GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natB in Dinoroseobacter shibae DFL-12

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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