Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_009490034.1 MICLODRAFT_RS06000 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SMc02869 (352 letters) >NCBI__GCF_000262405.1:WP_009490034.1 Length = 361 Score = 338 bits (866), Expect = 2e-97 Identities = 185/349 (53%), Positives = 231/349 (66%), Gaps = 23/349 (6%) Query: 17 VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76 +G++ ++ +RK++G+ EVL G+ L +KDGEFV VGPSGCGKSTLLR IAGLED T G + Sbjct: 1 MGTVDIRNVRKSYGNVEVLHGVALHIKDGEFVALVGPSGCGKSTLLRMIAGLEDVTEGDI 60 Query: 77 QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136 I V HVAP R IAMVFQ+YALYPH+ V++NMG L+Q +PK EIE +V AA + Sbjct: 61 VISDRVVNHVAPKDRNIAMVFQNYALYPHMNVRENMGFALRQRRMPKPEIESRVDNAARI 120 Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196 L LE L R+P LSGGQRQRVA+GRAIVREP +FLFDEPLSNLDA LRV R EI LH Sbjct: 121 LGLEHLLDRKPRALSGGQRQRVAMGRAIVREPNVFLFDEPLSNLDAKLRVQMRSEIKELH 180 Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256 + LK T +YVTHDQ+EAMTLAD++VVLN G IEQ GSP+ELY+RPA+ FVA FIGSP MN Sbjct: 181 QRLKTTTVYVTHDQIEAMTLADRVVVLNGGIIEQQGSPLELYDRPASRFVAAFIGSPPMN 240 Query: 257 FIEA-------AKLGDGEA-------------KTIGIRPEHIGLSRESGDWKGKVIHVEH 296 FIE +L DG TIG+RPEH LS + W V VE Sbjct: 241 FIEGTVVDASNVRLDDGTTLNVPMTDLGGQARVTIGVRPEHFELS--NAGWPATVSVVEP 298 Query: 297 LGADTIIYIESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRFDADG 345 G++T I + ++ + + G +++H T +H FD +G Sbjct: 299 TGSETQITARM-SGQIVRILVRGRTFVRPGEVIHLTVPSDLIHIFDDNG 346 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: 367 Number of extensions: 22 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: 352 Length of database: 361 Length adjustment: 29 Effective length of query: 323 Effective length of database: 332 Effective search space: 107236 Effective search space used: 107236 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