Align Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate GFF4323 PS417_22140 sugar ABC transporter permease
Query= TCDB::Q72KX3 (369 letters) >FitnessBrowser__WCS417:GFF4323 Length = 302 Score = 118 bits (296), Expect = 2e-31 Identities = 78/205 (38%), Positives = 119/205 (58%), Gaps = 16/205 (7%) Query: 176 LVVGLVL-LYVAYTAYREGERRRA-LWGLASA----GVLLLWAFAFGQGL-RLLPYPEVH 228 LV+G+ L +++ REG R L+ +A + G W G GL +LL Sbjct: 93 LVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAWKWLLNPGMGLDKLLRDWGWE 152 Query: 229 GFSL--------ALVGVILAAVWQMSGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFR 280 GF L + +++AAVWQ SG+ MA++LAGLRG+ ++ AA++DGAS +++ Sbjct: 153 GFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQSIVRAAQIDGASMPRIYW 212 Query: 281 RVIFPMLAPITLSAMIVLGHIALKIFDLVFAM-AGLDYAPTDVPAIYMYLLAFRGNQFAK 339 V+ P L P+ SA+++L HIA+K FDLV AM AG +D+PA++MY F Q Sbjct: 213 SVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGM 272 Query: 340 GAAIGILLLLLVAVVVVPYLATQLR 364 G+A IL+L + ++VPYL ++LR Sbjct: 273 GSASAILMLGAILAIIVPYLYSELR 297 Score = 87.4 bits (215), Expect = 4e-22 Identities = 57/160 (35%), Positives = 84/160 (52%), Gaps = 11/160 (6%) Query: 4 RILAFLVLLPSVLAVGVFVYGFIGQNLWVSLTDWGKDPAQALALRPELRFVGLENYRELF 63 R L LVL PS+ V V YG+I LW + + P ++ GL Y LF Sbjct: 18 RWLPKLVLAPSMFIVLVGFYGYI---LWTFVLSFTNS-----TFLPTYKWAGLAQYARLF 69 Query: 64 TGFVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFV 123 + R+ + NL F F+ +L +G+ LA+ +D+ R EGF RT++L+PMALS + Sbjct: 70 D---NDRWWVASKNLAVFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMI 126 Query: 124 VTGTIWRWLLQPQGGVNVLPTLFGLPPLSFPWLATREQVL 163 VTGT W+WLL P G++ L +G WL ++V+ Sbjct: 127 VTGTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVV 166 Lambda K H 0.331 0.146 0.458 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: 338 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 369 Length of database: 302 Length adjustment: 28 Effective length of query: 341 Effective length of database: 274 Effective search space: 93434 Effective search space used: 93434 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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