Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_109939631.1 DLD82_RS02995 ATP-binding cassette domain-containing protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_003173335.1:WP_109939631.1 Length = 378 Score = 132 bits (333), Expect = 8e-36 Identities = 91/249 (36%), Positives = 137/249 (55%), Gaps = 23/249 (9%) Query: 16 LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75 L++ + K Y + + L++Q G ++TLIG SGSGKTT L+ +N L E G+IL++ Sbjct: 18 LDLTGVSKWYNNSCAVSYLTLSIQGGELITLIGGSGSGKTTTLKMINRLIEPDSGEILIN 77 Query: 76 GESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHKD 135 G++ + N +R S G QQ LFPH++ +N+++ L + K+H+D Sbjct: 78 GQN--FLSFNPVALRRS----------IGYVIQQIGLFPHMSVAENISIPLT-LGKVHQD 124 Query: 136 EAVVLAEKWLERVGLLER--RDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDP 193 ++ L V L RD P +LSGGQQQRV +ARA+A +P L+L DE ALDP Sbjct: 125 RIRNRIDELLTLVSLSPDTFRDRKPSELSGGQQQRVGLARALAADPPLLLMDEPFGALDP 184 Query: 194 ----ELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFE 249 +L E L + K L G T++ VTH++ AF +SD+I + +G + P EL Sbjct: 185 LLRRQLQEEFLRIKKSL---GKTIIFVTHDIDEAFLLSDRIAVLREGSLHALTTPPELLV 241 Query: 250 RPQS-PRLA 257 Q+ P LA Sbjct: 242 AAQNDPYLA 250 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: 226 Number of extensions: 10 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: 378 Length adjustment: 27 Effective length of query: 238 Effective length of database: 351 Effective search space: 83538 Effective search space used: 83538 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