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::Q70HW1 (384 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 338 bits (867), Expect = 1e-97 Identities = 179/379 (47%), Positives = 249/379 (65%), Gaps = 24/379 (6%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA++ L ++ KTY G + V +++I D EF V VGPSGCGK+T LRM+AGLE I+ G Sbjct: 1 MAKLSLRNVQKTYAGNVK-VVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGG 59 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 ++IGD+ VN + P +RDIAMVFQNYALYPHM+VY NMA+GLK+R + K+EI++RV+ AA Sbjct: 60 EVHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAA 119 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 IL++A LL+RKP+ALSGGQRQRVA+GRAIVREP VFL DEPLSNLDAKLRVQMR E+++ Sbjct: 120 GILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKE 179 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH+RL+TT +YVTHDQ EAMT+ DR++V+ G ++Q TP VY++P + FVA FIGSP Sbjct: 180 LHRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPP 239 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLH------ 294 MN + G E + V + GA G P LG P LH Sbjct: 240 MNLVPVTRTNGGQG-------------EAQMRVEQKPGAQGAPATLGHLPMGLHLPERAL 286 Query: 295 ----DEEVFMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVK 350 E + +++ +++V +VE +G++ Y + ++G +V R++ G + Sbjct: 287 LGLRPEHIEPCAAHEAIAEIEVRLVEALGADSYAYGTLGGQPVVVRLDSNMPVSSGDRLP 346 Query: 351 LAIDLNKIHIFDAETEESI 369 + +H FDA++ + I Sbjct: 347 ITAAAEHLHFFDADSGKRI 365 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: 408 Number of extensions: 13 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: 367 Length adjustment: 30 Effective length of query: 354 Effective length of database: 337 Effective search space: 119298 Effective search space used: 119298 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