 G+ P+G +V + +T + F LL+ GV+V+ G AFG Sbjct: 312 GLKPVRPDGGMFVMVD----VRRTGLDAQA------FAERLLDDYGVSVLAGEAFGPSAA 361 Query: 372 PNFRISYATSEALLEEACRRIQRFCAA 398 + R+ + L +AC+RI CAA Sbjct: 362 GHIRLGLVVDQVKLADACQRITS-CAA 387 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: 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: 400 Length of database: 394 Length adjustment: 31 Effective length of query: 369 Effective length of database: 363 Effective search space: 133947 Effective search space used: 133947 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