Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate BWI76_RS23380 BWI76_RS23380 sugar ABC transporter permease
Query= TCDB::Q8RJU9 (308 letters) >FitnessBrowser__Koxy:BWI76_RS23380 Length = 296 Score = 136 bits (343), Expect = 5e-37 Identities = 83/279 (29%), Positives = 140/279 (50%), Gaps = 21/279 (7%) Query: 22 LLVVWPFIQSIYYSFTDWTGLSPDFKTVGFDNYERMLDDD-IFWKSLQHSLLFALLLPVV 80 + +PF+ S + SFT++ +SP G +NY ML +D +FWKS+ + + L + Sbjct: 21 VFTAFPFVSSFFLSFTEYDLMSPPVFN-GIENYRYMLTEDGLFWKSMGVTFAYVFLTIPL 79 Query: 81 TIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLSIAIVALLFAFAYNPD 140 + AL AF++N +RG GF++ Y+ P +L ++ + A Sbjct: 80 KLAFALGIAFVLNFK------------LRGIGFFRTAYYIPSILGSSVAIAVLWRALFAI 127 Query: 141 SGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTVGFFVVLFSAGMASIPADIYE 200 G +NS + +G V WLG+P LAL V + VW G +V+F A + ++P YE Sbjct: 128 DGLLNSFIGVLGFDPVN--WLGEPSLALMSVTLLRVWQ-FGSAMVIFLAALQNVPQSQYE 184 Query: 201 AALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGAESFAVVHIMTTGPGGPDYSTT 260 AA++DGA++ F ++T+PL+ + ++ A + F +++T GGP YST Sbjct: 185 AAMIDGASKWQMFMKVTVPLITPVIFFNFIMQTTQAF--QEFTGPYVIT--GGGPTYSTY 240 Query: 261 VMVLYVYQKAFRDGQAAYATTIGVALLIVTLAFAAVVMR 299 + LY+Y AF+ Y + L +V FAA+ + Sbjct: 241 LFSLYIYDTAFKYFDMGYGAALAWVLFLVVAVFAAIAFK 279 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: 308 Number of extensions: 18 Number of successful extensions: 6 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: 296 Length adjustment: 27 Effective length of query: 281 Effective length of database: 269 Effective search space: 75589 Effective search space used: 75589 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