Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)
Query= TCDB::Q8RJU8 (307 letters) >FitnessBrowser__Dyella79:N515DRAFT_3133 Length = 273 Score = 145 bits (367), Expect = 8e-40 Identities = 86/267 (32%), Positives = 141/267 (52%), Gaps = 7/267 (2%) Query: 43 HGILVLWAFMVVLPLLWAVMTSFK--DDASIFGSPWSLPDKLHFDNWSRAWTEAHMGDYF 100 +G+L+ + V PLLW + SF +AS P LP N+ + A MG Y Sbjct: 11 NGLLIGSTLVAVFPLLWMLSVSFMRPGEASALPPPL-LPTHATLANYHELFERAGMGRYL 69 Query: 101 LNTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVN 160 LN++ V + +L MA Y A+ F G ++ + +GG+ P +A++PLF ++ Sbjct: 70 LNSLGVSSAITLLSLAFNLMAGYAFAKLRFSGRERLFQVLLGGLVIPAQVAMLPLFLLLK 129 Query: 161 NMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPM 220 +GL+N+ +++ A + F +F + + R +P + EAA +DGA R F QI+LP+ Sbjct: 130 YLGLVNSYAAVVVP--AMATIFGIFLVRQYARGIPDDLMEAARIDGAGELRIFVQIVLPL 187 Query: 221 AKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLV 280 KP ++++ IF FL WN +M P + T + L L L S+ + D + AG V Sbjct: 188 LKPIMVTLAIFTFLTAWNDFMWPLIALTGQEHYTLPIALASL--SREHVQDSELMMAGSV 245 Query: 281 MAMLPVLAAYIIFQRQVVQGLTAGALK 307 + +LPVL ++ QR +QGL G++K Sbjct: 246 VTVLPVLVLFLALQRYYLQGLLLGSVK 272 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: 257 Number of extensions: 17 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: 307 Length of database: 273 Length adjustment: 26 Effective length of query: 281 Effective length of database: 247 Effective search space: 69407 Effective search space used: 69407 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