Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate AZOBR_RS27985 AZOBR_RS27985 ABC transporter permease
Query= TCDB::Q8RJU8 (307 letters) >FitnessBrowser__azobra:AZOBR_RS27985 Length = 280 Score = 132 bits (333), Expect = 7e-36 Identities = 82/271 (30%), Positives = 135/271 (49%), Gaps = 18/271 (6%) Query: 43 HGILVLWAFMVVLPLLWAVMTSFK------DDASIFGSPWSLPDKLHFDNWSRAWTEAHM 96 H + +V+ P W V + + DDA +F LP +N+ W + H Sbjct: 21 HAAALALLLLVLFPFAWMVQMALRPADAVLDDAVLF-----LPT---LENFVALW-QGHF 71 Query: 97 GDYFLNTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLF 156 FLN+VLV S +L LG AAYVL R+ F R + + P + +P F Sbjct: 72 PKSFLNSVLVSSLSTAASLALGVPAAYVLTRWRFRARRRVALWILATRMAPPIALTIPFF 131 Query: 157 YVVNNMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQI 216 +GL +++ GL L+Y+ +++ V+F+ FF +P S+ EAA++DG + F ++ Sbjct: 132 LAYRWVGLQDSVVGLALIYMTFNISIVVWFMQTFFAAIPRSLEEAAWIDGCGVWQAFRRV 191 Query: 217 MLPMAKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLF 276 LP+A PGL + +F F+ WN + +L T + + +G+ +W + Sbjct: 192 TLPLAAPGLAATAVFCFIFSWNDFFFALIL-TRTNAVTAPVAITNFLQYEGW--EWGKIA 248 Query: 277 AGLVMAMLPVLAAYIIFQRQVVQGLTAGALK 307 A + MLPVLA ++ ++ +V+GLTAG LK Sbjct: 249 AAGTLVMLPVLAFTLLVRKYLVRGLTAGGLK 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: 241 Number of extensions: 16 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: 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 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