Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_000230695.2:WP_015448118.1 Length = 255 Score = 138 bits (347), Expect = 2e-37 Identities = 85/233 (36%), Positives = 128/233 (54%), Gaps = 11/233 (4%) Query: 11 KRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIGERSVL-- 68 KRYG ++ L+ + +A +G L+GSSG GKST+L ++ GL P G + + R + Sbjct: 19 KRYGRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQRS 78 Query: 69 GVHPKDRDIAMVFQSYALYPNLSVARNIGF-----GLEMRRVPQAEHDKAVRDTARLLQI 123 V P R + V Q L+P+L+ N+ G R+ Q +A + A Sbjct: 79 DVLPLRRRVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQ----RAEQLAALTHLP 134 Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183 +L+R P++LSGGQRQRVA+ RAL+ +P L DEPL LD +R E++ ELK++ L Sbjct: 135 TGVLERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIFDQL 194 Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGS 236 TV+ VTHD EA A R+ ++R G + Q ++ +RPA +V FV + Sbjct: 195 GKTVIVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRFVAA 247 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: 212 Number of extensions: 13 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: 255 Length adjustment: 27 Effective length of query: 333 Effective length of database: 228 Effective search space: 75924 Effective search space used: 75924 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. 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