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 209328 DVU0392 aromatic aminotransferase
Query= BRENDA::Q9SIE1 (475 letters) >MicrobesOnline__882:209328 Length = 399 Score = 179 bits (454), Expect = 2e-49 Identities = 127/397 (31%), Positives = 211/397 (53%), Gaps = 25/397 (6%) Query: 72 LSPRVQSLKPSKTMVITDLAATLVQSGVPVIRLAAGEPDFDTPKVVAEAGINAIREGFT- 130 +S RVQ ++ S T ++ LAA + + L G P F TP+ + EA A+R+ Sbjct: 7 VSRRVQQIRISATKLMPMLAARVGGC----VSLGQGVPSFRTPEHIVEAVCRALRDKADA 62 Query: 131 -RYTLNAGITELREAICRKLKEENGLSYAPD-QILVSNGAKQSLLQAVLAVCSPGDEVII 188 RYTL G+ LREAI L G PD ++ V+ GA ++LL A+L V GDEVII Sbjct: 63 GRYTLQPGMPALREAIAADLAARKGYMVNPDSEVGVTVGAMEALLMALLTVVDRGDEVII 122 Query: 189 PAPYWVSYTEQARLADATPVVIPTKISNNFLLDPKDLESKLTEKSRLLILCSPSNPTGSV 248 P+P + S+ EQ +A+ PV +P + ++++ LD + + +T ++R +I+C+P NPTG+V Sbjct: 123 PSPGYASHAEQVLMAEGVPVHVPLR-ADDWGLDVDAIRAAVTPRTRAVIVCNPGNPTGTV 181 Query: 249 YPKSLLEEIARIIAKHPRLLVLSDEIYEHIIYAPATHTSFASLPDMYERTLTVNGFSKAF 308 Y + + + + A ++++SDE Y++++Y S ASLP+M + VN FSK + Sbjct: 182 YDDADVRALCEL-ALERNIMLISDETYDYMVYGGGEPLSPASLPEMRRHVIVVNSFSKKY 240 Query: 309 AMTGWRLGYLAGPKHIVAACSKLQGQVSSGASSIAQKAGVAALGLGKAGGETVAEMVKAY 368 A+TGWR+GY A + K+ + A +++Q A +AAL + V +M A Sbjct: 241 ALTGWRVGYCAADAAWMGELLKVHDAAAICAPAVSQYAALAAL---TGPQDCVDDMRAAL 297 Query: 369 RERRDFLVKSLGDI-KGVKISEPQGAFYLFIDFSAYYGSEAEGFGLINDSSSLALYFLDK 427 RR+ L + +P+GAFY+ + Y ++A S +A L++ Sbjct: 298 SARRNLACARLDAMAPHFDYVQPRGAFYI---MARYTFTDA-------PSDMVARRLLEE 347 Query: 428 FQVAMVPGDAFG--DDSCIRISYATSLDVLQAAVEKI 462 +V VPG +FG + +R+S+ L A +++ Sbjct: 348 GRVITVPGASFGPTGERHLRLSFGMEEAELDEAFDRM 384 Lambda K H 0.317 0.132 0.370 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: 396 Number of extensions: 22 Number of successful extensions: 5 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: 475 Length of database: 399 Length adjustment: 32 Effective length of query: 443 Effective length of database: 367 Effective search space: 162581 Effective search space used: 162581 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 (21.6 bits) S2: 51 (24.3 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