Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__PS:Dsui_2943 Length = 356 Score = 206 bits (525), Expect = 6e-58 Identities = 110/236 (46%), Positives = 149/236 (63%), Gaps = 7/236 (2%) Query: 20 LQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQID 79 L+L + + +G+H V+ GI ++ G +GPSGCGK+TLLR IAG ED +GS+ +D Sbjct: 4 LELADVMQRYGAHTVVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGSIALD 63 Query: 80 GVEVGH----VAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAG 135 G V +AP +R I MVFQ YAL+PHLTV DN+ GLK G E +++VA Sbjct: 64 GELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKG---GERQQRVAAMLD 120 Query: 136 MLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARL 195 ++ L + P ELSGGQ+QRVA+ RA+ P+L L DEP SNLD LR LE+ + Sbjct: 121 LVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSLEVREI 180 Query: 196 HRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIG 251 + T I VTHDQ EA +AD+I V++ GRI+Q +P LY++PAN FVA F+G Sbjct: 181 LKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFVG 236 Lambda K H 0.320 0.137 0.393 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: 356 Number of extensions: 14 Number of successful extensions: 3 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: 352 Length of database: 356 Length adjustment: 29 Effective length of query: 323 Effective length of database: 327 Effective search space: 105621 Effective search space used: 105621 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: 49 (23.5 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