GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdX in Acidovorax sp. GW101-3H11

Align D-serine transporter DsdX (characterized)
to candidate Ac3H11_3740 Gluconate permease

Query= SwissProt::P08555
         (445 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3740
          Length = 456

 Score =  225 bits (574), Expect = 2e-63
 Identities = 133/442 (30%), Positives = 239/442 (54%), Gaps = 10/442 (2%)

Query: 14  SIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFLAAVIGLG 73
           SI L++L I++++ H F+A++L SF V    GM   D+++ + +G+GGTLG +A ++ LG
Sbjct: 13  SIALLLLLIIRWQVHAFVAMMLVSFLVAFATGMPIGDIISTLIAGMGGTLGSVAILVALG 72

Query: 74  TILGKMMEVSGAAERIGLTL-QRCRWLSVDVIMVLVGLICGITLFVEVGVVLLIPLAFSI 132
           ++LG+M+EVSG A  +     Q      V + +    L+  I +F +VG ++L+P+ +  
Sbjct: 73  SMLGRMIEVSGGAASLANRFTQLLGPTRVPMALTAAALVLAIPVFFDVGFIILVPIVYGF 132

Query: 133 AKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLLVGLMASLI 192
            K    + +K  +P+   ++A H VVPPHP  +  A  +  DIG + + GL + +  + +
Sbjct: 133 CKAAGVNPIKFGLPVAGIMLAAHVVVPPHPGIVGGAAIVKGDIGWITIIGLAICIPLAAL 192

Query: 193 GGPLFLKFLGQRLPFKPVPTE-FADLKVRDEKTL------PSLGATLFTILLPIALMLVK 245
              +      +  P  P   E FA     ++ T       PS+G  +  I++P+AL++  
Sbjct: 193 SQVVAGWLNRKGYPMLPTTAEQFAAFGNSEDSTASKSGKAPSVGTIMALIIIPLALIMAG 252

Query: 246 TIAELNMARESGLYILVEFIGNPITAMFIAVFVAYYVLGIRQHMSMGTMLTHTENGFGSI 305
           T     + +   L  ++ FIG+PI A+ +AV +A ++LG  Q  +        E+     
Sbjct: 253 TTGATLLPKGDSLRNVLGFIGSPIFALMVAVGLAMFLLGRNQGWNRERTNAIMESALPPA 312

Query: 306 ANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSATVAMM 365
           A ++L+ GAGG F  +L +S +   L+  L+  H+  ILLA++++L L AA GSATVA++
Sbjct: 313 ATVILVTGAGGVFAKVLTASGIGAALSQSLTATHLPLILLAFIISLALRAAQGSATVAII 372

Query: 366 GATAIVAPMLP--LYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETFKYY 423
               ++A  +    Y  +   ++ +AIG G++G + V DS FW+V +Y G ++ +  + +
Sbjct: 373 TTCGLLADAMAGGGYSPLQVALLTVAIGFGSLGLSHVNDSGFWIVTRYLGLSVGDGLRTW 432

Query: 424 TTATFIASVVALAGTFLLSFII 445
           T  T +  +   A T LL  ++
Sbjct: 433 TVLTTVLGIAGFAMTALLWVLV 454


Lambda     K      H
   0.329    0.143    0.418 

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: 582
Number of extensions: 36
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: 445
Length of database: 456
Length adjustment: 33
Effective length of query: 412
Effective length of database: 423
Effective search space:   174276
Effective search space used:   174276
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: 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