Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_090272110.1 BLU11_RS03765 high-affinity branched-chain amino acid ABC transporter permease LivH
Query= TCDB::P74318 (286 letters) >NCBI__GCF_900105005.1:WP_090272110.1 Length = 308 Score = 142 bits (358), Expect = 9e-39 Identities = 88/295 (29%), Positives = 160/295 (54%), Gaps = 19/295 (6%) Query: 3 LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTSGINLWL- 61 L Q + NG+ VGS AL A+G T+ YGI+ + NFAHG+ + +Y+ + + L + Sbjct: 8 LLQQLLNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIVLAALALLGIE 67 Query: 62 SMALGCVGTIIAMFIG--------EWLLWKPMRARRATATTLIIISIGLALFLRNGILLI 113 S+ L + ++ I E + ++P+R +I +IG+++FL+N + L Sbjct: 68 SLPLLIIAALVVSMIVTSAYGYSIERVAYRPLRGGNRLIP--LISAIGMSIFLQNLVRLA 125 Query: 114 WGG------NNQNYRVPIVPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAM 167 G N + I PA F Y ++++ + + +M +L L + R+++G+A Sbjct: 126 QGSRDIAMPNLVRGGIDIGPATGFHAT-LSYMQIIIFVVTLISMTLLTLFITRSRMGRAC 184 Query: 168 RAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMT-TLKPNMGWFLILPMFA 226 RA A+++ + + GIN ++ T+++ A L A+ G + G+ + P +G+ L F Sbjct: 185 RACAEDLKMTNLLGINTNSIIALTFIIGAALAAVAGVLLGMYYGVINPYIGFMAGLKAFT 244 Query: 227 SVILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281 + +LGGIG+ GA+ GG+++GVA+ ++ +F YK VA L+I+IL RP G+ Sbjct: 245 AAVLGGIGSIPGAVLGGLLLGVAEAMTAGYFSGEYKDVVAFSLLILILLFRPSGI 299 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: 205 Number of extensions: 11 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: 286 Length of database: 308 Length adjustment: 26 Effective length of query: 260 Effective length of database: 282 Effective search space: 73320 Effective search space used: 73320 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