Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 158 bits (399), Expect = 3e-43 Identities = 95/275 (34%), Positives = 148/275 (53%), Gaps = 15/275 (5%) Query: 13 YGEVETLKGIDIA---LESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIGERSVLG 69 + + ET G+ A + GE V++G SG GKST++ ++ L EP+ G +LI ++ Sbjct: 37 FEKTETTVGVQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVA 96 Query: 70 VHP------KDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQI 123 ++ + ++MVFQS+AL P+++V +N FGLEM V + ++ + + Sbjct: 97 MNDDQLVKVRRAKLSMVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGL 156 Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183 E + P +LSGG +QRV + R L +P + L DE S LD +R EM+ EL +L Sbjct: 157 EAWAESMPDELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKA 216 Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYV-AGFVGSPPMNIL 242 + T+V+++HD EAM + RIA+M GR+ Q+ P+E+ PA YV A F G P NIL Sbjct: 217 KRTIVFISHDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRGVDPTNIL 276 Query: 243 DAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVK 277 A A ++ +P+ N A R VK Sbjct: 277 TAGDIATQTQV-----TIPITDGKNPRAGLQRLVK 306 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: 343 Number of extensions: 15 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: 415 Length adjustment: 30 Effective length of query: 330 Effective length of database: 385 Effective search space: 127050 Effective search space used: 127050 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: 50 (23.9 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