Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 211 bits (536), Expect = 3e-59 Identities = 121/323 (37%), Positives = 178/323 (55%), Gaps = 29/323 (8%) Query: 21 VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80 VKD +L ++ +GPSG GK+T LR+IAGLE G +++ R + +DR I Sbjct: 18 VKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFLTGRDATNESVRDRQIG 77 Query: 81 MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140 VFQ+YAL+ H+TV +N+AFGL+LRK K ++ RV+E +++ + L DR P LSGGQ Sbjct: 78 FVFQHYALFKHLTVRKNIAFGLELRKHTKEKVRARVEELLELVQLTGLGDRYPSQLSGGQ 137 Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200 RQRVAL RA+ +PQV L+DEP LDAK+R +R+ +RKLH + T ++VTHDQ EAM Sbjct: 138 RQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWLRKLHDEVHVTTVFVTHDQEEAM 197 Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDGDAFYFRAP 260 + D+IVVM G ++Q +P +Y P FV FIG V + F+A Sbjct: 198 EVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIGPVN--------VLPNSSHIFQAG 249 Query: 261 SISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFMTTYPDSVLQMQVEVVEHMGS 320 + PE + +RP HD E+ + P++V +++ + H+G Sbjct: 250 GLDTPHPE-----------------VFLRP---HDIEIAIDPIPETV-PARIDRIVHLGW 288 Query: 321 EVYLHTSIGPNTIVARVNPRHVY 343 EV + ++ PR Y Sbjct: 289 EVQAEVRLEDGQVLVAHLPRDRY 311 Lambda K H 0.321 0.138 0.395 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: 381 Number of extensions: 20 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: 384 Length of database: 338 Length adjustment: 29 Effective length of query: 355 Effective length of database: 309 Effective search space: 109695 Effective search space used: 109695 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