Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 209487 DVU0548 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= TCDB::P74318 (286 letters) >MicrobesOnline__882:209487 Length = 302 Score = 129 bits (323), Expect = 1e-34 Identities = 86/288 (29%), Positives = 158/288 (54%), Gaps = 13/288 (4%) Query: 5 QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWW-ANTSGINLWLSM 63 +L+F G+ GSI AL A+G T+ YGI+ L NFAHG+ + A+ A GI + Sbjct: 8 ELLFGGLTRGSIYALIALGYTMVYGIIELINFAHGEVYMIGAFTALIVAGVLGIYGFPEA 67 Query: 64 ALGCVGTIIAM-------FIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGG 116 + + I+A+ F E + +KP+R A + +I +IG+++FL+N ++L Sbjct: 68 GILIIAAIVAVIYCAAYGFTLEKVAYKPLRD--APRLSPLISAIGMSIFLQNYVILAQTS 125 Query: 117 NNQNYR--VPIVPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNV 174 + + VP + + + +L+I + MV L L ++ T++GKAMRA A N Sbjct: 126 DFVPFPRLVPDLAILEPIAHITGTSDVLIIVTSAITMVGLTLFIKYTRMGKAMRATAQNR 185 Query: 175 DLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGL-MTTLKPNMGWFLILPMFASVILGGI 233 +A + GI+ + V+ T+++ + L A+GG + + + +G+ + F + +LGGI Sbjct: 186 KMAMLLGIDADRVISLTFIIGSSLAAIGGVLIASHIGQVNFAIGFIAGIKAFTAAVLGGI 245 Query: 234 GNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281 G+ GA+AGG+++G+ + + + + Y+ +A L+++IL RP G+ Sbjct: 246 GSIPGAMAGGLVLGLCESFATGYVSSDYEDALAFALLVLILIFRPSGI 293 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: 204 Number of extensions: 14 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: 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 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