GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Desulfovibrio vulgaris Hildenborough

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate 209213 DVU0279 sulfate permease family protein

Query= SwissProt::P0AFR2
         (559 letters)



>MicrobesOnline__882:209213
          Length = 568

 Score =  390 bits (1002), Expect = e-113
 Identities = 226/552 (40%), Positives = 326/552 (59%), Gaps = 37/552 (6%)

Query: 21  KEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRF 80
           +E Y    F +DL AG+TVGI+A+PLAMA AI SG  P+ GL+TA VAG +I+L GGSR+
Sbjct: 22  REGYDGGTFFKDLAAGLTVGIVALPLAMAFAIASGTTPERGLFTAIVAGFLISLLGGSRY 81

Query: 81  SVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFT 140
            + GPT AFV+I++ V  + G  GL+V TLL+G  L++ GL RFG LI+YIP  VT GFT
Sbjct: 82  QIGGPTGAFVIIIFNVIMKHGYDGLVVTTLLAGAMLLVFGLCRFGALIKYIPYPVTTGFT 141

Query: 141 SGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWP 200
           +GI + I + Q+KDFLGL M  VP  + +K  A      T +     I  + LG ++   
Sbjct: 142 AGIAVLIFSQQVKDFLGLSMQSVPPDFFEKWQAYIHNAATFDPATCGIAFLALGAIILTR 201

Query: 201 RLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLVLP 260
           +   R+PG +  ++        V  LG  V TIGS+F           GIP  LP   LP
Sbjct: 202 KTIPRIPGPVVGVVLASLT---VWALGLDVETIGSRF----------GGIPTELPTFTLP 248

Query: 261 WDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLG 320
                   T+T + +R LLP A ++A+L  IESLL  VV DGMTG KH +N EL  QG  
Sbjct: 249 --------TVTLERVRQLLPDAMTIALLAGIESLLSCVVADGMTGDKHNSNVELAAQGAA 300

Query: 321 NIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMA 380
           NI +  FGGI AT AIAR+  N+R+G  +P++ +IH+ +++  +L LAPL S++PL+++A
Sbjct: 301 NIASVMFGGIPATGAIARTVTNIRSGGRTPVAGMIHAAVLVGFILYLAPLASFIPLASLA 360

Query: 381 ALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMR 440
           A+L++VAW+MSE HK + LL HAPK D++VM L  +LTV+ D+ +A+ VG++LASLLFMR
Sbjct: 361 AVLMVVAWDMSEMHKFLRLL-HAPKSDVLVMCLTFALTVVIDLTVAVYVGVMLASLLFMR 419

Query: 441 RIARMTRLAPVV--------------VDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEG 486
           R++ +T++   +              +DVP+ V V  + GP FF  A+     L +    
Sbjct: 420 RMSEVTQICTCLDGEATKVQGRETAELDVPEGVKVYEIDGPFFFGVADRFQNVLAALDRQ 479

Query: 487 KRIVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAGIQPIPGR 545
             + IL+   V  LD+  ++A + F ++   +G +L +  V      T+ R G   + G 
Sbjct: 480 PEVFILRMRKVSTLDSTAVNALEVFWRKCRSDGTQLLLSGVRETMRTTLRRMGTLSLIGE 539

Query: 546 LAFFPNRRAAMA 557
                N  AA+A
Sbjct: 540 GNICENIDAALA 551


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: 673
Number of extensions: 38
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: 559
Length of database: 568
Length adjustment: 36
Effective length of query: 523
Effective length of database: 532
Effective search space:   278236
Effective search space used:   278236
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: 53 (25.0 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