Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 305 bits (780), Expect = 2e-87 Identities = 170/365 (46%), Positives = 229/365 (62%), Gaps = 4/365 (1%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M + + ++ F V+ L + EF+VL+G SGCGKST L IAGL +V+ G+I Sbjct: 1 MAEIKLDQVNKRFKKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEI 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I R V PKDR I MVFQSYALYP M V KN++FGL +P EI++RVK+A+EI Sbjct: 61 SIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEI 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 L I LL+R+P++LSGGQRQRVA+GRA+VRD FLFDEPLSNLDAKLR ++R E+ +LH Sbjct: 121 LGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLH 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 + L++T++YVTHDQIEA+TLADRI VMK G I Q+ P+ +Y P N FVAGFIGSPSMN Sbjct: 181 ERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMN 240 Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHT-RLQPGQKVVLGLRPEHVKV---DEARDG 296 F + + G +V V + A R + V+ G+RPE VK D +G Sbjct: 241 FLDVRLVEEAGDLWVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVKERPGDALPEG 300 Query: 297 EPTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAE 356 +A VD+ EP+G++ ++ T + + RI+ + L+ +M +FD E Sbjct: 301 VEPLRAEVDVREPIGSEVIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMHLFDPE 360 Query: 357 SENRL 361 SE L Sbjct: 361 SEQAL 365 Lambda K H 0.320 0.137 0.392 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: 387 Number of extensions: 11 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: 361 Length of database: 368 Length adjustment: 29 Effective length of query: 332 Effective length of database: 339 Effective search space: 112548 Effective search space used: 112548 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 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