GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Dechlorosoma suillum PS

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate Dsui_1250 Dsui_1250 sulfate permease-like transporter, MFS superfamily

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__PS:Dsui_1250
          Length = 555

 Score =  374 bits (959), Expect = e-108
 Identities = 220/530 (41%), Positives = 322/530 (60%), Gaps = 41/530 (7%)

Query: 24  YTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVS 83
           Y  A+F RD+ AG+TVG++A+PLAMA AI SGV P  G++TA VAG +IA  GGSR  + 
Sbjct: 15  YDRAQFGRDVSAGLTVGVLALPLAMAFAIASGVDPAAGIWTAIVAGFIIAALGGSRVQIG 74

Query: 84  GPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGI 143
           GPT AF+VI+Y +  Q+GLA LL+AT+L+G+ LI MGLAR G LI +IPV+V +GFT+GI
Sbjct: 75  GPTGAFIVIVYGIVAQYGLANLLIATMLAGLILIGMGLARLGALIRFIPVTVVIGFTNGI 134

Query: 144 GITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFW---- 199
            + I   QIK+FLGL M  +P  +  K+  L   LP  ++   A+   +L +LV W    
Sbjct: 135 AVLIFISQIKEFLGLDMEALPAEFFAKMKVLAANLPNTDLPTLALASASLVLLVLWNKKV 194

Query: 200 ----PRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLP 255
               P LG +LPG L  L+AG       +LL   V TIGS+F           GIPQ LP
Sbjct: 195 AGKLPLLG-KLPGPLAVLIAGTVAQ---SLLEFPVETIGSRF----------GGIPQSLP 240

Query: 256 QLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELV 315
               P         LT  ++R L+  A ++A+LGAIESLL A V D     +H  N EL+
Sbjct: 241 AFAFP--------ELTLSTLRNLISPAITIALLGAIESLLSARVADSQIDDRHDPNQELL 292

Query: 316 GQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLP 375
            QG+ N++AP  GG  AT AIAR++ NVRAG  +P++ ++H++ ++  +LV APL S +P
Sbjct: 293 AQGVANVVAPLVGGFAATGAIARTSTNVRAGGRTPVAGMVHALTLLAVVLVAAPLASDVP 352

Query: 376 LSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLAS 435
           L+ ++A+L++VAWNM E H+  +L R++  +   ++L    +TV+FD+ +A+ +G+VLAS
Sbjct: 353 LATLSAILMVVAWNMGEWHEFKELPRYS-MNYRAILLSTFFITVVFDLTLAVEIGMVLAS 411

Query: 436 LLFMRRIARMTRLAPVVVDVPD-----DVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIV 490
           L F+ R++ +T++AP  + +PD      V    + G LFF A   L T L+   +G +++
Sbjct: 412 LFFIYRMSELTKVAP--LSLPDWAAGQPVAAYSLYGSLFFGAVGKLQTLLDQHAQGTQVL 469

Query: 491 ILKWDAVPVLDAGGLDAFQRFVKRLPE--GCELRVCNVEFQPLRTMARAG 538
           IL    V  LD  GLD  +   + L +  GC L +  +  QP   ++R+G
Sbjct: 470 ILDLHQVINLDTTGLDTLEALQRMLAKRGGC-LILAGLNAQPGSLVSRSG 518


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: 690
Number of extensions: 40
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: 559
Length of database: 555
Length adjustment: 36
Effective length of query: 523
Effective length of database: 519
Effective search space:   271437
Effective search space used:   271437
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