GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltJ in Herbaspirillum seropedicae SmR1

Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate HSERO_RS19250 HSERO_RS19250 glutamate ABC transporter permease

Query= reanno::pseudo1_N1B4:Pf1N1B4_772
         (248 letters)



>FitnessBrowser__HerbieS:HSERO_RS19250
          Length = 249

 Score =  237 bits (605), Expect = 1e-67
 Identities = 125/246 (50%), Positives = 166/246 (67%), Gaps = 4/246 (1%)

Query: 1   MNYNWDWGVFFKSTGVGSEIYFDWYLSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRI 60
           M+YNW+WG+F++ +  G   Y D  L+GL WT+A A  AWI+AL+LG+I G +RT     
Sbjct: 1   MHYNWNWGIFWEMSPDGIP-YIDTLLAGLKWTLATAACAWIMALILGTIFGTLRTTTKPW 59

Query: 61  VSGIATCYVELFRNVPLLVQLFIWYFLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGL 120
           V  IA  YVELFRN+PLLVQ+F+WYF++P+LLPA I +W K   +   ++F++  + LG 
Sbjct: 60  VVRIANGYVELFRNIPLLVQMFLWYFVMPELLPAFIGDWIK---SLPDASFVTATLALGF 116

Query: 121 FTTARVCEQVRTGIQALPRGQEAAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVF 180
           FT++RV  QV TGIQALPRGQ  A  A+G    Q Y  VLLP A+RIIIP LT+EF  + 
Sbjct: 117 FTSSRVAVQVTTGIQALPRGQRMAGAALGLTPVQTYRYVLLPMAFRIIIPALTNEFAAII 176

Query: 181 KNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRSVEKKVAVP 240
           KNSSVA  IGL+EL A T    EF+   FEA T AT+IY  +++  + + R +EK  AVP
Sbjct: 177 KNSSVALTIGLVELTAATYSMREFTFQTFEALTGATIIYVIISVIALFMARLLEKVTAVP 236

Query: 241 GLISVG 246
           G I+ G
Sbjct: 237 GYITGG 242


Lambda     K      H
   0.326    0.140    0.433 

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: 207
Number of extensions: 5
Number of successful extensions: 3
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: 248
Length of database: 249
Length adjustment: 24
Effective length of query: 224
Effective length of database: 225
Effective search space:    50400
Effective search space used:    50400
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: 46 (22.3 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