Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 278 bits (712), Expect = 1e-79 Identities = 150/326 (46%), Positives = 212/326 (65%), Gaps = 17/326 (5%) Query: 6 LEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIG 65 L + K Y P V + +L +Q EF +GPSGCGK+TTLR+IAGL+ T G++++G Sbjct: 8 LRQLRKAYSPSVVP-VANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIWLG 66 Query: 66 DRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDI 125 DR + +PP DRD+AMVFQ+YALYPH+ V QN+ GL++R+ AEI++R+Q+ A L++ Sbjct: 67 DREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNLEL 126 Query: 126 AHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRL 185 HLLDR+P LSGGQRQRVALGRA+VR+P VFL+DEPLSNLDA LR Q+RA+++ L + Sbjct: 127 DHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFSQQ 186 Query: 186 QTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIR 245 + V+YVTHDQTEA+++ RI ++ G +QQ D+P +Y P N FVAGFIGSP MN + Sbjct: 187 ASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNLLP 246 Query: 246 GEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFMTTYPD 305 I G A+ S +L +P + A V+ G+RPE L T + Sbjct: 247 LPI-HSGQAW---LGSRALPIP--------SHLAARSQVLWGLRPEHLK----LATPEVE 290 Query: 306 SVLQMQVEVVEHMGSEVYLHTSIGPN 331 + +Q+ + E++G + L +I N Sbjct: 291 RAIPVQLHLTENLGMQRLLTVAIAAN 316 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: 401 Number of extensions: 18 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: 355 Length adjustment: 30 Effective length of query: 354 Effective length of database: 325 Effective search space: 115050 Effective search space used: 115050 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