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 BWI76_RS07920 BWI76_RS07920 methionine aminotransferase
Query= BRENDA::Q9SIE1 (475 letters) >FitnessBrowser__Koxy:BWI76_RS07920 Length = 386 Score = 153 bits (386), Expect = 1e-41 Identities = 121/401 (30%), Positives = 190/401 (47%), Gaps = 26/401 (6%) Query: 70 MSLSPRVQSLK-PSKTMVITDLAATLVQSGVPVIRLAAGEPDFDTPKVVAEAGINAIREG 128 MS P + K PS I + L Q I L+ G PDFD P+ + E + +G Sbjct: 1 MSNKPLIPESKLPSLGTTIFSQMSALAQQH-QAINLSQGFPDFDGPRYLQERLAYHVAQG 59 Query: 129 FTRYTLNAGITELREAICRKLKEENGLSYAPD---QILVSNGAKQSLLQAVLAVCSPGDE 185 +Y G+ LREAI K +E G Y PD + V+ GA ++L A+ A+ GDE Sbjct: 60 ANQYAPMTGVAALREAIVDKTEELYG--YRPDANSDVTVTAGATEALYAAITALVRAGDE 117 Query: 186 VIIPAPYWVSYTEQARLADATPVVIPTKISNNFLLDPKDLESKLTEKSRLLILCSPSNPT 245 VI P + SY L+ I + +F +D + + L++K+RL+IL +P NP+ Sbjct: 118 VICFDPSYDSYAPAIELSGGVLKRIALQ-PPHFRVDWQQFAASLSDKTRLVILNTPHNPS 176 Query: 246 GSVYPKSLLEEIARIIAKHPRLLVLSDEIYEHIIYAPATHTSFASLPDMYERTLTVNGFS 305 +V+ + + + IA + VLSDE+YEHI +A H S + P + ER + V+ F Sbjct: 177 ATVWLREDFAALWQAIADR-EIYVLSDEVYEHICFAAEGHASVLAHPQLRERAVAVSSFG 235 Query: 306 KAFAMTGWRLGYLAGPKHIVAACSKLQGQVSSGASSIAQKAGVAALGLGKAGGETVAEMV 365 K F MTGW++GY P I K+ ++ ++ AQ +A + + E ++ Sbjct: 236 KTFHMTGWKVGYCVAPAAISGELRKVHQYLTFAVNTPAQ---LAIADMLRREPEHYRQLP 292 Query: 366 KAYRERRDFLVKSLGDIKGVKISEPQGAFYLFIDFSAYYGSEAEGFGLINDSSSLALYFL 425 YRERRD + +L + ++I +G ++L D+SA D S + Sbjct: 293 AFYRERRDLFIDALRSSR-LEILPCEGTYFLLADYSAVSDL---------DDVSFCRWLT 342 Query: 426 DKFQVAMVPGDAFGDD----SCIRISYATSLDVLQAAVEKI 462 + VA +P F D IR+ +A L AA E++ Sbjct: 343 TEIGVAAIPLSVFCADPFPHKLIRLCFAKQPATLLAAAERL 383 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: 354 Number of extensions: 20 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: 475 Length of database: 386 Length adjustment: 32 Effective length of query: 443 Effective length of database: 354 Effective search space: 156822 Effective search space used: 156822 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