Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_009764516.1 MICLODRAFT_RS24390 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SMc02869 (352 letters) >NCBI__GCF_000262405.1:WP_009764516.1 Length = 377 Score = 376 bits (965), Expect = e-109 Identities = 200/355 (56%), Positives = 250/355 (70%), Gaps = 27/355 (7%) Query: 22 LKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGV 81 LK ++K+FG +V+ G+DLDV+DGEFV+FVGPSGCGKSTLLR IAGLED T+G + IDG Sbjct: 6 LKNVQKSFGRVKVIHGVDLDVRDGEFVVFVGPSGCGKSTLLRLIAGLEDITAGELFIDGE 65 Query: 82 EVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSLEP 141 V + PA+RGIAMVFQSYALYPH+ V DNM GL+ A KA+I+ KV +AA +L ++ Sbjct: 66 RVNDLVPARRGIAMVFQSYALYPHMNVYDNMAFGLELAKASKAQIDAKVREAARLLQIDT 125 Query: 142 YLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSLKA 201 L R+P +LSGGQRQRVAIGRAIVR+PK+FLFDEPLSNLDAALRV TR+EIA+LH +A Sbjct: 126 LLDRKPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVQTRIEIAKLHNDTRA 185 Query: 202 TMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMNFIEA- 260 TMIYVTHDQVEAMTLAD+IVVLN GRIEQVG+P++LY+RPANLFVAGFIGSPQMNFIE Sbjct: 186 TMIYVTHDQVEAMTLADRIVVLNGGRIEQVGTPLDLYHRPANLFVAGFIGSPQMNFIECQ 245 Query: 261 -------------------------AKLGDGEAKTIGIRPEHIGLSRESGDWKGKVIHVE 295 A + GE T+G+RP+H+ +S + G G+V VE Sbjct: 246 VAGVGPDEVLVSLPSGGTLSVPVSPAAVQPGERITLGVRPDHVRVSPQGG-LSGRVELVE 304 Query: 296 HLGADTIIYIESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRFDADGRVIKS 350 LG + ++Y++ LTVR G+ R+ + S H F + G + S Sbjct: 305 ELGENHLLYVDVGQGRRLTVREPGDARHGAGSTIALEIDRESCHLFKSSGEALPS 359 Lambda K H 0.320 0.137 0.393 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: 438 Number of extensions: 18 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: 352 Length of database: 377 Length adjustment: 29 Effective length of query: 323 Effective length of database: 348 Effective search space: 112404 Effective search space used: 112404 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