GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Williamsia sterculiae CPCC 203464

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate WP_076480183.1 BW971_RS13035 cation:dicarboxylase symporter family transporter

Query= TCDB::Q848I3
         (444 letters)



>NCBI__GCF_900156495.1:WP_076480183.1
          Length = 482

 Score =  371 bits (953), Expect = e-107
 Identities = 197/437 (45%), Positives = 288/437 (65%), Gaps = 7/437 (1%)

Query: 11  LYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQNMK 70
           LY  VIVA+  G+++G   P  G  +  LG  F+ LIKM+I+PIIFCT+V GI  ++   
Sbjct: 45  LYLAVIVAVVAGVIVGLVAPGVGKDIAVLGTMFVSLIKMMISPIIFCTIVLGIGSVRKAA 104

Query: 71  SVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGKDQS 130
           +VG+ GG A +YF ++STIAL +GLVV N++QPG+G+H+  ++    +  A   A +   
Sbjct: 105 TVGRVGGLAFVYFLVMSTIALAVGLVVGNLIQPGSGLHLSATSAGKGQQLAD-DAHEAGG 163

Query: 131 IVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHVMFNI 190
           ++ F+  +IP +++ +   G++LQ L  +++ GFAL  +G  G+P+L  I     ++F I
Sbjct: 164 LMDFVQGIIPESLLSSLTAGNVLQTLFVALLVGFALQAMGTTGEPILTAIGYIQKLVFRI 223

Query: 191 INMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRAHGF- 249
           + M++ LAPIGA GA+A  +G  G  ++ +L  LM+ FY+TC++FV  VLGA+ RA    
Sbjct: 224 LTMVLWLAPIGAFGAIAGVVGQTGWSAVGELLMLMVAFYLTCLIFVFGVLGAVLRAVAHV 283

Query: 250 SVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDGTSI 309
           S+ KL+RY+  E L++  TSSSESALPR++ KME LG +++ VG+V+PTGYSFNLDGT+I
Sbjct: 284 SIFKLVRYLAREYLLIFATSSSESALPRLIAKMEHLGVQRTTVGVVVPTGYSFNLDGTAI 343

Query: 310 YLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP-- 367
           YLTMA++F+A A    + +  Q  LL+ ++++SKGAAGV+G+G   LA  L A  H P  
Sbjct: 344 YLTMASIFVADALGKPLSLAEQFGLLVFMIVASKGAAGVSGAGLATLAGGLQA--HRPDL 401

Query: 368 VAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGRAISDTR 427
           + G+ LI+GIDRFMSEARA+TN  GNAVAT++V  W   +D D++   LA        T 
Sbjct: 402 LNGVGLIVGIDRFMSEARAVTNFSGNAVATLLVGSWTHTIDPDRVDHVLAGRDPFDETTM 461

Query: 428 EEDDLGVAEGPTPTTVK 444
             DD G A G TPT  K
Sbjct: 462 VGDDHGAAVG-TPTDGK 477


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: 623
Number of extensions: 39
Number of successful extensions: 5
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: 444
Length of database: 482
Length adjustment: 33
Effective length of query: 411
Effective length of database: 449
Effective search space:   184539
Effective search space used:   184539
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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