Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate SMc04136 SMc04136 ABC transporter permease
Query= TCDB::Q8RJU9 (308 letters) >FitnessBrowser__Smeli:SMc04136 Length = 315 Score = 129 bits (325), Expect = 7e-35 Identities = 91/291 (31%), Positives = 155/291 (53%), Gaps = 31/291 (10%) Query: 8 FIVGFLAVPLGLYALLVVWPFIQSIYYSFTDWTGL-SPDFKTVGFDNYERMLD-DDIFWK 65 +++GF + LG P I S+Y SFT++ + +P++ +G NY R+ D F Sbjct: 39 WLIGFFGLTLG--------PAIASLYLSFTNFDLIRAPEW--IGTANYARIATADPKFAA 88 Query: 66 SLQHSLLFALLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLS 125 +++ + L+ +L + AL A +++ GVRG Y+ +++ P +L Sbjct: 89 AVKVTFLYVVLSVPFKLAFALLVAILLD------------RGVRGLTVYRAIFYLPSLLG 136 Query: 126 IAI-VALLFAFAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTVGFFV 184 ++ +A+L+ + D G INSLL G+ P W+ PD ++W ++ + VW G + Sbjct: 137 GSVAIAVLWRQLFAGD-GLINSLLAQFGIEG--PSWISHPDYSIWTLVVLSVWQ-FGSPM 192 Query: 185 VLFSAGMASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGAESFAV 244 ++F AG+ IP D+YEAA LDGA++ F++ITLPLL + V I A ++F Sbjct: 193 IIFLAGLRQIPTDMYEAASLDGASKFRQFYKITLPLLTPVIFFNAVVQTIDAF--KAFTP 250 Query: 245 VHIMTTGPGGPDYSTTVMVLYVYQKAFRDGQAAYATTIGVALLIVTLAFAA 295 I++ G GGP ST LY+YQ+AF + + YA+ + L+++ F A Sbjct: 251 AFIISGGTGGPINSTLFYTLYLYQEAFGNFRMGYASALAWILVLIIGLFTA 301 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: 330 Number of extensions: 22 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: 315 Length adjustment: 27 Effective length of query: 281 Effective length of database: 288 Effective search space: 80928 Effective search space used: 80928 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