Align LacK, component of Lactose porter (characterized)
to candidate WP_085638891.1 MGEO_RS13900 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q01937 (363 letters) >NCBI__GCF_002115805.1:WP_085638891.1 Length = 362 Score = 332 bits (852), Expect = 7e-96 Identities = 184/357 (51%), Positives = 237/357 (66%), Gaps = 6/357 (1%) Query: 1 MAEVRLTDIRKSY-GSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGE 59 MA ++LT++ K+Y G++ V+ +NL++ GE +VFVGPSGCGKSTLLRMIAGLE I+ G Sbjct: 1 MANLKLTNVEKTYAGAVNVLNNINLDIEKGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 60 Query: 60 LTIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAK 119 L I G V+ND+ P+ RGIAMVFQ+YALYPHMTVRENM FAL+ A + EI+ V AAK Sbjct: 61 LEIDGQVVNDMPPAMRGIAMVFQSYALYPHMTVRENMSFALKIAKKPQSEIDAAVERAAK 120 Query: 120 ILELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARL 179 +L+LD +DR PKALSGGQRQRVAIGR+IVR P V+LFDEPLSNLDA LRV R+EIA+L Sbjct: 121 MLQLDPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180 Query: 180 HKEL-NATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPR 238 +++ +T++YVTHDQVEAMTLA +IVV+ + QVGAPL LY+ P++ FVA FIGSP Sbjct: 181 KEQMPESTMIYVTHDQVEAMTLASRIVVLANKGIAQVGAPLELYERPNSEFVAQFIGSPS 240 Query: 239 MNFLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDT 298 MN LP ++G GQ T ++ T G V VGVRPE F+ SGD Sbjct: 241 MNLLPGEIVGT---GQQTTVKMDGGGVAVSDYPTTDADMGLKVNVGVRPEDFV-GTSGDH 296 Query: 299 QLTAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLF 355 V++ E LG + +Y +I + H G + +G S +F Sbjct: 297 IFEGRVEITEALGEVTLLYFEKQGDGHAVIGKLPGIHAELRGKTVKLGASPDKVHIF 353 Lambda K H 0.320 0.137 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: 387 Number of extensions: 17 Number of successful extensions: 3 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: 363 Length of database: 362 Length adjustment: 29 Effective length of query: 334 Effective length of database: 333 Effective search space: 111222 Effective search space used: 111222 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 (21.8 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