Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate WP_007695788.1 C447_RS16060 sugar ABC transporter permease
Query= reanno::WCS417:GFF4323 (302 letters) >NCBI__GCF_000336675.1:WP_007695788.1 Length = 324 Score = 150 bits (378), Expect = 5e-41 Identities = 94/267 (35%), Positives = 145/267 (54%), Gaps = 6/267 (2%) Query: 32 VLVGF--YGYILWTFVLSFTNSTFLPTYKWAGL--AQYARLFDNDRWWVASKNLAVFGGM 87 V++GF YG I W ++S T+ T + + L Y + + AS+N V + Sbjct: 51 VIMGFFVYGGIGWNLLVSLTDYTGFGSADYGDLDFEMYVQALSSPDVIAASRNTFVLLVV 110 Query: 88 FIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAWKWLLNPGMGLDKLLR 147 F + LV+G+ LAI LD++IR + I+TIYL PMALS +VT W W+ N G+ ++ Sbjct: 111 FTAVCLVLGLALAIVLDRQIRFKEQIQTIYLLPMALSFVVTAQFWLWMYNYNSGVINIIL 170 Query: 148 DWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQSIVRAAQIDGASM 207 D G R+ ++ DP V+ ++ A +WQ SG+ M ++L+GL+ + Q AA DGAS Sbjct: 171 DAVGIG-RIQFIGDPRFVLGAVIFALIWQFSGYTMIVYLSGLQSIPQDQFEAAATDGAST 229 Query: 208 PRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAG-GPGYSSDLPAMFMYSFTFS 266 +IYW V++P L+ SA ++L A+K+F + +M P SD+ A M F Sbjct: 230 VKIYWRVIIPQLKSASVSAAVVLMIFALKAFTFLYSMFGTYRPPNGSDILATLMVRQAFK 289 Query: 267 RGQMGMGSASAILMLGAILAIIVPYLY 293 + +A A L+L L +I PYLY Sbjct: 290 FQEWSYAAAVATLLLLMALVVIGPYLY 316 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: 282 Number of extensions: 19 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: 302 Length of database: 324 Length adjustment: 27 Effective length of query: 275 Effective length of database: 297 Effective search space: 81675 Effective search space used: 81675 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 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