Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_109939172.1 DLD82_RS00420 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_2050 (263 letters) >NCBI__GCF_003173335.1:WP_109939172.1 Length = 376 Score = 147 bits (372), Expect = 2e-40 Identities = 84/243 (34%), Positives = 141/243 (58%), Gaps = 10/243 (4%) Query: 19 LRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIMLDGESIG 78 +R++ G + LK + S+++G + L+G SG GK+TLLRC+N L G I+LDGE I Sbjct: 14 IRERTGHVVALKNISFSVKKGEIFVLMGLSGCGKSTLLRCLNRLISPTAGSILLDGEDIA 73 Query: 79 YDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPKDEAVAL 138 + +R+R R+ GM FQ F L PH NV GL +++ + +E + Sbjct: 74 --SVSTERMR------TIRRSRMGMVFQSFALLPHKNIQDNVAFGL-EIQGISAEERAGI 124 Query: 139 AEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPELVGEVL 198 A++ L+ VGL + +P QLSGG +QRV +ARAIA +P ++L DE SALDP + ++ Sbjct: 125 AKETLDLVGLSGYENSYPDQLSGGMKQRVGLARAIASSPDILLMDEAFSALDPMIRRDMQ 184 Query: 199 NVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSPRLAEF 257 N + + + T++ V+H++ A ++ +I M G I + G P+E+ +P++ + F Sbjct: 185 NELLDIQDRLEKTIIFVSHDLDEALKLGTRIGLMKAGEIVQIGTPEEILTQPKNEFVERF 244 Query: 258 LKN 260 +++ Sbjct: 245 VED 247 Lambda K H 0.320 0.138 0.392 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: 226 Number of extensions: 11 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: 263 Length of database: 376 Length adjustment: 27 Effective length of query: 236 Effective length of database: 349 Effective search space: 82364 Effective search space used: 82364 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