Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 333 bits (854), Expect = 4e-96 Identities = 186/367 (50%), Positives = 246/367 (67%), Gaps = 12/367 (3%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+ +++ + KR+ + ++ + + EF+VL+G SGCGKST L +IAGL E + G+I Sbjct: 1 MAEIKLDQVNKRFKKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEI 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 IG R V V PKDRDIAMVFQSYALYP+++V +N+ FGL R VP+ E D+ V+ A + Sbjct: 61 SIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEI 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 L I +LL R+P+QLSGGQRQRVA+GRA+VR+PQ FLFDEPLSNLDAKLR++MR EL +LH Sbjct: 121 LGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLH 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 + L++T+VYVTHDQIEAMTLA RI VM+DG+I Q+ P EVY+RPA +VAGF+GSP MN Sbjct: 181 ERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMN 240 Query: 241 ILDAEMT--ANGLKIEGCEEVLPLP----AAFNGAAWAGRRVKVGIRPEALRLAAGSE-- 292 LD + A L ++G L +P AF G R V GIRPE ++ G Sbjct: 241 FLDVRLVEEAGDLWVDGESFRLKVPRHRAPAFRG--HVNRPVIFGIRPEDVKERPGDALP 298 Query: 293 --AQRLTASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFD 350 + L A V+V E G E++ TATVGS TA + P AV + + +HLFD Sbjct: 299 EGVEPLRAEVDVREPIGSEVIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMHLFD 358 Query: 351 PESGRSL 357 PES ++L Sbjct: 359 PESEQAL 365 Lambda K H 0.320 0.136 0.385 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: 356 Number of extensions: 10 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: 360 Length of database: 368 Length adjustment: 29 Effective length of query: 331 Effective length of database: 339 Effective search space: 112209 Effective search space used: 112209 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