Align ABC transporter related (characterized, see rationale)
to candidate Dsui_2068 Dsui_2068 ABC-type metal ion transport system, ATPase component
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__PS:Dsui_2068 Length = 278 Score = 164 bits (415), Expect = 2e-45 Identities = 102/236 (43%), Positives = 139/236 (58%), Gaps = 17/236 (7%) Query: 2 NATAPVALSVKNIHKSF----GDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLL 57 N +P AL+++ + KSF G + LD G++ I+G SG+GKST LR NLL Sbjct: 5 NTDSP-ALALRGVSKSFRTPDGQQVGVHPTDLDVAPGEIHGIIGFSGAGKSTLLRLANLL 63 Query: 58 ETPDDGSVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLI 117 E PD G V + G++L L P+D R R ++GM+FQ+FNL + TV +N + Sbjct: 64 ERPDAGQVVVHGQDLMT-------LSPADLRTA---RQRIGMIFQHFNLLHNRTVADN-V 112 Query: 118 EGPMRVQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVML 177 P+R+ A E + L VGL+EK G YPA LSGGQ+QRVAIARALA P V+L Sbjct: 113 AFPLRIAGADEARINERVKTCLEFVGLSEKAGVYPAQLSGGQKQRVAIARALAPEPHVLL 172 Query: 178 FDEPTSALDPELVGEVLRVMRSLAEE-GRTMLVVTHEMGFARHVSNRVMFLHQGQV 232 DEPTSALDP +L V+ + G T+L+V+HEMG R + +RV + GQ+ Sbjct: 173 ADEPTSALDPRTTQSLLEVLADVNRRLGVTILLVSHEMGVIRRLCHRVSVMEAGQI 228 Lambda K H 0.318 0.133 0.377 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: 181 Number of extensions: 10 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: 263 Length of database: 278 Length adjustment: 25 Effective length of query: 238 Effective length of database: 253 Effective search space: 60214 Effective search space used: 60214 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 (21.7 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