Align LacK, component of Lactose porter (characterized)
to candidate YP_001312901.1 Smed_4163 ABC transporter-like protein
Query= TCDB::Q01937 (363 letters) >NCBI__GCF_000017145.1:YP_001312901.1 Length = 361 Score = 383 bits (983), Expect = e-111 Identities = 201/360 (55%), Positives = 255/360 (70%), Gaps = 8/360 (2%) Query: 4 VRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGELTIG 63 V L+DIRKSYG+LEVI G++L + G+FVVFVGPSGCGKSTLLRMIAGLE+++ GE+ I Sbjct: 10 VVLSDIRKSYGNLEVIHGIDLTIEEGDFVVFVGPSGCGKSTLLRMIAGLEEVTEGEIAIK 69 Query: 64 GTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKILEL 123 G + D+DPS+RGIAMVFQ+YALYPHM+V EN+GF L+ A +IERRV + IL++ Sbjct: 70 GRDVTDLDPSERGIAMVFQSYALYPHMSVGENLGFGLKMARTDPADIERRVAQVSAILKI 129 Query: 124 DALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLHKEL 183 D L+DR+P LSGGQRQRVAIGRAIVR+PDVFLFDEPLSNLDAELRV MR+EIARLH+EL Sbjct: 130 DPLLDRRPGQLSGGQRQRVAIGRAIVRKPDVFLFDEPLSNLDAELRVSMRIEIARLHREL 189 Query: 184 NATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMNFLP 243 T++YVTHDQ EAMTLAD+IVV+R G +EQ G+P +Y+DP NMFVAGFIGSPRMNFL Sbjct: 190 GNTMIYVTHDQTEAMTLADQIVVLRDGRIEQTGSPREVYEDPANMFVAGFIGSPRMNFLE 249 Query: 244 AVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDTQLTAH 303 A G + AL A D + GD + +G+RPEH G ++ A Sbjct: 250 AEWQGDGTVHIGSAALWAPID-------GSSLAPGDRLRLGMRPEHLTVCEPGAERIAAQ 302 Query: 304 VDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFDASGRRIR 363 V+ E+LG T Y+Y G+ +++EQ E + G+ ++ + F GRR+R Sbjct: 303 VEFSEYLGGTRYLYCQLEDGQSLVVEQRE-GPDWQVGERLSFSVPEDRRRFFAGDGRRLR 361 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: 390 Number of extensions: 18 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: 361 Length adjustment: 29 Effective length of query: 334 Effective length of database: 332 Effective search space: 110888 Effective search space used: 110888 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