Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease
Query= TCDB::Q8RJU8 (307 letters) >NCBI__GCF_001431535.1:WP_042615044.1 Length = 278 Score = 162 bits (411), Expect = 6e-45 Identities = 93/266 (34%), Positives = 153/266 (57%), Gaps = 8/266 (3%) Query: 44 GILVLWAFMVVLPLLWAVMTSFKD--DASIFGSPWSLPDKLHFDNWSRAWTEAHMGDYFL 101 G+LVL A + + PLLW V S +A+ F P + P + F N+ + MG F Sbjct: 18 GLLVL-ALVSLAPLLWMVSVSVMPAGEATTFPPPLT-PSHVTFANYHELFARTGMGVNFA 75 Query: 102 NTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVNN 161 N++LV +G+L+L +MA Y A+ F G ++ + + + P +A++PLF ++ Sbjct: 76 NSLLVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLFQVLMAALVIPAQVAMLPLFLLMKQ 135 Query: 162 MGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPMA 221 +GL+N+ G+I+ +A F +F + + R++P + EAA +DGA R FFQI+LPM Sbjct: 136 LGLVNSFGGVIVPALA--TVFGIFLVRQYARSIPDELLEAARMDGAGEMRIFFQIVLPML 193 Query: 222 KPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLVM 281 KP L+++ IF F+G WN +M P ++ TD + L L L S+ + D + AG V+ Sbjct: 194 KPVLVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLPVALATL--SREHIMDVEMMMAGAVV 251 Query: 282 AMLPVLAAYIIFQRQVVQGLTAGALK 307 ++PVLA +++ QR +QGL G++K Sbjct: 252 TVIPVLALFLLLQRYYIQGLMLGSVK 277 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: 261 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: 1 Length of query: 307 Length of database: 278 Length adjustment: 26 Effective length of query: 281 Effective length of database: 252 Effective search space: 70812 Effective search space used: 70812 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 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