Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate GFF1647 PGA1_c16700 binding protein-dependent transport system, inner membrane component
Query= TCDB::Q8RJU9 (308 letters) >FitnessBrowser__Phaeo:GFF1647 Length = 316 Score = 139 bits (350), Expect = 9e-38 Identities = 94/294 (31%), Positives = 151/294 (51%), Gaps = 19/294 (6%) Query: 12 FLAVPLGLYALLVVWPFIQSIYYSFTDWTGLSPDFKT--VGFDNYERMLDDDIFWKSLQH 69 +L+ + L +++ P I I YSF L+P F T VGF+NYE++ D FW +L++ Sbjct: 36 YLSPMILLIGSVMLIPLIVGISYSFQSIELLNP-FATGWVGFENYEKLWSDRKFWIALEN 94 Query: 70 SLLFALLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLSIAIV 129 + + L L A ++N T G ++ + F P + + Sbjct: 95 TFFWTFWSIFFQFFLGLGLAMLLN------------TQFFGKKLFQALVFLPWAVPTFLS 142 Query: 130 ALLFAFAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTVGFFVVLFSA 189 AL +A+ +NP G I L +G+ LGDPDLA+W + +W V FF + A Sbjct: 143 ALTWAWLFNPVIGPIPHWLAALGVLSEPYNILGDPDLAIWGPITANIWFGVPFFAITLLA 202 Query: 190 GMASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGAESFAVVHIMT 249 + SIP ++YEAA +DGA +F +ITLP L + + + + + +FA + + Sbjct: 203 ALQSIPGELYEAAEIDGATPWQSFTKITLPFLAPMIA---ITVMLRTIWIANFADLIFVM 259 Query: 250 TGPGGPDYSTTVMVLYVYQKAFRDGQAAYATTIGVALLIVTLAFAAVVMRLGRR 303 TG GGP ST ++ Y++ AFR YA+TI VALLI+ LA+A +++ + +R Sbjct: 260 TG-GGPANSTQILSTYIFTTAFRKLDFGYASTIAVALLIILLAYAVILLWMRKR 312 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: 347 Number of extensions: 29 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: 316 Length adjustment: 27 Effective length of query: 281 Effective length of database: 289 Effective search space: 81209 Effective search space used: 81209 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