GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Herbaspirillum seropedicae SmR1

Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate HSERO_RS17565 HSERO_RS17565 glutamate/aspartate ABC transporter permease GltJ

Query= SwissProt::P0AER3
         (246 letters)



>FitnessBrowser__HerbieS:HSERO_RS17565
          Length = 241

 Score =  286 bits (732), Expect = 3e-82
 Identities = 144/248 (58%), Positives = 184/248 (74%), Gaps = 9/248 (3%)

Query: 1   MSIDWNWGIFLQQAPFGNTTYLGWIWSGFQVTIALSICAWIIAFLVGSFFGILRTVPNRF 60
           M+  W W +FLQ AP    TYL W+ SG  VT+AL + AWI+A ++G+F GILRT+PNR 
Sbjct: 1   MAYQWQWSVFLQ-APSTGQTYLDWLLSGLGVTVALGLSAWILALVLGTFLGILRTLPNRA 59

Query: 61  LSGLGTLYVELFRNVPLIVQFFTWYLVIPELLPEKIGMWFKA--ELDPNIQFFLSSMLCL 118
           LSG    YVELFRNVPL+VQ F WY  +PELLP     W  A   L P  Q F+ +MLCL
Sbjct: 60  LSGFAACYVELFRNVPLLVQIFIWYFAMPELLP-----WGDAVKALPPMTQQFVMAMLCL 114

Query: 119 GLFTAARVCEQVRAAIQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMN 178
           G+FTAARVCEQVR+ I+SLPRGQK A LA+GLTL Q Y +VLLP A R+++PP+TSE +N
Sbjct: 115 GMFTAARVCEQVRSGIESLPRGQKGAGLALGLTLGQTYLFVLLPMAMRIVLPPLTSEFLN 174

Query: 179 LVKNSAIASTIGLVDMAAQAGKLLDYSAHAWESFTAITLAYVLINAFIMLVMTLVERKVR 238
           + KNSA+ASTIGL+++AAQ  +L+DY+A  +E+F A+TLAY+LIN  +M +M ++ERK  
Sbjct: 175 IFKNSAVASTIGLLELAAQGRQLVDYTAQPYEAFIAVTLAYMLINICVMSLMRILERKTS 234

Query: 239 LPGNMGGK 246
           LPG M GK
Sbjct: 235 LPG-MAGK 241


Lambda     K      H
   0.328    0.140    0.443 

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: 256
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: 246
Length of database: 241
Length adjustment: 23
Effective length of query: 223
Effective length of database: 218
Effective search space:    48614
Effective search space used:    48614
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: 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