Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 339 bits (869), Expect = 8e-98 Identities = 179/370 (48%), Positives = 254/370 (68%), Gaps = 15/370 (4%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA + L+ + K++ G+T+ +K LD+ D EF V VGPSGCGK+T LRM+AGLE +TEG Sbjct: 1 MAGLKLQAVTKSWDGKTQ-VIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEG 59 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 +++I D+RV ++ PKDR IAMVFQNYALYPHM+V +NMA+GLK+R + K +I RV+EAA Sbjct: 60 DIWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAA 119 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 +IL++ LL R+P+ LSGGQRQRVA+GRAIVR+P VFL DEPLSNLDAKLRVQMR E+++ Sbjct: 120 RILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQ 179 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH+RL+TT +YVTHDQ EAMT+ R++VM GV +Q TP VY +P ++FVA FIGSPA Sbjct: 180 LHRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPA 239 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLP-EGRYGVLKASGAIGKPVVLGVRPEDLHDEEVF 299 MN + G + +G F + LP G Y G+ + LG+RP E + Sbjct: 240 MNLLTGRVNNEGTHFELDG---GIELPLNGGY-----RQYAGRKMTLGIRP-----EHIA 286 Query: 300 MTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIH 359 +++ + + M ++ +E +G++ H G +V R+ + GS++ L + N++H Sbjct: 287 LSSQAEGGVPMVMDTLEILGADNLAHGRWGEQKLVVRLAHQERPTAGSTLWLHLAENQLH 346 Query: 360 IFDAETEESI 369 +FD ET + + Sbjct: 347 LFDGETGQRV 356 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: 382 Number of extensions: 17 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: 384 Length of database: 356 Length adjustment: 30 Effective length of query: 354 Effective length of database: 326 Effective search space: 115404 Effective search space used: 115404 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