Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_035241766.1 Q366_RS17910 aminotransferase
Query= curated2:P63499 (429 letters) >NCBI__GCF_000745975.1:WP_035241766.1 Length = 405 Score = 381 bits (978), Expect = e-110 Identities = 181/399 (45%), Positives = 271/399 (67%), Gaps = 1/399 (0%) Query: 31 SAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALPYAQ 90 S ++++V +IRGPV + A ++ + G +L+LN GNPA FGF PD + +I + A Sbjct: 7 SDRMENVHSDIRGPVFEKAMQMVSAGIDVLRLNTGNPATFGFTMPDSVRTALISNVDKAV 66 Query: 91 GYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQVLIP 150 GY D +G+ AR+A+ Y + G +DDV++GNGVSE++ M + L+ GD++LIP Sbjct: 67 GYCDLKGMPDARKAICD-YHVGKGILDLTMDDVFIGNGVSEVVNMAMTTFLNPGDEMLIP 125 Query: 151 SPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTGAVY 210 SP Y LWT +AG TPV Y CDE W PD+AD+ KIT +T+A+++INPNNPTG++Y Sbjct: 126 SPSYSLWTNMAYIAGATPVLYRCDEASEWYPDVADIRRKITPKTRAILIINPNNPTGSLY 185 Query: 211 SCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKAYRVA 270 S +++ Q+V +AR+H+L++ +DEIYD+++ D+ +H+S A++APD+ TFNGLSK++ V Sbjct: 186 SKDVIEQIVQIAREHKLIMCSDEIYDRLVMDELEHVSTAALAPDLPVFTFNGLSKSHIVC 245 Query: 271 GYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVLPGGR 330 G+R GWLAI+GP+ I + LA MRLC N Q I AL +S + L+ PGGR Sbjct: 246 GFRCGWLAISGPRRQIGGLIASMTKLAAMRLCGNALTQLVIPAALEDEESTKALIAPGGR 305 Query: 331 LLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKILVTQ 390 + EQR+ L++I G++ VK + A Y FP++D ++I D++ VLDLL S+ IL+ Sbjct: 306 IYEQREATIKALDQIEGITYVKNSAAFYLFPKIDTRKFNITSDKKFVLDLLESKHILLVA 365 Query: 391 GTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYRQ 429 G+GF+WP PDH R+V LP S+ L+ AI+ +G+FL +YRQ Sbjct: 366 GSGFDWPEPDHFRIVMLPESKVLSGAIQEIGDFLSTYRQ 404 Lambda K H 0.320 0.138 0.419 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: 481 Number of extensions: 13 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: 429 Length of database: 405 Length adjustment: 31 Effective length of query: 398 Effective length of database: 374 Effective search space: 148852 Effective search space used: 148852 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