Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate WP_007675527.1 BN137_RS07340 carbohydrate ABC transporter permease
Query= TCDB::Q8RJU8 (307 letters) >NCBI__GCF_000319285.1:WP_007675527.1 Length = 280 Score = 125 bits (313), Expect = 1e-33 Identities = 79/273 (28%), Positives = 131/273 (47%), Gaps = 21/273 (7%) Query: 46 LVLWAFMVVLPLLWAVMTSFKDDASIFGSPWSLPDKLHFDNWSRAWTEAHMGD------- 98 L L+ +LP +MTSFK LH + + WT AH D Sbjct: 17 LALFLIATLLPFFVMLMTSFKSPKEAIS--------LHPTLFPQHWTLAHYLDIFNPIIF 68 Query: 99 ----YFLNTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVP 154 YF N+++V + + +G + AY L++ F G I F F +L +VP Sbjct: 69 PFVTYFRNSLVVSVIASGVAVFIGILGAYALSKLRFKGRMTINASFYAVYMFSGILLVVP 128 Query: 155 LFYVVNNMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFF 214 LF ++ +G+ +T +I+ + +LP VF L ++F T+P + EAA +DG + + F Sbjct: 129 LFKIITALGIYDTQLAIIVTMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLNRLQIIF 188 Query: 215 QIMLPMAKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSG 274 +I +P+A GL+SV ++ F+ WN Y+ ++ + L GL L + Y W Sbjct: 189 RITVPLAVSGLVSVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNTLFSTPDY--IWGR 246 Query: 275 LFAGLVMAMLPVLAAYIIFQRQVVQGLTAGALK 307 + A ++ LPV+ Y + +R + GLT G +K Sbjct: 247 MMAASLVTALPVVVMYALSERFIKSGLTDGGVK 279 Score = 23.1 bits (48), Expect = 0.008 Identities = 11/21 (52%), Positives = 13/21 (61%) Query: 170 GLILVYIAYSLPFTVFFLTAF 190 GL L IA LPF V +T+F Sbjct: 16 GLALFLIATLLPFFVMLMTSF 36 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: 263 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 307 Length of database: 280 Length adjustment: 26 Effective length of query: 281 Effective length of database: 254 Effective search space: 71374 Effective search space used: 71374 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 24 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