Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 179 bits (454), Expect = 1e-49 Identities = 107/271 (39%), Positives = 154/271 (56%), Gaps = 14/271 (5%) Query: 22 IDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIGERSVL----GVHPKDRDI 77 + LE+GE L L+G SGCGK+TLL +IAG G I + +V + P+ R + Sbjct: 27 VSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQRSLPPETRSV 86 Query: 78 AMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQIENLLDRKPSQLSGG 137 MVFQ YAL+P+L+V N+ FGL R+ A R L+ +E L R P +LSGG Sbjct: 87 GMVFQDYALFPHLTVLDNVCFGLRDRKGSAA----VARQALALVGLEGLERRYPHELSGG 142 Query: 138 QRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQMLRTTVVYVTHDQIEA 197 Q+QRVA+ RAL P + L DEPLSNLD ++R+ +R EL+ + + + T + VTHDQ EA Sbjct: 143 QQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQATAILVTHDQEEA 202 Query: 198 MTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILDAEMTANGLK-IEGC 256 +++ R+AVMR GR EQ+ P+E++ PA+ +VA F+ N L E + + + G Sbjct: 203 LSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLSQ--ANFLATEYQGDAWRTVLGD 260 Query: 257 EEVLPLPAAFNGAAWAGRRVKVGIRPEALRL 287 E P G+ G V +R E + L Sbjct: 261 FEA---PGGLEGSRTGGEPPVVMVRQEDVLL 288 Lambda K H 0.320 0.136 0.385 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: 331 Number of extensions: 21 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: 360 Length of database: 368 Length adjustment: 29 Effective length of query: 331 Effective length of database: 339 Effective search space: 112209 Effective search space used: 112209 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