GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Shewanella oneidensis MR-1

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate 202663 SO3562 proton/glutamate symporter, putative (NCBI ptt file)

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__MR1:202663
          Length = 413

 Score =  248 bits (632), Expect = 3e-70
 Identities = 134/396 (33%), Positives = 217/396 (54%), Gaps = 11/396 (2%)

Query: 12  QVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMESMKAVG 71
           +VLT   +G L+G    E    +KPLGD F+  IKM++AP++FC++V  I  + S   + 
Sbjct: 14  KVLTGFILGALVGVLLGESATVLKPLGDLFISAIKMLVAPLVFCSIVVSITSLGSQTNLK 73

Query: 72  RTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKDQGIVA 131
           R     L  F +  TIA +IGL + +++  G  M +  AT + +       +    G   
Sbjct: 74  RLSIKTLGMFMLTGTIASLIGLAVGSLIDMGGTMQL--ATTEVR-------ERNIPGFAQ 124

Query: 132 FIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIFGIINM 191
            ++D+IP +   + A G +LQ+++FA L G A++++G K + +   IE+ ++V+F +  M
Sbjct: 125 VLLDMIPINPFASLAEGKVLQIIVFAALVGIAINKVGEKAEPLKRTIEAGAEVMFQLTRM 184

Query: 192 IMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKATGFSIFK 251
           +++L PIG FG MA+ +G+YG+ TL+ LG+ I   YI  ++ ++ V G   K  G S  +
Sbjct: 185 VLKLTPIGVFGLMAWVVGEYGLSTLLPLGKFIAAIYIAALVHMIFVYGGFVKLAGLSPIQ 244

Query: 252 FIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT-SIYLT 310
           F R      L+   TSSS   LP     +E +G  K     V+P G + N+DG   IY  
Sbjct: 245 FFRKALPAQLVAFSTSSSFGTLPASTRAVETMGVSKRYSAFVMPLGATMNMDGCGGIYPA 304

Query: 311 MAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPVAGLA 370
           +AA+FIAQ     +D +  + + +   ++S G AGV GS  ++L  TL  +G LP+ G+A
Sbjct: 305 IAAIFIAQIYGIPLDTLDYVMIAVTATIASVGTAGVPGSAMVMLTVTLGVIG-LPLEGIA 363

Query: 371 LILGIDRFMSEARALTNLVGNGVATIVVAKWVKELD 406
            I  IDR +   R  TN+ G+ +  +V+ K   ELD
Sbjct: 364 FIASIDRIIDMIRTTTNVTGDMMTAVVIGKSENELD 399


Lambda     K      H
   0.327    0.142    0.401 

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: 23
Number of successful extensions: 6
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: 428
Length of database: 413
Length adjustment: 32
Effective length of query: 396
Effective length of database: 381
Effective search space:   150876
Effective search space used:   150876
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: 50 (23.9 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