Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate BWI76_RS03135 BWI76_RS03135 sugar ABC transporter permease
Query= TCDB::Q8RJU9 (308 letters) >FitnessBrowser__Koxy:BWI76_RS03135 Length = 290 Score = 137 bits (344), Expect = 4e-37 Identities = 91/289 (31%), Positives = 149/289 (51%), Gaps = 24/289 (8%) Query: 16 PLGLYALLVVW-PFIQSIYYSFTDWTGLSPDFKTVGFDNYERMLDDDIFWKSLQHSLLFA 74 P L+ LL W P +S+Y S D +S + VG +N+ R+ D +FW+SL ++LL+ Sbjct: 13 PSLLFLLLFTWFPLGRSVYDSLFDTRMVSDGGQYVGLENFSRLFADSVFWQSLVNNLLYI 72 Query: 75 LLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLSIAIVALLFA 134 LL V + LAL A + R R + + +FFP ++ + A L+ Sbjct: 73 LLTVVPGVTLALLLAVALTENHRVNR------------WLRTAFFFPMIIPMVSAAALWL 120 Query: 135 FAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTVGFFVVLFSAGMASI 194 F + P G ++ L + G + WLG + AL + + VW G++++ F AG+ SI Sbjct: 121 FIFMPGLGLLDHYLAKL-FGPMNNNWLGRSNSALLALALIGVWKFAGYYMLFFLAGLQSI 179 Query: 195 PADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGAESFAVVHIMTTGPGG 254 PA EAA+++GA R FF++TLPLL T+ ++ AL + H+ GG Sbjct: 180 PASTREAAIMEGATRTQVFFKVTLPLLRPTLS----FVITTALIYSITQIDHVAVMTRGG 235 Query: 255 PDYSTTVMVLYVYQKAFRD---GQAAYATTIGVALLIVTLAFAAVVMRL 300 PD +TTV++ Y+ A+ G+A+ AT + +A L AF+ + ++L Sbjct: 236 PDNATTVLLYYIQNLAWDTHDLGKASAATFLTLAGL---FAFSLINLKL 281 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: 16 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: 290 Length adjustment: 27 Effective length of query: 281 Effective length of database: 263 Effective search space: 73903 Effective search space used: 73903 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