Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >FitnessBrowser__psRCH2:GFF16 Length = 278 Score = 251 bits (640), Expect = 2e-71 Identities = 138/254 (54%), Positives = 170/254 (66%), Gaps = 2/254 (0%) Query: 7 PSNTQPLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQ 66 P QPL+ G+ K+YG L VL G+DL ++ G V +IG SGSGK+TLLR + LE Sbjct: 18 PEQAQPLVRFAGVTKRYGELTVLDGLDLQIEEGEKVAIIGPSGSGKSTLLRVLMTLEGID 77 Query: 67 GGQIVLDGESIGY-DDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGLL 125 G I +DGE + + D G+ V + + R R GM FQ FNLFPH+ ALQNV + Sbjct: 78 EGVIEVDGEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPV 137 Query: 126 KVKKLPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEV 185 +V L K EA AE+ L VGL ++ +HFP QLSGGQQQRVAIARA+AM P +MLFDEV Sbjct: 138 QVLGLSKAEARGRAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEV 197 Query: 186 TSALDPELVGEVLNVIKGLAE-DGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKE 244 TSALDPEL GEVLNVI+ L E +TML+VTH+M FA E +D++ F +QGRI EQG P E Sbjct: 198 TSALDPELCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDE 257 Query: 245 LFERPQSPRLAEFL 258 LF PQ R EFL Sbjct: 258 LFNNPQEERTREFL 271 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: 238 Number of extensions: 8 Number of successful extensions: 3 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: 278 Length adjustment: 25 Effective length of query: 238 Effective length of database: 253 Effective search space: 60214 Effective search space used: 60214 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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