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::Q8NMV1 (376 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 316 bits (809), Expect = 7e-91 Identities = 176/375 (46%), Positives = 238/375 (63%), Gaps = 19/375 (5%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA + + + S+ G K +K L++ADGEF+V+VGPSGCGKST LRM+AGLE VT+G Sbjct: 1 MAGLKLQAVTKSWDG-KTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEG 59 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 I+I D+ VT + P+DR IAMVFQNYALYPHM+V ENM + LKI G + +I +RV EAA Sbjct: 60 DIWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAA 119 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 L L L+R+P+ LSGGQRQRVAMGRAIVR+P VFL DEPLSNLDAKLRVQ R ++ Sbjct: 120 RILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQ 179 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 L R+L T++YVTHDQ EA+T+ R+ V+ G +Q+G P E+Y++PA++FVA FIGSPA Sbjct: 180 LHRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPA 239 Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSI 300 MNL T V + + T + ++T+G RPE + + + E + Sbjct: 240 MNLLTGRV-NNEGTHFELDGGIELPLNGGYRQYAGRKMTLGIRPEHIALSSQAEG---GV 295 Query: 301 PIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVFHARIV 360 P+ +D +E LG+D+ +G+ GE ++VVR A P GS + Sbjct: 296 PMVMDTLEILGADNLAHGRW-GE-------------QKLVVRLAHQERPTAGSTLWLHLA 341 Query: 361 EGGQHNFSASTGKRL 375 E H F TG+R+ Sbjct: 342 ENQLHLFDGETGQRV 356 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: 376 Number of extensions: 15 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: 376 Length of database: 356 Length adjustment: 30 Effective length of query: 346 Effective length of database: 326 Effective search space: 112796 Effective search space used: 112796 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