GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Shewanella loihica PV-4

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate 5208721 Shew_1224 sodium:dicarboxylate symporter (RefSeq)

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__PV4:5208721
          Length = 416

 Score =  228 bits (581), Expect = 3e-64
 Identities = 131/411 (31%), Positives = 224/411 (54%), Gaps = 22/411 (5%)

Query: 6   PLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAG 65
           P ++ +    I+ + +G++LG    +    LKPLGD FI  IKM++AP+IFC +V  I  
Sbjct: 9   PFWQKVLAGFILGVGLGVVLG----EQATQLKPLGDLFIAAIKMLVAPLIFCAIVVSITS 64

Query: 66  MQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTA 125
           + N  S+ +     L  F +  TIA LIGL + +++  G  + +  + +           
Sbjct: 65  LGNDVSLKRLSIKTLAMFMLTGTIASLIGLAIGSLIDMGGSLELATTEV----------- 113

Query: 126 GKDQSIVGF---ILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDR 182
            +++++ GF   +L++IP     + A G +LQ+++F+ + G A++++G   +P+   I+ 
Sbjct: 114 -RERNVPGFAQVLLDMIPVNPFASLAEGKVLQIIVFAALVGIAINKIGEKAEPLKRTIEA 172

Query: 183 FAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGA 242
            A VMF +  M+++L PIG  G MA+ +G YG+ +L+ LG+ +   YI  ++ ++ V G 
Sbjct: 173 GAEVMFQLTRMVLQLTPIGVFGLMAWVVGEYGLSTLLPLGKFIGAIYIAALIHMVFVYGG 232

Query: 243 ICR-AHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYS 301
           + R   G S ++  R      L+   T+SS   LP      E +G  K     V+P G +
Sbjct: 233 LVRFGAGLSAVQFFRKAMPAQLVAFTTASSFGTLPASTRATETMGVSKKYGAFVLPLGAT 292

Query: 302 FNLDGT-SIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATL 360
            N+DG   IY  +AA+FIAQ     +++T  + + +   ++S G AGV GS  ++L+ TL
Sbjct: 293 MNMDGCGGIYPAIAAIFIAQIYGIPLEMTDYMLIAVTATVASVGTAGVPGSAMVMLSVTL 352

Query: 361 SAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQ 411
             VG LP+ G+A I  IDR +   R  TN+ G+ +  VVV K   +LD++Q
Sbjct: 353 GVVG-LPLEGIAFIASIDRVIDMIRTATNVTGDMMTAVVVGKSEGQLDQEQ 402


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: 430
Number of extensions: 31
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: 416
Length adjustment: 32
Effective length of query: 412
Effective length of database: 384
Effective search space:   158208
Effective search space used:   158208
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 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