Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_035242342.1 Q366_RS18995 aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000745975.1:WP_035242342.1 Length = 399 Score = 347 bits (891), Expect = e-100 Identities = 166/384 (43%), Positives = 243/384 (63%), Gaps = 3/384 (0%) Query: 9 ADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHG 68 A R+ LPPY+F ++++K + R +G D+IDLGMGNP TP V++ ++ +DPK+H Sbjct: 10 ASRMDYLPPYLFGMINKMKMEKRRKGDDVIDLGMGNPMDPTPDAVIEKLVEVAKDPKSHR 69 Query: 69 YPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPS 128 YP G +R I +Y R Y + LD D E +GSKEG+SHL +A + PGD VLVP+ Sbjct: 70 YPESSGLPHLKREIAKYYGRHYNIGLDADKETYFTIGSKEGISHLCLAIMGPGDCVLVPA 129 Query: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188 PA+P H VIAG V + L+PE +L + + E K+L NYP NPTG Sbjct: 130 PAFPIHIYAAVIAGANVMRIPLEPEKGFLDRIIKVCEACYPSPKVLMLNYPHNPTGVVTD 189 Query: 189 REFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMA 248 + F++EIV A++++ ++++D YA++ +DGY S LEI GAKD+GVEF + SK+YNMA Sbjct: 190 KNFYKEIVKLAKRFKFMVINDFAYAKITYDGYVAPSFLEIEGAKDVGVEFGSFSKSYNMA 249 Query: 249 GWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDF 308 GWR+G+ VGN +++ L +K DYGIF+A+Q A AL+ D + E+ + Y RRD Sbjct: 250 GWRIGYCVGNEKIVEALGKIKGYFDYGIFSAIQVAGIIALRDCDDTIPELVKIYENRRDV 309 Query: 309 LIQGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTPGNAFGVAGE 365 L GL +GWD+ K KA M++W K P MGS +FA+ L+ V V PG F GE Sbjct: 310 LCSGLERIGWDIQKPKAGMFVWAKIPEPFNKMGSMEFAIQLMNNGNVAVAPGAGFSEEGE 369 Query: 366 GYVRISLIADCDRLGEALDRIKQA 389 GY+R++L+ + +RL +A+ ++K+A Sbjct: 370 GYLRLALVENEERLRQAVRQMKKA 393 Lambda K H 0.321 0.140 0.427 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: 459 Number of extensions: 17 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: 403 Length of database: 399 Length adjustment: 31 Effective length of query: 372 Effective length of database: 368 Effective search space: 136896 Effective search space used: 136896 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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