Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_000759345.1:WP_043527041.1 Length = 354 Score = 314 bits (805), Expect = 2e-90 Identities = 183/374 (48%), Positives = 233/374 (62%), Gaps = 26/374 (6%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA++ +Y G E VK +LEIADGEF+VLVGPSGCGKST LRM+AGLE +TDG Sbjct: 1 MASIQLTGLKKTYAGNVE-AVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDG 59 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 + I D+ V + P +RDIAMVFQNYALYPHMTV N+ + LK G ++EI +RV +AA Sbjct: 60 TLKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAA 119 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 A L + FLERKP+ LSGGQRQRVAMGRA+VR P FL DEPLSNLDAKLRVQ R +I Sbjct: 120 AMLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQ 179 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 LQR+L T++YVTHDQ EALT+GDR+ VL G ++QVG P E+Y++PA++FVA FIGSPA Sbjct: 180 LQRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPA 239 Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSI 300 MN+ + +G + LAA T IG RP+ L I E L + Sbjct: 240 MNMLPVAYLRERGANGLL------DHLAADTD------VIGIRPDDLRIEAPDED-HLVV 286 Query: 301 PIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVFHARIV 360 ++ E G++S LY L G D P V+R + A G ++ Sbjct: 287 TGTVELFEAAGAESHLYVSLEG--------SDQP----TVIRTSARPPVAEGETMRFHVL 334 Query: 361 EGGQHNFSASTGKR 374 H F+ ++GKR Sbjct: 335 PSALHPFNQASGKR 348 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: 344 Number of extensions: 7 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: 354 Length adjustment: 30 Effective length of query: 346 Effective length of database: 324 Effective search space: 112104 Effective search space used: 112104 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 24 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