Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate 3607839 Dshi_1247 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q8RJU9 (308 letters) >FitnessBrowser__Dino:3607839 Length = 308 Score = 125 bits (313), Expect = 2e-33 Identities = 90/298 (30%), Positives = 153/298 (51%), Gaps = 25/298 (8%) Query: 12 FLAVPLGLYALLVVWPFIQSIYYSFTDWTGLS-PDFKTVGFDNYERMLDDDIFWKSLQHS 70 FL + +A+ V+ P QS S +W GL P+F VG NY+ + DD F+ SL+++ Sbjct: 30 FLIPGILFFAVYVIIPIFQSFQISLLEWDGLGEPEF--VGLRNYDELRYDDAFYTSLKNN 87 Query: 71 LLFALLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLSIAIVA 130 +++ L L ++ I LF A +N +TG+R YK ++FFP V+S +V Sbjct: 88 IIW-LALYLLAIPAGLFIALFLN---------QTVTGIR---LYKSLFFFPFVISQVVVG 134 Query: 131 LLFAFAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTVGFFVVLFSAG 190 L+F + Y+P+ G +N++L +GLG + LGD ++A +W + ++L+ G Sbjct: 135 LVFTWFYDPNFGMLNTMLGWVGLGPI--AVLGDERYVTIGIIAAGLWPQTAYCMILYLTG 192 Query: 191 MASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGAESFAVVHIMTT 250 + ++ + EA LDGA + + LP L +V I AL SF ++ IMT Sbjct: 193 LNAVDPEQIEAGRLDGAKGWRMLWHVVLPQLRPATFIAFVVTIIGAL--RSFDLISIMT- 249 Query: 251 GPGGPDYSTTVMVLYVYQKAFRD--GQAAYATTIGVALLIVTLAF-AAVVMRLGRRER 305 GGP S+ V+ Y+++ A + + Y I V L ++ + F ++++ R ER Sbjct: 250 -QGGPFGSSRVLSFYMFEVALSEYGFRMGYGAAIAVVLFLIMMVFITGFLVKMYRDER 306 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: 290 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: 308 Length adjustment: 27 Effective length of query: 281 Effective length of database: 281 Effective search space: 78961 Effective search space used: 78961 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