Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 304 bits (778), Expect = 3e-87 Identities = 159/356 (44%), Positives = 241/356 (67%), Gaps = 3/356 (0%) Query: 1 MSALEIRNIRKRY-GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGD 59 M+ L+++ + K + G+ + +K + + + GEF+V++G SGCGKSTLL ++AGL + GD Sbjct: 1 MAGLKLQAVTKSWDGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGD 60 Query: 60 ILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTAR 119 I I ++ V + PKDR IAMVFQ+YALYP++SV N+ +GL++R + + + + V++ AR Sbjct: 61 IWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAAR 120 Query: 120 LLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRL 179 +L+++ LL R+P +LSGGQRQRVA+GRA+VR+P VFLFDEPLSNLDAKLR++MR EL++L Sbjct: 121 ILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQL 180 Query: 180 HQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPM 239 H+ L+TT +YVTHDQ+EAMTLA R+ VM G EQ+ P EVY++PA+L+VA F+GSP M Sbjct: 181 HRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAM 240 Query: 240 NILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTAS 299 N+L + G E + + LP +AGR++ +GIRPE + L++ +E + Sbjct: 241 NLLTGRVNNEGTHFE-LDGGIELPLNGGYRQYAGRKMTLGIRPEHIALSSQAEG-GVPMV 298 Query: 300 VEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGR 355 ++ +E+ G + + G Q++ L + GS LHLFD E+G+ Sbjct: 299 MDTLEILGADNLAHGRWGEQKLVVRLAHQERPTAGSTLWLHLAENQLHLFDGETGQ 354 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: 363 Number of extensions: 13 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: 360 Length of database: 356 Length adjustment: 29 Effective length of query: 331 Effective length of database: 327 Effective search space: 108237 Effective search space used: 108237 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: 49 (23.5 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