Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate RR42_RS14420 RR42_RS14420 branched-chain amino acid transporter permease subunit LivH
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__Cup4G11:RR42_RS14420 Length = 308 Score = 149 bits (375), Expect = 1e-40 Identities = 89/296 (30%), Positives = 174/296 (58%), Gaps = 19/296 (6%) Query: 4 QTIQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNT------- 56 Q Q +VNG+ +G+I AL A+G T+ YGI+ + NFAHG+ +GAY+ T Sbjct: 7 QFTQQLVNGLTLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIGAYVGLVTLTAIGASAG 66 Query: 57 --FGVNIWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIIS-IGLALFLRNGII 113 + + +++V+V+ T E++ + R +R + +IS IG+++FL+N + Sbjct: 67 YPLPLVLGAALLVSVLVTGLYGFAVERVAY---RPLRGGPRLVPLISAIGMSIFLQNYVQ 123 Query: 114 LIWGGRNQNYNLPITPALDI-----FGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKA 168 + G R+ + + I+ A++ F V VP ++LL++ + ++ + AL + ++++G+A Sbjct: 124 IGQGARDMSVPVLISGAIEFQMGSDFTVTVPYSRLLIVGVTLVLMLALTLFIGHSRMGRA 183 Query: 169 MRAVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGL-ITAVRPNMGWFLILPLF 227 RA A+D+ +A + GID +VI +T+++ + ++GG + GL I + P +G+ + F Sbjct: 184 CRACAEDMRMANLLGIDTNRVISFTFVLGAMLAAVGGVLIGLTIGKLNPYIGFVAGIKAF 243 Query: 228 ASVILGGIGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283 + +LGGIG+ GA+ ++G+ + ++ ++ ++YK VA +++L+LL RP GL Sbjct: 244 TAAVLGGIGSIPGAMLGGVLLGLAETFASGYMPAEYKDVVAFGLLVLILLFRPTGL 299 Lambda K H 0.328 0.144 0.426 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: 253 Number of extensions: 13 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: 288 Length of database: 308 Length adjustment: 26 Effective length of query: 262 Effective length of database: 282 Effective search space: 73884 Effective search space used: 73884 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 (21.7 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