Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 276 bits (705), Expect = 8e-79 Identities = 158/366 (43%), Positives = 225/366 (61%), Gaps = 20/366 (5%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 LELR + K Y P + + N+ L++ GEFL L+GPSGCGKST + IAGL+ + G+I Sbjct: 6 LELRQLRKAYSPSVVP-VANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIW 64 Query: 64 VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123 + D +I+ + P DRD+AMVFQSYALYP ++VR N+ GL+IR+ AEI++ + +V+ L Sbjct: 65 LGDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNL 124 Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 +++HLL R+P QLSGGQ+QRVA+GRAL R+P ++L DEPLSNLDA LR ++R +MK + Sbjct: 125 ELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFS 184 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243 + + VYVTHDQ EA++L ++A++ G +QQ +P IY PAN FVA FIGSP MN Sbjct: 185 QQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNL 244 Query: 244 IPLRLQRKDGRLLALLDSGQA---RCELPLGMQDAGLEDREVILGIRPEQIILANGEANG 300 +PL + SGQA LP+ A +V+ G+RPE + LA E Sbjct: 245 LPLPIH-----------SGQAWLGSRALPIPSHLAARS--QVLWGLRPEHLKLATPEVE- 290 Query: 301 LPTIRAEVQVTEPTGPDTLVFVNL-NDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDA 359 I ++ +TE G L+ V + + +V RL + L + F+P F Sbjct: 291 -RAIPVQLHLTENLGMQRLLTVAIAANPEVRLRLLMPSDQPIPTDLQVTFEPESQHWFCP 349 Query: 360 KTGERL 365 TG+RL Sbjct: 350 STGDRL 355 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: 360 Number of extensions: 16 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 ( 7.4 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