Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate Dsui_2068 Dsui_2068 ABC-type metal ion transport system, ATPase component
Query= reanno::pseudo5_N2C3_1:AO356_09895 (257 letters) >FitnessBrowser__PS:Dsui_2068 Length = 278 Score = 156 bits (394), Expect = 5e-43 Identities = 96/235 (40%), Positives = 136/235 (57%), Gaps = 16/235 (6%) Query: 5 TPALEIRNLHKRY----GQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPN 60 +PAL +R + K + GQ + L G++ I+G SG+GKST LR NLLE P+ Sbjct: 8 SPALALRGVSKSFRTPDGQQVGVHPTDLDVAPGEIHGIIGFSGAGKSTLLRLANLLERPD 67 Query: 61 QGQILVAGEELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPR 120 GQ++V G++L L AD + R IG +FQ+FNL + +V DN+ P Sbjct: 68 AGQVVVHGQDLMT-------LSPAD---LRTARQRIGMIFQHFNLLHNRTVADNVA-FPL 116 Query: 121 RVLGQSKAEAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEP 180 R+ G +A E + L VG+++K YPA+LSGGQ+QR AIAR LA +P V+L DEP Sbjct: 117 RIAGADEARINERVKTCLEFVGLSEKAGVYPAQLSGGQKQRVAIARALAPEPHVLLADEP 176 Query: 181 TSALDPEMVQEVLSVIRALAEE-GRTMLLVTHEMGFARQVSSEVVFLHQGLVEEQ 234 TSALDP Q +L V+ + G T+LLV+HEMG R++ V + G + E+ Sbjct: 177 TSALDPRTTQSLLEVLADVNRRLGVTILLVSHEMGVIRRLCHRVSVMEAGQIVER 231 Lambda K H 0.317 0.132 0.363 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: 155 Number of extensions: 7 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: 257 Length of database: 278 Length adjustment: 25 Effective length of query: 232 Effective length of database: 253 Effective search space: 58696 Effective search space used: 58696 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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