Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_000017185.1:WP_011974043.1 Length = 238 Score = 144 bits (363), Expect = 2e-39 Identities = 90/241 (37%), Positives = 143/241 (59%), Gaps = 15/241 (6%) Query: 5 QVSTQNASQALLEIRDLHKQYGPLE----VLKGVDLTMQRGNVVTLIGSSGSGKTTLLRC 60 ++ + + L+E +++ K YG E VL+G++L ++ G V ++G SG GK+TLL Sbjct: 7 KIENKIEKKELIEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNI 66 Query: 61 VNMLEEFQGGQILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQ 120 + +L+ G + + G+ N + V R ++G FQQFNL LTAL+ Sbjct: 67 LGLLDVPNKGMVYIKGKKTTMFSENDRAVFR--------RKISGFIFQQFNLINTLTALE 118 Query: 121 NVTLGLLKVKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPS 180 NV L L+ +K +K+ + A+K L+ + L R ++YP QLSGGQQQRVAIARA++ NP Sbjct: 119 NVELPLVLDEK-NKNYRIKKAKKLLKIINLGHRENYYPNQLSGGQQQRVAIARALSNNPK 177 Query: 181 LMLFDEVTSALDPELVGEVLSVIKGLAE-DGMTMLLVTHEMRFAFEVSDKIVFMNQGRIE 239 ++ DE T LD + EV+ ++K L E +G+T+++VTHE FA + + +I+ M G I Sbjct: 178 IIFADEPTGNLDSKNSREVMDILKELNEKEGITVIMVTHEPEFA-KYASRIINMKDGEIV 236 Query: 240 E 240 E Sbjct: 237 E 237 Lambda K H 0.319 0.135 0.379 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: 132 Number of extensions: 7 Number of successful extensions: 4 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: 265 Length of database: 238 Length adjustment: 24 Effective length of query: 241 Effective length of database: 214 Effective search space: 51574 Effective search space used: 51574 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: 46 (22.3 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