Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate Synpcc7942_1414 Synpcc7942_1414 ATPase
Query= reanno::pseudo3_N2E3:AO353_16275 (244 letters) >FitnessBrowser__SynE:Synpcc7942_1414 Length = 241 Score = 147 bits (371), Expect = 2e-40 Identities = 89/220 (40%), Positives = 129/220 (58%), Gaps = 8/220 (3%) Query: 1 MISIKNVNKWYGD----FQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKG 56 +I ++V+K YG+ + L +V+ GE + G SGSGKST + + L+ G Sbjct: 8 VIQFEHVSKIYGEGETTVRALDHVDFQVRAGEYCAIMGASGSGKSTAMNLIGCLDRPTAG 67 Query: 57 DVVVDGTSIADPKTD-LPKLRSR-VGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEAT 114 +DGT +AD D L +R+R +G VFQ F L P L+ EN+ + I G S++E Sbjct: 68 RYYLDGTDVADLDDDALAAVRNRKIGFVFQQFHLLPQLSAVENVMLPMIYA-GISQQERR 126 Query: 115 KKGLQLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNE 174 + + L +VGL+ P QLSGGQQQRVAIARA+ P+++L DEPT ALD + E Sbjct: 127 DRAVAALTQVGLAQRLDNKPNQLSGGQQQRVAIARAIVNQPVLLLADEPTGALDSQTTEE 186 Query: 175 VLDVMVQLANEGMTMMCVTHEMGFARKVADRVIFMDQGKI 214 VL++ QL G+T++ VTHE A + A+RVI+ G+I Sbjct: 187 VLNIFDQLHQRGITIVIVTHEAEVADR-AERVIWFRDGQI 225 Lambda K H 0.321 0.136 0.394 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: 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: 244 Length of database: 241 Length adjustment: 23 Effective length of query: 221 Effective length of database: 218 Effective search space: 48178 Effective search space used: 48178 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: 46 (22.3 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