Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000744815.1:WP_037573817.1 Length = 369 Score = 211 bits (536), Expect = 3e-59 Identities = 121/324 (37%), Positives = 191/324 (58%), Gaps = 18/324 (5%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M + ++++ G A+D +++ I +GE ++GPSG GK+T +R++AGL+ + G Sbjct: 1 MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 + +R V +PP+DR I MVFQ +ALYP++T +N+ F L ++K EIR + Sbjct: 61 AIRIGERDVTH-----LPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSK 115 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 VEE AKILD+ L+ P+ LSGGQ+QRVA+ RA+V++P + L+DEP SNLDA++R S R Sbjct: 116 VEEAAKILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTR 175 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 + +Q RLG+T + V+HD + + DRV VL G L QV P ++YD P ++ VA Sbjct: 176 TQIAGLQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGF 235 Query: 241 IGE--INELEGKVTNEGVVIGSLRFPVS--------VSSDRAI-IGIRPE--DVKLSKDV 287 IG +N +E +T+ GV G VS + D+ + +G+RPE D+ + Sbjct: 236 IGSPAMNLVEVPITDGGVKFGESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEG 295 Query: 288 IKDDSWILVGKGKVKVIGYQGGLF 311 +D + V V+ +G G ++ Sbjct: 296 GGEDKGLAVTVNVVEELGADGYVY 319 Lambda K H 0.319 0.139 0.390 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: 287 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: 353 Length of database: 369 Length adjustment: 29 Effective length of query: 324 Effective length of database: 340 Effective search space: 110160 Effective search space used: 110160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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