Align LacK, component of Lactose porter (characterized)
to candidate H281DRAFT_04155 H281DRAFT_04155 sorbitol ABC transporter ATP-binding protein /mannitol ABC transporter ATP-binding protein
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__Burk376:H281DRAFT_04155 Length = 369 Score = 384 bits (986), Expect = e-111 Identities = 208/360 (57%), Positives = 253/360 (70%), Gaps = 3/360 (0%) Query: 1 MAEVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGEL 60 MA V L +IRK+Y EV++ +NL+++ GEFVVFVGPSGCGKSTL+RMIAGLEDIS G+L Sbjct: 1 MASVTLRNIRKAYDDTEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60 Query: 61 TIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKI 120 TI GT MNDV P+KRGIAMVFQ+YALYPHMT+ +NM F L+ AG K EI+ V AAKI Sbjct: 61 TINGTRMNDVPPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI 120 Query: 121 LELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLH 180 L +D L+DRKPK LSGGQRQRVAIGRAI R+P VFLFDEPLSNLDA LRV MR+E ARLH Sbjct: 121 LHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLH 180 Query: 181 KELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMN 240 EL T++YVTHDQVEAMTLADKIVV+ G +EQVG+P LY P N FVAGFIGSP+MN Sbjct: 181 DELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMN 240 Query: 241 FLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDTQL 300 F+ VV G VTV + ++ V Q GD VTVG+RPEH L G D + Sbjct: 241 FMEGVVQSVTHDG-VTVRYETGETQRVAVEPGAVKQ-GDKVTVGIRPEH-LHVGMTDDGV 297 Query: 301 TAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFDASGR 360 +A VE LG+ +Y+YA + +I + G+ +G + + LFD+ G+ Sbjct: 298 SARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHAKGETQKLGATPEHCHLFDSEGK 357 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: 430 Number of extensions: 20 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: 369 Length adjustment: 30 Effective length of query: 333 Effective length of database: 339 Effective search space: 112887 Effective search space used: 112887 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