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 Ac3H11_3135 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q9SIE1 (475 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3135 Length = 394 Score = 171 bits (432), Expect = 5e-47 Identities = 122/408 (29%), Positives = 200/408 (49%), Gaps = 26/408 (6%) Query: 70 MSLSPRVQSLKPSKTMVITDLAATLVQSGV----PVIRLAAGEPDFDTPKVVAEAGINAI 125 M S R + ++P M + A L + P+I L GEPDF P +V EA A+ Sbjct: 1 MKFSTRAERIEPFYVMEVAKAAQALAREVAGTREPMIFLNIGEPDFTAPPLVQEAAARAV 60 Query: 126 REGFTRYTLNAGITELREAICRKLKEENGLSYAPDQILVSNGAKQSLLQAVLAVCSPGDE 185 G T+YT G+ LRE I + G++ +I+V+ GA +L A LA+ GDE Sbjct: 61 HSGATQYTNALGLDALRERISSWYQSRFGVNVPARRIVVTAGASAALQLACLALIESGDE 120 Query: 186 VIIPAPYWVSYTEQARLADATPVVIPTKISNNFLLDPKDLESKLTEKSRLLILCSPSNPT 245 +++P P + A+ V++PT + + L + + EK+R ++L SPSNPT Sbjct: 121 ILMPDPSYPCNRHFVSAAEGKAVLLPTTAAERYQLSADKVRAAWNEKTRGVLLASPSNPT 180 Query: 246 GSVYPKSLLEEIARIIAKHPRLLVLSDEIYEHIIYAPA-THTSFASLPDMYERTLTVNGF 304 G+ L I ++ H + ++ DEIY + Y HT+ A + + +++N F Sbjct: 181 GTSIAPDELRRIHDVVRSHDGITMI-DEIYLGLSYEEEFGHTALA----IDDNIISINSF 235 Query: 305 SKAFAMTGWRLGYLAGPKHIVAACSKLQGQVSSGASSIAQKAGVAALGLGKAGGETVAEM 364 SK F MTGWRLG++ P+ +V +L + AS+++Q A +A E++AE Sbjct: 236 SKYFNMTGWRLGWMVVPEAMVPVVERLAQNLFICASTVSQYAALACF-----EAESIAEY 290 Query: 365 VK---AYRERRDFLVKSLGDIKGVKISEPQGAFYLFIDFSAYYGSEAEGFGLINDSSSLA 421 + ++ RRDF + +L + +P GAFY + D + A+ G + S A Sbjct: 291 ERRRAEFKARRDFFIPALEKLGLAVPVKPDGAFYAWADCT----QAAQRLG-VTGSWDFA 345 Query: 422 LYFLDKFQVAMVPGDAFG---DDSCIRISYATSLDVLQAAVEKIRKAL 466 + + +A+ PG FG + IR S A S+ L+ +V ++R L Sbjct: 346 FELMRRAHIAVTPGRDFGTFDPERFIRFSTANSMAQLEESVARLRTLL 393 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: 333 Number of extensions: 9 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: 475 Length of database: 394 Length adjustment: 32 Effective length of query: 443 Effective length of database: 362 Effective search space: 160366 Effective search space used: 160366 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