GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Pseudomonas simiae WCS417

Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate GFF217 PS417_01100 amino acid ABC transporter permease

Query= SwissProt::P0AER3
         (246 letters)



>FitnessBrowser__WCS417:GFF217
          Length = 221

 Score =  100 bits (248), Expect = 3e-26
 Identities = 73/230 (31%), Positives = 118/230 (51%), Gaps = 27/230 (11%)

Query: 11  LQQAPFGNTTYLGWIWSGFQVTIALSICAWIIAFLVGSFFGILRTVPNRFLSGLGTLYVE 70
           L  APF        +  G   T+ LS+       L+G    ++R    + +S L  +YV 
Sbjct: 9   LDSAPF--------LLKGAYYTVILSLGGMFFGLLLGFGLALMRLSRFKLVSWLARVYVS 60

Query: 71  LFRNVPLIVQFFTWYLVIPELLPEKIGMWFKAELDPNIQFFLSSMLCLGLFTAARVCEQV 130
            FR  PL+VQ F  Y  +P+     +G+    ELDP      ++M+   L  AA  CE +
Sbjct: 61  FFRGTPLLVQLFLIYYGLPQ-----VGI----ELDP----IPAAMIGFSLNMAAYACEIL 107

Query: 131 RAAIQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMNLVKNSAIASTIG 190
           RAAI S+ RGQ  AA ++G+T  Q  R  +LP A R  +PP+ +  ++LVK++A+A+TI 
Sbjct: 108 RAAIGSIERGQWEAAASIGMTRAQTLRRAILPQAMRTALPPLGNSFISLVKDTALAATIQ 167

Query: 191 LVDMAAQAGKLLDYSAHAWESFT---AITLAYVLINAFIMLVMTLVERKV 237
           + ++  QA  +   SA  +E FT   +  L Y ++ + +  +   +E +V
Sbjct: 168 VPELFRQAQLV---SARTFEIFTMYLSAALIYWILASILAHLQNRLEDRV 214


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: 152
Number of extensions: 9
Number of successful extensions: 2
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: 221
Length adjustment: 23
Effective length of query: 223
Effective length of database: 198
Effective search space:    44154
Effective search space used:    44154
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