Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate SMc04395 SMc04395 ABC transporter permease
Query= reanno::WCS417:GFF4323 (302 letters) >FitnessBrowser__Smeli:SMc04395 Length = 292 Score = 360 bits (923), Expect = e-104 Identities = 168/282 (59%), Positives = 220/282 (78%) Query: 16 LQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLPTYKWAGLAQYARLFDNDRWW 75 LQ LPKLVLAPS IVLV YG+I +T LS T+S LP+Y + GL+ Y+RL+ WW Sbjct: 7 LQELLPKLVLAPSFLIVLVFVYGFIAYTGFLSMTDSKMLPSYNFVGLSNYSRLWALPHWW 66 Query: 76 VASKNLAVFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAWKWL 135 A NLA+F ++I + V+G+ LAI LDQKIR EGF+R +YLYPMALS IVTGTAWKW Sbjct: 67 RAVSNLAIFATLYIAVCSVLGLALAILLDQKIRAEGFLRPVYLYPMALSFIVTGTAWKWF 126 Query: 136 LNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQS 195 L+PG+GL+ + WGWE F +W+ D + +YC+VIAAVWQ++GFIMAMFLAGLRGVD Sbjct: 127 LDPGIGLENTMHLWGWESFSFNWIKDRNYAIYCVVIAAVWQSTGFIMAMFLAGLRGVDNE 186 Query: 196 IVRAAQIDGASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAGGPGYSSDL 255 I++AAQIDGA+ P IY +++P +RPVF SA ++LAH+AIK++DL+ A+T GGPG +++L Sbjct: 187 IIKAAQIDGATTPTIYRRIIIPLMRPVFLSAFVVLAHLAIKAYDLIIALTGGGPGQATEL 246 Query: 256 PAMFMYSFTFSRGQMGMGSASAILMLGAILAIIVPYLYSELR 297 PA FMYS+TF+R QM +G++SAI+ML I +IIVPYLYSE+R Sbjct: 247 PATFMYSYTFTRNQMAIGASSAIVMLVMIFSIIVPYLYSEVR 288 Lambda K H 0.330 0.141 0.455 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: 365 Number of extensions: 17 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: 302 Length of database: 292 Length adjustment: 26 Effective length of query: 276 Effective length of database: 266 Effective search space: 73416 Effective search space used: 73416 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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