Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate GFF726 PGA1_c07410 binding protein dependent transport system permease
Query= reanno::WCS417:GFF4323 (302 letters) >FitnessBrowser__Phaeo:GFF726 Length = 315 Score = 139 bits (349), Expect = 1e-37 Identities = 90/297 (30%), Positives = 154/297 (51%), Gaps = 12/297 (4%) Query: 8 SKASPFDALQRWL--------PKLVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLPTYKW 59 S A+ A + WL P L LAP + L IL +F LSF L ++ Sbjct: 12 SSATSPGASESWLRRNRQALAPWLFLAPGVIFFLFYVIFPILQSFNLSFYRWDGLGDPQF 71 Query: 60 AGLAQYARLFDNDRWWVASKNLAVFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLY 119 G+ Y L D+ + V+ N + +++ + + G+ +A+FL+Q + ++++ + Sbjct: 72 IGMENYRELMDDRAFEVSLWNNLKWLLLYL-LAIPAGLFIALFLNQTVTGIRLYKSLFFF 130 Query: 120 PMALSMIVTGTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASG 179 P +S +V G + W +P GL + W G ++ L DP V Y ++IA +W + Sbjct: 131 PFVISQVVVGLVFSWFYDPTFGLLNQVLAWVGLG-PINVLGDPTLVTYGIIIAGLWPQTA 189 Query: 180 FIMAMFLAGLRGVDQSIVRAAQIDGASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFD 239 + M ++L GL VD V AA++DGA ++ W V++P LRP F A ++ A++SFD Sbjct: 190 YCMILYLTGLNAVDPEQVEAARLDGAKGAKMLWYVIIPQLRPATFVAFVVTIIGALRSFD 249 Query: 240 LVAAMTAGGPGYSSDLPAMFMYSFTFSR--GQMGMGSASAILMLGAILAIIVPYLYS 294 L++ MT GGP SS + + +M+ S +MG G+A A+++ +L I +L+S Sbjct: 250 LISIMTNGGPFGSSRVLSFYMFEKALSEYGFRMGYGAAIAVVLFLIMLCFIAYFLWS 306 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: 311 Number of extensions: 21 Number of successful extensions: 4 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: 315 Length adjustment: 27 Effective length of query: 275 Effective length of database: 288 Effective search space: 79200 Effective search space used: 79200 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