Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Ac3H11_1936 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= TCDB::P73650 (240 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1936 Length = 272 Score = 181 bits (460), Expect = 1e-50 Identities = 104/235 (44%), Positives = 147/235 (62%), Gaps = 4/235 (1%) Query: 4 LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEII 63 LL +++V + Y + ++G++ + GE+ V+G NGAGK+T+ KTI G++ P +G I Sbjct: 20 LLRLQNVESAY-GPIKAIRGVSLQVRRGEIAAVLGSNGAGKTTILKTISGIIDPRKGSIE 78 Query: 64 FKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKD--RIYT 121 F+G++IT IVRRG+ +VP+ VF L+V +NL MGA+ +D ++ Sbjct: 79 FQGQDITARDPAAIVRRGLMHVPEGREVFPLLSVRDNLLMGAYTRADKDGVARDIETVFG 138 Query: 122 MFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKA 181 FP L +R Q AG LSGG++QMLA+ RALM P+L+LLDEPS LSP L K++F + Sbjct: 139 YFPILKERAAQDAGLLSGGQQQMLAISRALMAAPELILLDEPSLGLSPKLTKEIFEIVVR 198 Query: 182 IN-ATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 IN G I+LVEQNA AL +D GYVLENGR +E S + L + E YLG Sbjct: 199 INRERGTTILLVEQNANMALNASDYGYVLENGRIVMEDSCERLREKDDIKEFYLG 253 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: 181 Number of extensions: 8 Number of successful extensions: 3 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: 272 Length adjustment: 24 Effective length of query: 216 Effective length of database: 248 Effective search space: 53568 Effective search space used: 53568 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: 47 (22.7 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