GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Dechlorosoma suillum PS

Align sodium:C4-dicarboxylate symporter (dctA) (characterized)
to candidate Dsui_3482 Dsui_3482 Na+/H+ dicarboxylate symporter

Query= reanno::pseudo5_N2C3_1:AO356_18980
         (450 letters)



>FitnessBrowser__PS:Dsui_3482
          Length = 437

 Score =  290 bits (742), Expect = 6e-83
 Identities = 165/400 (41%), Positives = 244/400 (61%), Gaps = 9/400 (2%)

Query: 41  DGFIKLIKMVIAPIIFCTVVSGIGGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNV 100
           D F++LIKM+IAP+IF T+V+G+  M + K+VG+ GG AL +F   S  +L IGL+  NV
Sbjct: 46  DIFLRLIKMIIAPLIFATLVAGLANMGDAKAVGRVGGRALGWFICASFCSLFIGLLFANV 105

Query: 101 VQPGAGMHIDVSTLDTSKIAGFISAGKDQSIIAFILNVIPNTIVGAFANGDILQVLMFSV 160
           +QPG  + + +        AG        ++  FI +V P +I+ A A  ++LQ+L+F+V
Sbjct: 106 LQPGHALSVPLP----ESAAGLNLKTSALNLKDFITHVFPKSIMEAMAGNEVLQILVFAV 161

Query: 161 LFGFAL-HRLGAYGKPVLDFIDRFAHVMFIIINMIMKLAPLGAFGAMAFTIGAYGVGSLV 219
            FG AL H      + +++ +D   HVM  + + +M+ AP G FGA+A  I   G+G L+
Sbjct: 162 FFGLALGHLHNQAARSLVNTMDEVVHVMLKVTDYVMRFAPFGVFGAVAGAITTNGLGMLL 221

Query: 220 QLGQLMICFYITCVVFVLVVLGAICRAHGFSVIKLIRYIREELLIVLGTSSSESALPRML 279
             G+ M+ FY+       +++ A     G  V +LI+ +R  LL+   T+SSES  P+++
Sbjct: 222 VFGKFMLSFYVALAALWALLILAGFIVLGKDVFRLIKLVRGPLLVGFSTASSESVYPKLM 281

Query: 280 IKMERLGAKKSVVGLVIPTGYSFNLDGTSIYLTMAAVFIAQATDTPMDLTHQITLLLVLL 339
            ++E+ G K  V G V+P GYSFNLDG+ +Y T  A+FIAQA D PM LT QIT+LLVL+
Sbjct: 282 EQLEKFGIKTRVTGFVLPLGYSFNLDGSMMYTTFLALFIAQAYDIPMSLTAQITMLLVLM 341

Query: 340 LSSKGAAGVTGSGFIVLAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATIV 399
           +SSKG AGV  +  +V+AA L  + +LP AGL L+LGID F+   R +TN++GN++AT V
Sbjct: 342 VSSKGIAGVPRASLVVVAAVL-PMFNLPEAGLLLVLGIDHFLDMGRTVTNVLGNSIATAV 400

Query: 400 VAKWVKELDEDQLQTELASGGRGISDVREDDEQIAAAQIA 439
           VAKW   +  D +  ELA     +  V EDD  + A   A
Sbjct: 401 VAKWEGAI--DPVSEELAEAEESL-PVPEDDSLVTAKAAA 437


Lambda     K      H
   0.326    0.142    0.402 

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: 494
Number of extensions: 27
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: 450
Length of database: 437
Length adjustment: 32
Effective length of query: 418
Effective length of database: 405
Effective search space:   169290
Effective search space used:   169290
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: 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