Align LacK, component of Lactose porter (characterized)
to candidate WP_048081463.1 EJ01_RS05505 molybdenum ABC transporter ATP-binding protein
Query= TCDB::Q01937 (363 letters) >NCBI__GCF_000745485.1:WP_048081463.1 Length = 361 Score = 169 bits (427), Expect = 1e-46 Identities = 89/273 (32%), Positives = 151/273 (55%), Gaps = 7/273 (2%) Query: 19 IKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGELTIGGTVMNDVDPSKRGIA 78 + VNL + ++V +GP+G GKS LL IAG G++ + G + +++P RGI+ Sbjct: 17 LDNVNLSLDKNSYMVIIGPTGSGKSVLLETIAGFYRAEKGKIFLEGKEITELNPENRGIS 76 Query: 79 MVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKILELDALMDRKPKALSGGQ 138 +V+Q Y L+PHM + EN+ + L+ ++ I+ +V AK+L++D L+ R P LSGG+ Sbjct: 77 IVYQDYVLFPHMNIFENISYGLKKKTKDEEIIKSKVLKMAKLLKIDHLLHRNPDTLSGGE 136 Query: 139 RQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLHKELNATIVYVTHDQVEAM 198 +QR AI R+++ +P + L DEP S +D ++ I + + T ++VTH+ + Sbjct: 137 KQRTAIARSLIVEPRILLMDEPFSAVDVSTHAYLTKLIKNVIADYETTCIHVTHNFNDVW 196 Query: 199 TLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMNFLPAVVIGQAEGGQVTVA 258 LADK+ VM+ G + Q P ++ P + FVA F+G N +I + EG + Sbjct: 197 NLADKVAVMKEGKILQQDIPTEVFSKPSHNFVADFVGI--HNIFEGEII-EKEGSLTKIK 253 Query: 259 LKARPDTQLTVACATPPQGGDAVTVGVRPEHFL 291 L D+ L V + + + VG+RPE+ + Sbjct: 254 L----DSDLIVYSSDSSEDSGKILVGIRPENVI 282 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: 243 Number of extensions: 6 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