Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 317 bits (811), Expect = 4e-91 Identities = 182/386 (47%), Positives = 233/386 (60%), Gaps = 32/386 (8%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA ++ ++ +Y G + V ++EI DGEF+V+VGPSGCGKST LRM+AGLE ++ G Sbjct: 1 MAKLSLRNVQKTYAGNVK-VVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGG 59 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 + IGDK V H+ P +RDIAMVFQNYALYPHM+V +NM + LKI G + EI +RV AA Sbjct: 60 EVHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAA 119 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 L L LERKP+ALSGGQRQRVAMGRAIVR P VFL DEPLSNLDAKLRVQ R ++ Sbjct: 120 GILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKE 179 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 L R+L T++YVTHDQ EA+T+ DR+ VL G ++Q+G P E+Y RPA+ FVA FIGSP Sbjct: 180 LHRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPP 239 Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMT-----------PEDNGRITIGFRPEALEI 289 MNL + +G R++ P A PE R +G RPE +E Sbjct: 240 MNLVPVTRTNGGQGEAQMRVEQKPGAQGAPATLGHLPMGLHLPE---RALLGLRPEHIEP 296 Query: 290 IPEGESTDLSIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAP 349 E+ I++ VE LG+DS+ YG L G+ +VVR N Sbjct: 297 CAAHEAI---AEIEVRLVEALGADSYAYGTLGGQ--------------PVVVRLDSNMPV 339 Query: 350 APGSVFHARIVEGGQHNFSASTGKRL 375 + G H F A +GKR+ Sbjct: 340 SSGDRLPITAAAEHLHFFDADSGKRI 365 Lambda K H 0.316 0.135 0.380 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: 399 Number of extensions: 14 Number of successful extensions: 2 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: 376 Length of database: 367 Length adjustment: 30 Effective length of query: 346 Effective length of database: 337 Effective search space: 116602 Effective search space used: 116602 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 (21.6 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