Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Pf6N2E2_3579 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= TCDB::P74318 (286 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3579 Length = 304 Score = 134 bits (338), Expect = 2e-36 Identities = 88/291 (30%), Positives = 156/291 (53%), Gaps = 16/291 (5%) Query: 5 QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTS----GINLW 60 Q + NG+ +GS+ L A+G T+ YGI+ + NFAHG+ ++AYL + GI + Sbjct: 7 QQLINGLTLGSVYGLIAIGYTMVYGIIGMINFAHGEVYMISAYLAAISLALLAYFGIESF 66 Query: 61 LSMALGC-VGTIIAMFIGEWLL----WKPMRARRATATTLIIISIGLALFLRNGILLIWG 115 M LG V T++ + W++ +KP+R +T +I +IG++L L+N + G Sbjct: 67 PLMILGTLVFTVVVTGVYGWVIERVAYKPLR--NSTRLAPLISAIGISLILQNYAQISQG 124 Query: 116 GNNQNYRVPIVPAQDF-MG---IKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVA 171 Q + A +G ++ Y ++ ++ A A M VL I++ TK+G+ RA Sbjct: 125 ARQQGVPTLLEGAMRLDIGSGFVQLTYTKIFILIAAFAGMAVLTYIIKYTKLGRMCRATQ 184 Query: 172 DNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGL-MTTLKPNMGWFLILPMFASVIL 230 + +A + GIN + V+ + +++ A + AL G + + T G+ + + F + +L Sbjct: 185 QDRKMASILGINTDRVISYVFIIGAAMAALAGVLITMNYGTFDFYAGFIIGIKAFTAAVL 244 Query: 231 GGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281 GGIG+ GA+ GGII+G+++ + + YK + L+++IL RPQGL Sbjct: 245 GGIGSLPGAMLGGIILGISESLFSGLINSDYKDVFSFSLLVLILIFRPQGL 295 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: 211 Number of extensions: 12 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: 304 Length adjustment: 26 Effective length of query: 260 Effective length of database: 278 Effective search space: 72280 Effective search space used: 72280 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