Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate GFF2752 PGA1_c27950 ABC transporter permease protein
Query= TCDB::Q8RJU8 (307 letters) >FitnessBrowser__Phaeo:GFF2752 Length = 280 Score = 167 bits (424), Expect = 2e-46 Identities = 93/274 (33%), Positives = 153/274 (55%), Gaps = 10/274 (3%) Query: 39 NVFSHGILVLWAFMVVLPLLWAVMTSFKDDASIFGSPWSLPDKLHFDNWSRAW--TEAHM 96 ++ +HG L+ + + + P+ ++ SFK +IF P LP D +S T Sbjct: 12 SILAHGALITYTLIALFPVFVILVNSFKTRKAIFRDPLGLPTS---DTFSLVGYQTVLKQ 68 Query: 97 GDYFL---NTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALV 153 GD+FL N+++V SL L+ G+MAA+ LA + F GN + G+ PI + V Sbjct: 69 GDFFLYFQNSMIVTVVSLALVLLFGAMAAFALAEYRFKGNMLLGLYLALGIMIPIRIGTV 128 Query: 154 PLFYVVNNMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTF 213 + ++ + GL+NTL LILVY A LP VF L+ F + + + A +DG S F Sbjct: 129 AILELMVDTGLVNTLTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYTIF 188 Query: 214 FQIMLPMAKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWS 273 F+++LP+ +P + +V +FN + WN P +L + + LT G Q+ + Q + DW+ Sbjct: 189 FRLVLPLVRPAMATVAVFNMIPIWNDLWFPLILAPAEETKTLTLG-SQVFIGQ-FVTDWN 246 Query: 274 GLFAGLVMAMLPVLAAYIIFQRQVVQGLTAGALK 307 + + L MA+LPV+ Y+IF RQ+++G+T+GA+K Sbjct: 247 AVLSALSMAILPVMVLYVIFSRQLIRGITSGAVK 280 Lambda K H 0.326 0.141 0.440 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: 272 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: 307 Length of database: 280 Length adjustment: 26 Effective length of query: 281 Effective length of database: 254 Effective search space: 71374 Effective search space used: 71374 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 (21.6 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