Align LacK, component of Lactose porter (characterized)
to candidate 3607842 Dshi_1250 ABC transporter related (RefSeq)
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__Dino:3607842 Length = 351 Score = 373 bits (958), Expect = e-108 Identities = 210/364 (57%), Positives = 253/364 (69%), Gaps = 15/364 (4%) Query: 1 MAEVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGEL 60 M+ + L K YG +V+ GV+L ++ GEF VFVGPSGCGKSTLLRMIAGLE+ S G + Sbjct: 1 MSGITLRGAVKRYGETQVVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEGSI 60 Query: 61 TIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKI 120 IG + +DPS+RG+AMVFQTYALYPHMTV ENMGF L+ G+ K EI+ +V AA++I Sbjct: 61 HIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAASEI 120 Query: 121 LELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLH 180 L+LD + RKPKALSGGQRQRVAIGRAIVR P+VFLFDEPLSNLDAELRV MRVEIARLH Sbjct: 121 LKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLH 180 Query: 181 KELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMN 240 KE+ AT++YVTHDQVEAMTLADKIVV+R G VEQVGAPL LY DPDN+FVAGFIGSP MN Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFIGSPAMN 240 Query: 241 FLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDTQL 300 FL + A V L P L V A G VTVGVRP+H GD L Sbjct: 241 FLDGRIENDA------VHLAGLP--PLPVPGAAGRSG--PVTVGVRPQHIALEPGGDGYL 290 Query: 301 TAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFDA-SG 359 V++ E LG SY+Y G ++ +E E G + + ++ LF+A +G Sbjct: 291 ---VELTESLGGVSYLYLRGADGSRLTVEAGEEDPIAE-GTPVGLSLAPDRVMLFEAETG 346 Query: 360 RRIR 363 +R+R Sbjct: 347 QRLR 350 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: 406 Number of extensions: 17 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: 363 Length of database: 351 Length adjustment: 29 Effective length of query: 334 Effective length of database: 322 Effective search space: 107548 Effective search space used: 107548 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 17 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