Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 190 bits (483), Expect = 5e-53 Identities = 125/358 (34%), Positives = 196/358 (54%), Gaps = 24/358 (6%) Query: 6 LRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVD 65 L V K + + + +++ GE L LVGPSGCGK+TL+ IAG E++ G+I + Sbjct: 9 LDRVCKQFSGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLA 68 Query: 66 DADIS----GMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSK 121 ++ + P+ R + MVFQ YAL+P ++V DN+ FGL+ RK A + +A Sbjct: 69 GETVATAQRSLPPETRSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSAAVARQALA---- 124 Query: 122 LLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLM 181 L+ +E L R P +LSGGQQQRVA+ RALA +P + L DEPLSNLD ++R+ +R E++ + Sbjct: 125 LVGLEGLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDI 184 Query: 182 HQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPM 241 ++ + T + VTHDQ EA+++ D+VAVM+ G +Q G P++++ +PA+ FVA F+ Sbjct: 185 LRQAQATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLSQ--A 242 Query: 242 NFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIIL-ANGEANG 300 NF+ Q R + E P G++ + ++ +R E ++L + E G Sbjct: 243 NFLATEYQGDAWRTVL------GDFEAPGGLEGSRTGGEPPVVMVRQEDVLLHPHPEGTG 296 Query: 301 LPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAP-DVAPAVGETLTLQFDPAKVLLF 357 L V+ + G D FV L L P A AVG + +Q + L+ Sbjct: 297 L------VRDRQFLGRDYRYFVQLPAGLEIQVLGPVSEAIAVGTAVQVQLRTGQARLY 348 Lambda K H 0.319 0.138 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: 320 Number of extensions: 11 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: 386 Length of database: 368 Length adjustment: 30 Effective length of query: 356 Effective length of database: 338 Effective search space: 120328 Effective search space used: 120328 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: 50 (23.9 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