Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 326 bits (836), Expect = 5e-94 Identities = 173/334 (51%), Positives = 226/334 (67%), Gaps = 12/334 (3%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA VT YP E V + +I DGEF+VLVGPSGCGKST LRM+AGLE++T+G Sbjct: 1 MAQVTLNSVRKVYPNGVE-AVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEG 59 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 + IGD+ V +V P DRDIAMVFQNYALYPHMTV +N+ + LK + EI ++V EAA Sbjct: 60 TLEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAA 119 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 L L E+L+RKP LSGGQRQRVAMGRAIVR+P +FL DEPLSNLDAKLR Q R +I A Sbjct: 120 KMLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKA 179 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 LQR+LGVT++YVTHDQ EA+TM DRI VL G ++Q+G P E+Y PA+VFVA F+G+P Sbjct: 180 LQRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPP 239 Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSI 300 MNL ++ +G T ++ A+ G + +G RPE ++++ EG + Sbjct: 240 MNLLDATIANGQVTLPDG------VSMGALDTSAQGAVKLGIRPEDVQLVAEG-----GL 288 Query: 301 PIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVP 334 I ++ +EELG+ L+GKL G+ +D+P Sbjct: 289 AIDVELIEELGAHRLLHGKLGGQPFTIHVLKDIP 322 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: 381 Number of extensions: 13 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: 348 Length adjustment: 29 Effective length of query: 347 Effective length of database: 319 Effective search space: 110693 Effective search space used: 110693 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