Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 175 bits (443), Expect = 2e-48 Identities = 110/314 (35%), Positives = 168/314 (53%), Gaps = 30/314 (9%) Query: 19 LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDG----TVVNDVPPAQ 74 + ++ +++ GE++ VGPSGCGK+TLLRMIAG E + G++++ G T +PP Sbjct: 24 VDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQRSLPPET 83 Query: 75 RGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKAL 134 R + MVFQ YAL+PH+TV +N+ F L+ K S A A + L R P L Sbjct: 84 RSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSA----AVARQALALVGLEGLERRYPHEL 139 Query: 135 SGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHD 194 SGGQ+QRVA+ R++ P + L DEPLSNLD +R+ R E+ + ++T + VTHD Sbjct: 140 SGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILR-QAQATAILVTHD 198 Query: 195 QVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGKIIGTGAQT 254 Q EA+++ R+ V+ G Q+G P EL++ P + FVA+F+ + N L + G +T Sbjct: 199 QEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLS--QANFLATEYQGDAWRT 256 Query: 255 TVEMTDGGRAVSDYPSDDSLMGAAVN-----VGVRPED-MVEAAPGGDYVFEGKVAITEA 308 + D+ + L G+ V VR ED ++ P G G V + Sbjct: 257 ---------VLGDFEAPGGLEGSRTGGEPPVVMVRQEDVLLHPHPEG----TGLVRDRQF 303 Query: 309 LGEVTLLYFEAPSG 322 LG + + P+G Sbjct: 304 LGRDYRYFVQLPAG 317 Lambda K H 0.316 0.135 0.379 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: 341 Number of extensions: 14 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: 373 Length of database: 368 Length adjustment: 30 Effective length of query: 343 Effective length of database: 338 Effective search space: 115934 Effective search space used: 115934 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 (21.6 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