Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 267 bits (683), Expect = 3e-76 Identities = 151/347 (43%), Positives = 212/347 (61%), Gaps = 11/347 (3%) Query: 4 LEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63 +EIR++RK YG V+ ++G+ ++E G+ LV+LG SGCGK+TLL +IAGL + G I I Sbjct: 3 IEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIA 62 Query: 64 ERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQI 123 V + P R+I+MVFQSYAL+P+L+V NI FGL++R+VP E ++ ++ LL + Sbjct: 63 GTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGL 122 Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183 LD KP +LSGG +QRVA+GRA++ V L DEPLSNLDAKLR MR E+ L + L Sbjct: 123 SGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRL 182 Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILD 243 T++YVTHDQ+EAMT+A RI +MRDG+I Q +P+ Y+RPA +VA F+G+PPMNI+ Sbjct: 183 GITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIVP 242 Query: 244 AEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASVEVV 303 T G +E +L F G R GIRPE LRLA + +T Sbjct: 243 LCPTQGGAALEPGGRLL-----FPG--MDPDRYLFGIRPENLRLAESGQPAMVTGR---- 291 Query: 304 ELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFD 350 E G + + + Q + R + G+ T+D ++LFD Sbjct: 292 EYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFD 338 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: 365 Number of extensions: 17 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: 365 Length adjustment: 29 Effective length of query: 331 Effective length of database: 336 Effective search space: 111216 Effective search space used: 111216 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