Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Pf6N2E2_1429 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= TCDB::P73650 (240 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1429 Length = 253 Score = 152 bits (383), Expect = 8e-42 Identities = 89/242 (36%), Positives = 136/242 (56%), Gaps = 9/242 (3%) Query: 4 LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGE-- 61 +L + D+ Y + ++ ++ + G++V ++G NGAGKST K L+ +GE Sbjct: 7 ILQIDDIEVLYEQTILAVRSVSLEVGKGQVVVLLGANGAGKSTTLKAASNLVRAERGEVV 66 Query: 62 ---IIFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLK-- 116 I+++G ++T + G+ V + + F LTV ENL GA Q P + L Sbjct: 67 RGRIVYQGRDVTRSAPHTLAASGLVQVLEGRHCFAQLTVEENLLAGALARQVPRRQLLAD 126 Query: 117 -DRIYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDV 175 + +Y FP+L RR AG SGGE+QM+A+GRALM P L+LLDEPS L+P +V+++ Sbjct: 127 LESVYGHFPRLKLRRKSLAGYTSGGEQQMIAIGRALMAKPQLVLLDEPSMGLAPQIVEEI 186 Query: 176 FAQIKAIN-ATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYL 234 F ++ +N G + ++ EQN AL A GYVLE+GR EGS + L + + YL Sbjct: 187 FEIVRQLNQRDGVSFLIAEQNINIALRYAHHGYVLESGRVVSEGSAEQLAARGDLQDFYL 246 Query: 235 GA 236 GA Sbjct: 247 GA 248 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: 165 Number of extensions: 7 Number of successful extensions: 4 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: 253 Length adjustment: 24 Effective length of query: 216 Effective length of database: 229 Effective search space: 49464 Effective search space used: 49464 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