Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 305 bits (782), Expect = 1e-87 Identities = 168/306 (54%), Positives = 210/306 (68%), Gaps = 12/306 (3%) Query: 17 KEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRD 76 K V+ F L +AD EF+VLVGPSGCGKSTTLRM+AGLE VT G I IG + V HV P+D Sbjct: 15 KNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEISIGGRVVNHVPPKD 74 Query: 77 RDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKAL 136 RDIAMVFQ+YALYPHM V +NM F L G +DEI++RV +AA LG+++ L+R+P L Sbjct: 75 RDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEILGISDLLQRRPAQL 134 Query: 137 SGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQ 196 SGGQRQRVAMGRAIVR+PQ FL DEPLSNLDAKLRVQ R ++A L +L T VYVTHDQ Sbjct: 135 SGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLHERLQSTIVYVTHDQ 194 Query: 197 TEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKD--GDA- 253 EA+T+ DRI V+KDG + QVG P E+Y+RPAN FVAGFIGSP+MN + + GD Sbjct: 195 IEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMNFLDVRLVEEAGDLW 254 Query: 254 TSGHA-RIKLSPETLAAMTPEDNGRITIGFRPEAL-----EIIPEGESTDLSIPIKLDFV 307 G + R+K+ A N + G RPE + + +PEG + ++D Sbjct: 255 VDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVKERPGDALPEGVE---PLRAEVDVR 311 Query: 308 EELGSD 313 E +GS+ Sbjct: 312 EPIGSE 317 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: 414 Number of extensions: 8 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: 368 Length adjustment: 30 Effective length of query: 346 Effective length of database: 338 Effective search space: 116948 Effective search space used: 116948 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