Align ABC transporter for D-sorbitol, ATPase component (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1960 (365 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 276 bits (707), Expect = 5e-79 Identities = 148/351 (42%), Positives = 215/351 (61%), Gaps = 13/351 (3%) Query: 4 LKIENLKKGFEGLSI-IKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTIEL 62 L++ L+K + + + + L+++ EF+ +GPSGCGKST LRLIAGL+ TSG+I L Sbjct: 6 LELRQLRKAYSPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIWL 65 Query: 63 DGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARILE 122 R+IT + P RD+AMVFQ+YALYPH+ VR+NL+ L + ++E+++ + A LE Sbjct: 66 GDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNLE 125 Query: 123 LGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLHKE 182 L LLDR+P QLSGGQRQRVA+GRA+VR P +FL DEPLSNLDA LR Q R ++ L + Sbjct: 126 LDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFSQ 185 Query: 183 LQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMGFL 242 + ++YVTHDQ EA++L+ ++ +LN G ++Q+ SP +Y PAN FVAGF+G+P+M L Sbjct: 186 QASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNLL 245 Query: 243 QATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLS---AEGQVPVT 299 +H+ A + L IP S L+ V G+RPEHL L+ E +PV Sbjct: 246 PLPIHSGQA------WLGSRALPIP---SHLAARSQVLWGLRPEHLKLATPEVERAIPVQ 296 Query: 300 TDVTERLGSDTFCHVNVDSGESLTVRVQGDCEVPYAARRYLTLDVAHCHLF 350 +TE LG V + + + +R+ + P +T + H F Sbjct: 297 LHLTENLGMQRLLTVAIAANPEVRLRLLMPSDQPIPTDLQVTFEPESQHWF 347 Lambda K H 0.319 0.135 0.380 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: 326 Number of extensions: 16 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: 365 Length of database: 355 Length adjustment: 29 Effective length of query: 336 Effective length of database: 326 Effective search space: 109536 Effective search space used: 109536 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