Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 282 bits (721), Expect = 1e-80 Identities = 159/364 (43%), Positives = 228/364 (62%), Gaps = 16/364 (4%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 LELR + K Y + + N+ L ++ GEFL L+GPSGCGKST + IAGL+ T G+I Sbjct: 6 LELRQLRKAYSPSVVP-VANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIW 64 Query: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123 +GD++++ + P DRD+AMVFQSYALYP ++VR+N+ GL+IR+ A+I+ + +VA L Sbjct: 65 LGDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNL 124 Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 +++HLL+R+P QLSGGQ+QRVA+GRAL R+P ++L DEPLSNLDA LR ++R +MK + Sbjct: 125 ELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFS 184 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243 + + VYVTHDQ EA++L ++A++ G +QQ +P IY PAN FVA FIGSP MN Sbjct: 185 QQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNL 244 Query: 244 VPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVIL-GLRPEQIMLAAGEGDSAS 302 +PL + SGQA + L R +L GLRPE + LA E + A Sbjct: 245 LPLPIH-----------SGQAWLGSRALPIPSHLAARSQVLWGLRPEHLKLATPEVERA- 292 Query: 303 SIRAEVQVTEPTGPDTLVFVQL-NDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDANT 361 I ++ +TE G L+ V + + +V RL + L + F+P F +T Sbjct: 293 -IPVQLHLTENLGMQRLLTVAIAANPEVRLRLLMPSDQPIPTDLQVTFEPESQHWFCPST 351 Query: 362 GERL 365 G+RL Sbjct: 352 GDRL 355 Lambda K H 0.318 0.135 0.382 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: 2 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: 355 Length adjustment: 30 Effective length of query: 356 Effective length of database: 325 Effective search space: 115700 Effective search space used: 115700 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 (21.7 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