Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate 3608623 Dshi_2016 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q8RJU8 (307 letters) >FitnessBrowser__Dino:3608623 Length = 284 Score = 140 bits (353), Expect = 3e-38 Identities = 84/274 (30%), Positives = 141/274 (51%), Gaps = 7/274 (2%) Query: 32 KKEGTVLNVFSHGILVLWAFMVVLPLLWAVMTSFKDDASIFGSPWSL-PDKLHFDNWSRA 90 +K G L + G+++ AF + P+ A + S I P L P +N++RA Sbjct: 9 EKRGLGLWLTHLGLIIGVAF-IFFPIWLAFVASTVSQPEIVRPPMPLLPGDQLVENYTRA 67 Query: 91 WTEAHMGDYFL---NTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFP 147 T L N++++ G +G + + ++A+ + F FPG ++L + P Sbjct: 68 LTAGINAPVALMLGNSLIMALGIALGKIAISLLSAFAIVYFRFPGRMLFFWLIFLTLMLP 127 Query: 148 IMLALVPLFYVVNNMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGA 207 + + +VP + V+ N G+LN+ GLIL +A + F FF T+P +AEAA VDGA Sbjct: 128 VEVRIVPTYEVIANFGMLNSYQGLILPLVASAT--ATFLFRQFFMTVPDELAEAARVDGA 185 Query: 208 SHTRTFFQIMLPMAKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQG 267 R FF I+LPM++ + ++ + F+ WNQY+ P ++ TDP+ + G+ Q+ S Sbjct: 186 RPMRFFFDILLPMSRTNIAALFVILFIYGWNQYLWPLLITTDPEMNTIVMGIKQMFPSGD 245 Query: 268 YKGDWSGLFAGLVMAMLPVLAAYIIFQRQVVQGL 301 DW + A ++AM+P + I QR V+GL Sbjct: 246 DTADWPVIMATSILAMVPPVIVVITMQRLFVRGL 279 Lambda K H 0.326 0.141 0.440 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: 285 Number of extensions: 15 Number of successful extensions: 2 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: 307 Length of database: 284 Length adjustment: 26 Effective length of query: 281 Effective length of database: 258 Effective search space: 72498 Effective search space used: 72498 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 (21.6 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