Align NatB aka SLR0559, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 3608583 Dshi_1977 Extracellular ligand-binding receptor (RefSeq)
Query= TCDB::Q55387 (454 letters) >FitnessBrowser__Dino:3608583 Length = 420 Score = 159 bits (402), Expect = 2e-43 Identities = 119/387 (30%), Positives = 187/387 (48%), Gaps = 24/387 (6%) Query: 66 KLGALLPATGDLSSIGQNMPLAVQLAVDTINACGGVNGQDVTVVIEDDQTDPTAGVSAMT 125 K+GA+LP + D G+ + Q AVD +N GGVNG + +V+ D Q DP GV A Sbjct: 32 KIGAVLPTSVDW---GKPIAATAQFAVDQVNEAGGVNGCQIEMVLRDTQVDPKVGVDAAK 88 Query: 126 KLAEADQVAGVVGSFASSVSSAAV-PIAVRNNIMMISPGSTSPVFTDQAKKGEFKGFWAR 184 L + D V ++G+ +S VS + + + +M +S S+S FT A +G+ +G W R Sbjct: 89 ALVDLDGVRVLLGAVSSGVSMPILTSVTLPAGVMQMSCCSSSTAFTQLAAEGKTEGLWFR 148 Query: 185 TAPPDTYQAQALAALAKKQGFTDAATVVINNDYGVGFEKVFVESFTADGGNVTNKDNPVR 244 T QA A +A +G+ A N+D+G K+ A G VT Sbjct: 149 TFATSGVQAAMGAKVAADRGYKSVAIFYKNDDWGQDIGKLVAADLEALGIEVTGSVALND 208 Query: 245 YDPKAATLDTEAAQGFANSPDAVAAILYADTGSVLVQSAYRQGLMDGVT--LLLTDGVYS 302 P TEA QG P+A+ LY G +A R+ L G T +++ + + S Sbjct: 209 GQPSYRAEVTEALQG---QPEAIYLALYPKEGI----AAVREWLSLGGTQNMIVANSLKS 261 Query: 303 PDFVEKVGKDANGVSLLSGALGT-VPGADGKSLEAFTAQWKDATGGKDVTAFVPHTYDAT 361 +F E V G+ L LGT +S +AF ++ + + ++YDAT Sbjct: 262 DEFAENV-----GLQFLGNTLGTDTASPRAESADAFVTRYTERFESAPTGPGLANSYDAT 316 Query: 362 VLMMLAAEAA-KSNTGAGIQSKIRDVSNGPGEEVT----DACEAIAMVREGKDINYQGAS 416 ++ +LA +AA + +GA I +++ V+N G ++ A+ ++ G D+ YQGA+ Sbjct: 317 MIALLAMQAAGEGASGAEIAAQVGRVTNPEGTPISADGAGFAAAVEVLSSGGDVFYQGAT 376 Query: 417 GNVDIDENGDVVGTYDVWTVKGDGTLE 443 GNV DENGDV +W+ +G E Sbjct: 377 GNVQFDENGDVSAPAVIWSFTEEGITE 403 Lambda K H 0.313 0.131 0.374 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: 436 Number of extensions: 25 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: 454 Length of database: 420 Length adjustment: 32 Effective length of query: 422 Effective length of database: 388 Effective search space: 163736 Effective search space used: 163736 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 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