GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Sulfurimonas denitrificans DSM 1251

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_011372369.1 SUDEN_RS03855 SulP family inorganic anion transporter

Query= SwissProt::P0AFR2
         (559 letters)



>NCBI__GCF_000012965.1:WP_011372369.1
          Length = 545

 Score =  340 bits (873), Expect = 6e-98
 Identities = 194/525 (36%), Positives = 313/525 (59%), Gaps = 31/525 (5%)

Query: 28  RFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVSGPTA 87
           R + D+ AGI VGI+A+PL++A A+ SGV+P+ GL TA VAG +I++ GGSR  + GPT 
Sbjct: 21  RLSSDIFAGIVVGIVALPLSIAFAVASGVSPEKGLITAIVAGFIISILGGSRVQIGGPTG 80

Query: 88  AFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGIGITI 147
           AF+VILY + +++G+ GL+++T+++G+FL++ G  R G L++Y P  + +GFTSGI + I
Sbjct: 81  AFIVILYAIVEEYGIDGLMISTIMAGVFLVIFGFLRLGNLLKYFPHPLIVGFTSGIAVVI 140

Query: 148 GTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWPRLGIRLP 207
            + QIKD LGL +  +P  +  K    F  +   N+    + IVT+ I ++  ++  ++P
Sbjct: 141 FSTQIKDALGLNIEKLPSEFFHKWLTYFSNIGDTNLYALLLSIVTILITIYSKKVTTKVP 200

Query: 208 GHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLVLPWDLPNSE 267
           G   A++   AV   V +    V TI + F      G   N      P + L        
Sbjct: 201 GSFIAII---AVTLFVQIASIPVTTIETFF------GEIPNSFALQFPNIEL-------- 243

Query: 268 FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLGNIIAPFF 327
                 ++   L  A ++A+LG +ESLL AVV DGM G  H++N+EL+ QG+ NI+ PFF
Sbjct: 244 -----SNLYMYLAPALTIALLGGVESLLSAVVADGMIGGNHRSNTELIAQGVANIVTPFF 298

Query: 328 GGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMAALLLMVA 387
           GGI AT AIAR+A NV+ G  +PI+ ++HS+ ++L +L+ A     +P+SA+A +L++V+
Sbjct: 299 GGIAATGAIARTATNVKNGGRTPIAGIVHSLTLLLIMLIFASYAKLIPMSALAGILIVVS 358

Query: 388 WNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMRRIARM-- 445
           +NMSE    V +LR     DIIV+L    LTV  D+ IAI +G+VL+SLLFM+R+A +  
Sbjct: 359 YNMSEWRSFVSILR-GSNFDIIVLLSTFLLTVFVDLTIAIQIGVVLSSLLFMKRMADIGI 417

Query: 446 -TRLAPVVV----DVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVILKWDAVPVL 500
            T++   V+    +VP  + +  + GP FFA+A+     +++     +I+I++   VP +
Sbjct: 418 KTQVDSDVLEDYSEVPKGISIYEISGPFFFASAKQYTEVIKNVGIKSKILIIRMRHVPFV 477

Query: 501 DAGGLDAFQRFVKRLPE-GCELRVCNVEFQPLRTMARAGIQPIPG 544
           D+  L  FQ  +K L +   ++ +  V+   L  + + GI  + G
Sbjct: 478 DSTALHNFQETIKTLQQLDVKIVLSGVQNSVLEDLKKDGITSLIG 522


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: 588
Number of extensions: 18
Number of successful extensions: 4
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: 545
Length adjustment: 36
Effective length of query: 523
Effective length of database: 509
Effective search space:   266207
Effective search space used:   266207
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 Apr 09 2024. 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