Align ABC transporter for Lactose, ATPase component (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 271 bits (692), Expect = 3e-77 Identities = 145/306 (47%), Positives = 201/306 (65%), Gaps = 11/306 (3%) Query: 4 LQLSDVRKSYGGLEV-IKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTI 62 L+L +RK+Y V + + L ++ GEF+ +GPSGCGKST LR+IAGL++ +SG + + Sbjct: 6 LELRQLRKAYSPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIWL 65 Query: 63 DDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILE 122 D + + P R +AMVFQSYALYPH+ VR+N+ L+ AEIE+R+ + AH LE Sbjct: 66 GDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNLE 125 Query: 123 LGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQ 182 L LLDR+P QLSGGQRQRVA+GRA+VR P +FL DEPLSNLDA LR +R ++ L Q Sbjct: 126 LDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFSQ 185 Query: 183 LATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFL 242 A+ +VYVTHDQ EA++L+ +I ++ G ++Q+ SP +Y PAN FVAGFIGSP+MN L Sbjct: 186 QASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNLL 245 Query: 243 KGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFDEAGP---AALDLAID 299 + I QA+ G +P+ AA + V G+RPEH A P A+ + + Sbjct: 246 P--LPIHSGQAW-----LGSRALPIPSHLAARSQVLWGLRPEHLKLATPEVERAIPVQLH 298 Query: 300 MLEHLG 305 + E+LG Sbjct: 299 LTENLG 304 Lambda K H 0.321 0.139 0.396 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: 323 Number of extensions: 11 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: 358 Length of database: 355 Length adjustment: 29 Effective length of query: 329 Effective length of database: 326 Effective search space: 107254 Effective search space used: 107254 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: 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