Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like
Query= TCDB::Q8RJU9 (308 letters) >FitnessBrowser__SynE:Synpcc7942_0526 Length = 293 Score = 162 bits (411), Expect = 7e-45 Identities = 99/292 (33%), Positives = 167/292 (57%), Gaps = 19/292 (6%) Query: 12 FLAVPLGLYALLVVWPFIQSIYYSFTDWT-GLSPDFKTVGFDNYERMLDDDIFWKSLQHS 70 FLA L + L V WP +Q+ Y+SFT + L+ + VG +N++R+L+D +FWK+L ++ Sbjct: 13 FLAPALTILGLTVFWPALQAFYFSFTRFDYNLTRSPQWVGLENFQRLLNDAVFWKTLGNT 72 Query: 71 LLFALLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLSIAIVA 130 ++ + + + + L L A ++N +RG +++ Y+ P ++SI + Sbjct: 73 FIYLIGVVPLLVFLPLGLAILVN------------RPLRGITLFRLAYYTPVIVSIVVAG 120 Query: 131 LLFAFAYNPDSGAINSLLRGIGLGDVQPV-WLGDPDLALWCVMAVIVWSTVGFFVVLFSA 189 + + + Y ++G +N L + + QP+ WL P LAL+ VMAV VW +G+++V++ A Sbjct: 121 IAWRWLY-AETGLLNQLGQLVFGEGFQPIPWLTSPALALFSVMAVTVWKGLGYYMVIYLA 179 Query: 190 GMASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGAESFAVVHIMT 249 G+ IP ++YEAA LDG++ ITLPL+ + V I A + F V IMT Sbjct: 180 GLQGIPLELYEAAALDGSDGWRRHLDITLPLMRPYLVLVAVISAISA--TKVFEEVFIMT 237 Query: 250 TGPGGPDYSTTVMVLYVYQKAFRDGQAAYATTIGVALLIVTLAFAAVVMRLG 301 GGP S+ +V YVYQ+AF+ + +YA T+G+AL +V L + + +R G Sbjct: 238 --QGGPLNSSKTVVYYVYQQAFQKLEVSYACTVGLALFLVVLTLSLLRLRFG 287 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: 289 Number of extensions: 17 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: 293 Length adjustment: 27 Effective length of query: 281 Effective length of database: 266 Effective search space: 74746 Effective search space used: 74746 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