Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate 208683 DVU3163 ABC transporter, permease protein
Query= TCDB::Q8RJU9 (308 letters) >MicrobesOnline__882:208683 Length = 293 Score = 135 bits (339), Expect = 2e-36 Identities = 93/286 (32%), Positives = 145/286 (50%), Gaps = 33/286 (11%) Query: 8 FIVGFLAVPLGLYALLVVWPFIQSIYYSFTDWTGLSPDFKTVGFDNYERMLDDDIFWKSL 67 FIV F VP V FI S D G +P VG ++Y + +D++F K+L Sbjct: 22 FIVAFTHVP-------AVNTFIHSF---MLDGKGGAPA-TFVGLEHYMYLFEDEVFRKAL 70 Query: 68 QHSLLFALLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLSIA 127 ++LLFA ++IGLA+ AFM+N G + G ++ YF P VL + Sbjct: 71 VNNLLFASGTIPLSIGLAMLMAFMVNAG------------LAGQSVLRLCYFVPTVLPMI 118 Query: 128 IVALLFAFAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTVGFFVVLF 187 VA ++ F + P+ G + + +G V WLG+ AL CV+AV VW GFF++ + Sbjct: 119 AVANIWLFFFTPEYGLLEQVRGALGFSGVN--WLGNESTALPCVIAVAVWKDAGFFMIFY 176 Query: 188 SAGMASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGAESFAVVHI 247 A + I + EAA+L+GA+R+ + R+ +PLL T V I A V H+ Sbjct: 177 LAALQQISPSLGEAAMLEGASRLYFYRRVVIPLLMPTTLFVLVNATINAFR----MVDHL 232 Query: 248 MTTGPGGPDYSTTVMVLYVYQKAFRDGQAAYATTIGVALLIVTLAF 293 GGP+ ++++++ Y+Y+ +F+ Y G AL +V LAF Sbjct: 233 FVLTQGGPNNASSLLLYYIYEVSFKYWDTGY----GAALTMVLLAF 274 Lambda K H 0.330 0.145 0.458 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: 277 Number of extensions: 17 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: 308 Length of database: 293 Length adjustment: 27 Effective length of query: 281 Effective length of database: 266 Effective search space: 74746 Effective search space used: 74746 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