Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein
Query= TCDB::Q8RJU9 (308 letters) >FitnessBrowser__Dyella79:N515DRAFT_3134 Length = 292 Score = 137 bits (344), Expect = 4e-37 Identities = 92/298 (30%), Positives = 154/298 (51%), Gaps = 25/298 (8%) Query: 12 FLAVPLGLYALLVVWPFIQSIYYSFTDWTGLS----PDFKTVGFDNYERMLDDDIFWKSL 67 FLA L + L + P I ++ S TD+ + D + V NY +L +FW +L Sbjct: 10 FLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNYWELLHRPLFWSAL 69 Query: 68 QHSLLFALLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLSIA 127 H+L F L+ ++I +L A ++N P+ R ++ F P V ++ Sbjct: 70 GHTLYFVLVGVPLSIVASLGAALLLN--------SPL---ARCKPLFRTALFAPVVTTVV 118 Query: 128 IVALLFAFAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTVGFFVVLF 187 VA+++ + +N G N L G+G+ V WLGDP A+ ++ VW G+ +++F Sbjct: 119 AVAVIWRYLFNTKYGLANYALGGLGIHPVD--WLGDPRWAMPTIILFAVWKNFGYNMIIF 176 Query: 188 SAGMASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGA--ESFAVV 245 A + +IPAD+YEAA +DGA+ + F ITLP+L T+ + +GIL + + FA Sbjct: 177 LAALQAIPADLYEAARIDGASPLRQFRHITLPMLGPTL----LMVGILTVSGYFQLFAEP 232 Query: 246 HIMTTGPGGPDYSTTVMVLYVYQKAFRDGQAAYATTIGVALLIVTLAFAAVVMRLGRR 303 +MT GGP STT ++ +Y++ F+ A+ + L ++ A AV++R+ RR Sbjct: 233 FVMT--EGGPLQSTTSVLYLMYEEGFKWWNLGSASAVAFLLFLIMFAVTAVMLRVARR 288 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: 271 Number of extensions: 20 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: 308 Length of database: 292 Length adjustment: 27 Effective length of query: 281 Effective length of database: 265 Effective search space: 74465 Effective search space used: 74465 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