GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Flavobacterium beibuense F44-8

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate WP_035131390.1 Q763_RS03785 cation:dicarboxylase symporter family transporter

Query= TCDB::Q848I3
         (444 letters)



>NCBI__GCF_000769915.1:WP_035131390.1
          Length = 470

 Score =  296 bits (757), Expect = 1e-84
 Identities = 158/401 (39%), Positives = 246/401 (61%), Gaps = 8/401 (1%)

Query: 9   KSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQN 68
           +SL   ++V + IG  +GH +P+ G  L+ L   F+KLIK ++ P+IF T+V GIAG  N
Sbjct: 55  RSLTTWILVCLVIGAAIGHEWPEAGQGLQVLSKIFLKLIKTIVGPLIFATLVYGIAGHSN 114

Query: 69  MKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGKD 128
           +K VG+ G  +LLYFEIV+T+AL IGL  +N+ + G G+      +  + +   + A + 
Sbjct: 115 IKQVGRMGWKSLLYFEIVTTLALFIGLAAINITKAGEGI------IQPTDIKETIQAAEP 168

Query: 129 QSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVL-DFIDRFAHVM 187
           Q+    IL++ P  I  + A G++LQ+++FSVIFG AL  +    + V+ DF    + VM
Sbjct: 169 QTWQQIILHIFPENIAKSMAEGEVLQIVVFSVIFGIALIMVPEKKRKVMVDFTQSLSEVM 228

Query: 188 FNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRAH 247
           F   N++M  APIG   AMA+T+G  G+  L+ L +L++  Y   ++FV++V   I    
Sbjct: 229 FKFTNIVMYFAPIGVGAAMAYTVGHMGLSVLIPLLKLLLTLYGALLVFVIIVFIPIALFI 288

Query: 248 GFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDGT 307
              +   I+ I E + I   T+SSE+ALPR +  ME +G  + +V  V+P GYSFNLDGT
Sbjct: 289 KLDLRAFIKAIGEPVSIAFATTSSEAALPRAMEAMESIGVPRKIVSFVMPMGYSFNLDGT 348

Query: 308 SIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 367
           ++YL++A+VF+AQA    + I  Q+ ++  L+++SKG AG+  +  ++L  T +A  +LP
Sbjct: 349 TLYLSLASVFVAQAAGIDLSIGEQLIMVFTLMVTSKGVAGIPRASLVILMGT-AASFNLP 407

Query: 368 VAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELD 408
           V  + +ILGID  M  AR   N+VGN +A+ V+AKW  E D
Sbjct: 408 VWPIFIILGIDELMDMARTSINVVGNCLASAVIAKWEGEFD 448


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: 530
Number of extensions: 20
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: 444
Length of database: 470
Length adjustment: 33
Effective length of query: 411
Effective length of database: 437
Effective search space:   179607
Effective search space used:   179607
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