Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_164924745.1 NGR_RS30975 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_000018545.1:WP_164924745.1 Length = 355 Score = 317 bits (812), Expect = 3e-91 Identities = 186/382 (48%), Positives = 244/382 (63%), Gaps = 36/382 (9%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 M VT ++ + Y + + + I DGEF+VLVGPSGCGKST LRMLAGLE ++ G Sbjct: 1 MTDVTIRNVTKRYGALT--VIPQLSFRIEDGEFVVLVGPSGCGKSTLLRMLAGLEEISGG 58 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 + +G + ++RD+A+VFQNYALYPHMTV ENMGFALK+ + + EI++RVD+AA Sbjct: 59 DLLMGADVINDRPAKERDMAIVFQNYALYPHMTVAENMGFALKLRKRPRAEIDERVDKAA 118 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 A LGL + L+R P+ALSGGQRQRVAMGRAIVR+PQVFL DEPLSNLDAKLRVQ R +I A Sbjct: 119 AILGLGKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKA 178 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 L ++L +TTVYVTHDQ EA+TM D+I V+ +G ++Q+G P ELYDRPAN+FVAGFIGSP+ Sbjct: 179 LHQRLKITTVYVTHDQIEAMTMADKIVVMNEGRVEQMGTPLELYDRPANIFVAGFIGSPS 238 Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMTPEDNG-------RITIGFRPEALEIIPEG 293 MN +V AT+G + +PE +A P D G +T G RPE L++ G Sbjct: 239 MNFLPATVA---ATNG--PLLKTPEGVA--LPIDGGPTLTGRSEVTYGIRPEHLQL---G 288 Query: 294 ESTDLSIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGS 353 E+ IP ++ VE GS++ LY + G ++V PG Sbjct: 289 ET---GIPAEVVVVEPTGSETQLYVTVGGR--------------EVVAVLRDRVDVRPGE 331 Query: 354 VFHARIVEGGQHNFSASTGKRL 375 +G H F +TG R+ Sbjct: 332 KIWLTPRKGCAHLFDPNTGARI 353 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: 443 Number of extensions: 18 Number of successful extensions: 1 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: 355 Length adjustment: 30 Effective length of query: 346 Effective length of database: 325 Effective search space: 112450 Effective search space used: 112450 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 Apr 09 2024. 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