Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= BRENDA::P68187 (371 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 270 bits (689), Expect = 6e-77 Identities = 148/358 (41%), Positives = 221/358 (61%), Gaps = 20/358 (5%) Query: 3 SVQLQNVTKAWGEVVVS-KDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLF 61 +++L+ + KA+ VV +++L + GEF+ +GPSGCGKST LR+IAGL+ TSG ++ Sbjct: 5 ALELRQLRKAYSPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIW 64 Query: 62 IGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEVL 121 +G++ + PP +R + MVFQSYALYPHL+V +N++ GL++ I QR+ QVA L Sbjct: 65 LGDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNL 124 Query: 122 QLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHK 181 +L HLLDR+P LSGGQRQRVA+GR LV +PSVFLLDEPLSNLDA LR Q+R ++ L Sbjct: 125 ELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFS 184 Query: 182 RLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNF 241 + ++YVTHDQ EA++L+ +I +L+ G + Q+ P +Y PA+ FVAGFIGSP+MN Sbjct: 185 QQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNL 244 Query: 242 LPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHL-LPSDIADVIL 300 LP+ + + LP+P+ + + + G+RPEHL L + + + Sbjct: 245 LPLPIHSGQAWLGSRALPIPSH-----------LAARSQVLWGLRPEHLKLATPEVERAI 293 Query: 301 EGEVQVVEQLGNETQIHIQI---PSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLF 355 ++ + E LG + + + I P +R L+ + + + TF PE H F Sbjct: 294 PVQLHLTENLGMQRLLTVAIAANPEVRLRLLMPSDQPIPTDLQVTF----EPESQHWF 347 Lambda K H 0.320 0.137 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: 377 Number of extensions: 13 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: 371 Length of database: 355 Length adjustment: 29 Effective length of query: 342 Effective length of database: 326 Effective search space: 111492 Effective search space used: 111492 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