Align LacK, component of Lactose porter (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= TCDB::Q01937 (363 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 231 bits (589), Expect = 2e-65 Identities = 138/361 (38%), Positives = 196/361 (54%), Gaps = 15/361 (4%) Query: 3 EVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGELTI 62 ++RLT + K +GS + GV+L ++ G F +G SGCGK+T LRMI+GLE ++G + + Sbjct: 18 DLRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHL 77 Query: 63 GGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKILE 122 G + D P +R + VFQ YAL+PH+ + EN+ F LR G+ +++ V ++E Sbjct: 78 GDQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGIRS--VKKPVEDMLDLVE 135 Query: 123 LDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLHKE 182 L L RKP LSGGQ+QR+A+ RA++ QP V L DEPL LD +LR M++E+ R+ E Sbjct: 136 LGHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLE 195 Query: 183 LNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMNFL 242 + T V+VTHDQ EAMT+AD I VM G +EQ+G+P LY++P+ FVA F+G L Sbjct: 196 VGLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQSN---L 252 Query: 243 PAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPA------GSG 296 A + G V VA R C T V +GVRPE A SG Sbjct: 253 IAGTVESVSGDVVQVAAHGRSLALPAARCRTT---SGPVILGVRPEKVRIAKTEAEVPSG 309 Query: 297 DTQLTAHVDVVEHLGNTSYVYAHTVPGEQI-IIEQEERRHGGRYGDEIAVGISAKTSFLF 355 LT V +G ++ GE++ + EQ + R G E+ V F Sbjct: 310 ANHLTGKVTDASFIGVSTQYLVELPSGEELAVFEQNTGQEIQRPGAEVVVHWDPSQGFGL 369 Query: 356 D 356 D Sbjct: 370 D 370 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: 321 Number of extensions: 15 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: 386 Length adjustment: 30 Effective length of query: 333 Effective length of database: 356 Effective search space: 118548 Effective search space used: 118548 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: 50 (23.9 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