Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 197 bits (502), Expect = 3e-55 Identities = 117/297 (39%), Positives = 172/297 (57%), Gaps = 28/297 (9%) Query: 6 LEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIG 65 L+ + K + G + V + +++ E VGPSGCGKTT LRMIAG E + G++ + Sbjct: 9 LDRVCKQFSGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLA 68 Query: 66 DRRV----NDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAK 121 V +PP+ R + MVFQ+YAL+PH+TV N+ FGL+ RK A ++A Sbjct: 69 GETVATAQRSLPPETRSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSAAV----ARQALA 124 Query: 122 ILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKL 181 ++ + L R P LSGGQ+QRVAL RA+ +P + L+DEPLSNLD ++R+++R E+R + Sbjct: 125 LVGLEGLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDI 184 Query: 182 HQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAM 241 ++ Q T I VTHDQ EA+++ DR+ VMR G +Q P+ ++ P + FVA F+ Sbjct: 185 LRQAQATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLSQ--A 242 Query: 242 NFIRGEIVQDGDAFY-----FRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDL 293 NF+ E GDA+ F AP G L+ S G+P V+ VR ED+ Sbjct: 243 NFLATE--YQGDAWRTVLGDFEAP-----------GGLEGSRTGGEPPVVMVRQEDV 286 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: 326 Number of extensions: 11 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: 384 Length of database: 368 Length adjustment: 30 Effective length of query: 354 Effective length of database: 338 Effective search space: 119652 Effective search space used: 119652 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: 50 (23.9 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