Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 267 bits (682), Expect = 4e-76 Identities = 153/358 (42%), Positives = 219/358 (61%), Gaps = 30/358 (8%) Query: 4 IQFSNIKKSFGSADV-LKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISI 62 ++ ++K++ + V + + L + PGEFL L+GPSGCGKST LR +AGL+ SG+I + Sbjct: 6 LELRQLRKAYSPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIWL 65 Query: 63 DGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQ 122 ++I + P +RD+AMVFQSYALYPH+ V +N+ GL+++ +AAEI +R+ +++ L+ Sbjct: 66 GDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNLE 125 Query: 123 IKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHN 182 + HLLDR+P +LSGGQRQRVALGRAL RQ V L DEPLSNLDA LR Q+R ++K L Sbjct: 126 LDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFSQ 185 Query: 183 SKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFL 242 S ++YVTHDQ EA +L RIA+L G ++Q+ +P IY P N F+A FIGSP MN L Sbjct: 186 QASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNLL 245 Query: 243 E----------GAVLEKIPWPEARKADQILGIRPDAFALNQGPLGTQEVALG-DFQIDIS 291 G+ IP A ++ + G+RP+ L T EV Q+ ++ Sbjct: 246 PLPIHSGQAWLGSRALPIPSHLAARSQVLWGLRPEHL-----KLATPEVERAIPVQLHLT 300 Query: 292 ENLGGQQMLHGTLAGN---NVRILVDSMDNFSMKQTLPLKIDLT----KAHLFDKKTG 342 ENLG Q++L +A N +R+L+ S Q +P + +T H F TG Sbjct: 301 ENLGMQRLLTVAIAANPEVRLRLLMPS------DQPIPTDLQVTFEPESQHWFCPSTG 352 Lambda K H 0.318 0.136 0.383 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: 327 Number of extensions: 17 Number of successful extensions: 1 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: 347 Length of database: 355 Length adjustment: 29 Effective length of query: 318 Effective length of database: 326 Effective search space: 103668 Effective search space used: 103668 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