Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate RR42_RS16960 RR42_RS16960 ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >FitnessBrowser__Cup4G11:RR42_RS16960 Length = 238 Score = 194 bits (494), Expect = 1e-54 Identities = 101/220 (45%), Positives = 147/220 (66%), Gaps = 2/220 (0%) Query: 18 VPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQI 77 + ++GI+ I GELVT+IG NGAGK+T K I GL + G++ + G++I G+ S + Sbjct: 18 IQAVKGIDLEIKEGELVTLIGANGAGKTTTMKAITGLQGWAGGDVEYMGKSIKGVPSYTL 77 Query: 78 VRRGMCYVPQVCNVFGSLTVAENLDMGAFLH--QGPTQTLKDRIYTMFPKLAQRRNQRAG 135 +++G+ VP+ VF +T+ ENL MGA+ + + DR++ +FP+L +R NQ AG Sbjct: 78 LKQGLAMVPEGRGVFARMTITENLQMGAYTRTDEAGIKADIDRMFGIFPRLKERANQLAG 137 Query: 136 TLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIILVEQN 195 T+SGGE+QMLAM RALM P LLLLDEPS LSPI+V +F ++ ++A G ++LVEQN Sbjct: 138 TMSGGEQQMLAMARALMSQPKLLLLDEPSMGLSPIMVAKIFEVVRDVSALGVTVLLVEQN 197 Query: 196 AKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 A+ AL A RGYV+E+G + G + +L+DP V YLG Sbjct: 198 ARLALQAAHRGYVMESGLVTMSGDAKQMLDDPKVRAAYLG 237 Lambda K H 0.320 0.139 0.393 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: 163 Number of extensions: 9 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: 240 Length of database: 238 Length adjustment: 23 Effective length of query: 217 Effective length of database: 215 Effective search space: 46655 Effective search space used: 46655 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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