GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Pseudomonas putida KT2440

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate PP_0075 PP_0075 putative choline sulfate transporter

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__Putida:PP_0075
          Length = 521

 Score =  195 bits (496), Expect = 3e-54
 Identities = 148/505 (29%), Positives = 243/505 (48%), Gaps = 40/505 (7%)

Query: 20  WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79
           W  + +     +DL+ G++  I+A+P ++A A+ +G+  +YGLY A V  ++  L G S 
Sbjct: 13  WLPRQSGRSLRQDLLVGLSGAILALPQSIAYALIAGLPAEYGLYAAIVPVLIACLWGSSW 72

Query: 80  FSVSGPTAAFVVILYPVSQQFGLAG-------LLVATLLSGIFLILMGLARFGRLIEYIP 132
           + + GPTAA  ++LY       +AG       +L+ T L GIF +L+GL RFG L+ ++ 
Sbjct: 73  YLICGPTAAISIVLYASISPLAVAGSADYITLVLLLTFLGGIFQLLLGLLRFGALVNFVS 132

Query: 133 VSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVT 192
            SV LGFT G  I I   Q+ + LG+ +       L  V  L      +++    +G+ T
Sbjct: 133 HSVVLGFTLGAAIVIALGQLPNLLGMALPSQATA-LMTVQDLASHAGEVDLPSLLLGLAT 191

Query: 193 LGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQ 252
           + I   +     R P  L +L+    +  ++    GHV  + +                Q
Sbjct: 192 VVIGAAFKLWRPRWPSLLISLILVSLLAWLLPGFFGHVPRVAAF-------------TGQ 238

Query: 253 LLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANS 312
           L P   LP         L  + +  LLP+A ++ MLG + SL  A  L   +      + 
Sbjct: 239 LPPFSPLP--------LLDMELMLRLLPSAVAVGMLGLVTSLSIARSLSARSEQLIDPDQ 290

Query: 313 ELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLS 372
           E+  QGL NI   FF G  +  +  RS  +  AGA SP++ V  ++ V L  +  A L++
Sbjct: 291 EIRAQGLSNIAGAFFSGYLSAGSFTRSGLSYEAGARSPMAGVFSALWVALFAVTGAGLIA 350

Query: 373 WLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIV 432
            LP+ AMA  +L++ W + + H+ +  L    + + +VM L  + T+L ++  AI  G++
Sbjct: 351 HLPIPAMAGSILLICWGLVD-HRGIRALFRVSRSEFLVMALTAAATLLLELQTAIYAGVL 409

Query: 433 LASLLFMRRIARMTRLAPVVVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVIL 492
            +   +++R +R      +      D  VLRV G +FF AA  L   L+ R +G  +VI 
Sbjct: 410 ASLFFYLKRTSR----PRIQQSREGDADVLRVGGSIFFGAAHYLQVRLQ-RCQGPHVVI- 463

Query: 493 KWDA--VPVLDAGGLDAFQRFVKRL 515
             DA  V  +D  G+D   R  +RL
Sbjct: 464 --DARQVNFIDYSGVDMLHREARRL 486


Lambda     K      H
   0.328    0.142    0.425 

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: 658
Number of extensions: 40
Number of successful extensions: 3
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: 559
Length of database: 521
Length adjustment: 35
Effective length of query: 524
Effective length of database: 486
Effective search space:   254664
Effective search space used:   254664
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: 52 (24.6 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