Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_164924542.1 NGR_RS28300 aspartate transaminase
Query= BRENDA::Q02635 (400 letters) >NCBI__GCF_000018545.1:WP_164924542.1 Length = 402 Score = 412 bits (1060), Expect = e-120 Identities = 208/396 (52%), Positives = 270/396 (68%) Query: 5 ADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKY 64 A +SR+K S + A + +ARELKA GRD++ + GEPDFDTPDN+K AA AIDRGETKY Sbjct: 7 ASRVSRIKVSPSTAAAARARELKAAGRDIVDMTVGEPDFDTPDNVKAAAHAAIDRGETKY 66 Query: 65 TPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPY 124 TPV+G P LR+AI F+R L Y + VG G KQILF A MA++ EV+IPAPY Sbjct: 67 TPVNGTPALRKAIIGDFERRLGLSYADNEICVGGGAKQILFLALMASVEYDAEVIIPAPY 126 Query: 125 WVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHE 184 WVSYP+MV G PV V QE FKL E L+ AITPKT W V N+PSNP+GAAYS Sbjct: 127 WVSYPDMVIANDGKPVIVQCPQEQGFKLTPEALEAAITPKTLWLVLNAPSNPTGAAYSRA 186 Query: 185 ELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMT 244 EL+AL VL++HP V+VL+DD+Y+ + + D T V P L R L NGVSK+YAMT Sbjct: 187 ELEALGQVLLRHPQVFVLSDDIYDQVWFRDEPMTTLVAAVPELKGRVLLTNGVSKSYAMT 246 Query: 245 GWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDL 304 GWRIGY AGP L+ A++ +Q Q +S +S++Q AA AL+ Q F+ + ++++ RRD Sbjct: 247 GWRIGYGAGPAPLVAAINKLQSQMSSCPSSVSQAAAAHALSSDQSFVAESVKVYKERRDY 306 Query: 305 VVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVH 364 + LN G+SC P+GAFY++P+CAG++G+ P GK IETD DF+ LL+ GVA + Sbjct: 307 ACARLNAVPGLSCLVPDGAFYLFPNCAGVMGRKTPEGKTIETDLDFILYLLDGVGVAALQ 366 Query: 365 GSAFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400 GSA+GL P FR+S ATS + EAC RI+R AA + Sbjct: 367 GSAYGLSPYFRLSIATSMEAITEACDRIERAVAALK 402 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: 499 Number of extensions: 17 Number of successful extensions: 1 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: 402 Length adjustment: 31 Effective length of query: 369 Effective length of database: 371 Effective search space: 136899 Effective search space used: 136899 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 Jul 25 2024. The underlying query database was built on Jul 25 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