Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate YP_004144382.1 Mesci_5234 inner-membrane translocator
Query= TCDB::P74318 (286 letters) >NCBI__GCF_000185905.1:YP_004144382.1 Length = 302 Score = 172 bits (436), Expect = 8e-48 Identities = 96/295 (32%), Positives = 170/295 (57%), Gaps = 18/295 (6%) Query: 5 QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTS--------- 55 Q + +G+ GS+I LGA+G+TLTY ILR SNFAHGDFM Y T ++ Sbjct: 4 QFVVDGLLTGSMIGLGAIGVTLTYSILRFSNFAHGDFMAWGTYATLAVVSAIGATVGKVA 63 Query: 56 -------GINLWLSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRN 108 G L +++ +G T + + + +L+ +R++ A +++ S G ++ LR+ Sbjct: 64 PIAPLSFGWPLIVALVVGMAFTALLALLLDKVLFSRLRSQ-GQAIIVVMASFGASMALRS 122 Query: 109 GILLIWGGNNQNYRVPIVPAQDF-MGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAM 167 + + + I A GI+ ++ ++ + ++ +HL++ RT+ G++M Sbjct: 123 LLEFTFTSRPTYFSRAIQIAMPVGFGIRITSDQIALLLLTAVLVLAVHLLMTRTQTGRSM 182 Query: 168 RAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFAS 227 +A++ N LA++ GI+V VV TWV+ L + G M G++ ++P MG+ ++LPMFA+ Sbjct: 183 QALSQNAALARIVGIDVASVVRVTWVIGGALACVAGVMIGILVQIRPFMGFDMLLPMFAA 242 Query: 228 VILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGLF 282 ILGGIG+ GA+ GG+IIG+A+ +V G ++ V+ ++++ +LF+RP GLF Sbjct: 243 AILGGIGSIPGAVLGGLIIGLAEAGAVQLIGAEWRAAVSFIILMAVLFVRPIGLF 297 Lambda K H 0.329 0.143 0.450 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: 201 Number of extensions: 9 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: 286 Length of database: 302 Length adjustment: 26 Effective length of query: 260 Effective length of database: 276 Effective search space: 71760 Effective search space used: 71760 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 (21.8 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