Align Uncharacterized aminotransferase MJ0959; EC 2.6.1.- (characterized, see rationale)
to candidate H281DRAFT_04750 H281DRAFT_04750 aspartate aminotransferase
Query= uniprot:Y959_METJA (385 letters) >FitnessBrowser__Burk376:H281DRAFT_04750 Length = 407 Score = 140 bits (352), Expect = 8e-38 Identities = 111/366 (30%), Positives = 178/366 (48%), Gaps = 10/366 (2%) Query: 9 LLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFL-ITGSGT 67 L+M GP +P V A + VI H ++ + VF T + L + G G+ Sbjct: 31 LMMGAGPVPIPAAVAKANTI-VINHLGATMVKVIGQVKTMARYVFQTNSKWVLGVAGPGS 89 Query: 68 AAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEIL 127 AAM+MAISN+ G +VL+I G F R A + + L+V +A + + E + Sbjct: 90 AAMEMAISNLAWEGTRVLSIKNGFFSGRMAEMGRRVGARVTELEVADRTVASLDEIAEAI 149 Query: 128 DKYDDIKAVTVVHNETSTGARN-PIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 + + + VTVV ETS N +K+I + K AL IVD V +L + +D + ID Sbjct: 150 -RRERPEIVTVVQGETSNTVWNYQLKDIAALAKAAGALVIVDAVCTLSTMPLAMDAWGID 208 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIK-KNDDKVGFYLDLLAYKKYYEEKKQTPYTP 245 +TG QK L++ PG++ I S+ AWE +K + + LD + ++ YT Sbjct: 209 AVITGGQKGLSSIPGVSLIAFSDAAWERVKGRTAPNAHWCLDASLAENFWHNAGY-HYTA 267 Query: 246 SVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSAK 305 V+ AL+ AL LV E +E R RH + + A + G+ A+G++L+A R +V + Sbjct: 268 PVSGVLALHEALRLVCAETLEKRFARHLKCSVALQEGVTALGLQLYAPVACRLNSVVGIE 327 Query: 306 YPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMG-ICGEKEVLATLACVELALK 364 P G+ +S ++ + ++G I RIG MG C E + TL + + Sbjct: 328 VPAGLSPGDVCAHISRQHQVEISGS---FGLPIVRIGQMGEQCREHNLFRTLHALGRTMV 384 Query: 365 ELGFEV 370 +LG +V Sbjct: 385 DLGVKV 390 Lambda K H 0.316 0.135 0.379 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: 325 Number of extensions: 22 Number of successful extensions: 2 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: 385 Length of database: 407 Length adjustment: 31 Effective length of query: 354 Effective length of database: 376 Effective search space: 133104 Effective search space used: 133104 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: 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