Aligments for a candidate for dauA in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|MicrobesOnline__882:209213 DVU0279 sulfate permease family
           protein
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources