GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Algiphilus aromaticivorans DG1253

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_043765232.1 U743_RS02380 C4-dicarboxylic acid transporter DauA

Query= SwissProt::P0AFR2
         (559 letters)



>NCBI__GCF_000733765.1:WP_043765232.1
          Length = 574

 Score =  478 bits (1231), Expect = e-139
 Identities = 262/563 (46%), Positives = 362/563 (64%), Gaps = 15/563 (2%)

Query: 11  PFRALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGI 70
           P    + A  K  Y  A   RD++AGITVG +AIPL+MALAI +GV PQ+GLYTA VAG 
Sbjct: 5   PLFTALRASLKAGYGIATLRRDVLAGITVGTVAIPLSMALAIATGVPPQHGLYTAIVAGA 64

Query: 71  VIALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEY 130
           V ALTGG+RF+V+GPTAAFVVIL+P+  ++G+ GLLVATL++G+ L+ +G +  GRL+++
Sbjct: 65  VAALTGGARFNVTGPTAAFVVILFPIVAEYGIGGLLVATLMAGLILVALGASGMGRLVQF 124

Query: 131 IPVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGI 190
           IP  V LGFT+GI + I  +Q+  FLG+       H+L  + ++  +LP +     A G+
Sbjct: 125 IPYPVVLGFTAGIALVIAVLQVPQFLGIADGEGAGHFLSGLASIGRSLPELEPLTLATGV 184

Query: 191 VTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLL---GGHVATIGSQFHYVLADGSQG 247
           +TL  L+ WPRL + +P  L  L  G       N +      VATI SQF +  A+G  G
Sbjct: 185 ITLATLLLWPRLQLPVPAPLAGLAVGAVAAWFFNAMQAGDAPVATIASQFEWT-AEGRSG 243

Query: 248 NGIPQLLPQLVLPWDLPNSE---FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMT 304
           +GIP L P  VLPW LP ++     + +  IR L   AF++AML AIESLLC+VV DGMT
Sbjct: 244 SGIPPLAPGFVLPWRLPGADGAPLVVDFALIRDLAGPAFAIAMLAAIESLLCSVVADGMT 303

Query: 305 GTKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILAL 364
            T+H +N EL+GQGL N+ APFFGGITATAAIAR+A  +R+GA SPI+A++HS++V+LA+
Sbjct: 304 RTRHDSNGELIGQGLSNLAAPFFGGITATAAIARTATGIRSGAQSPIAAIVHSLVVLLAM 363

Query: 365 LVLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMV 424
           L+LAPLL  +P+SA+AALL +VAWNMSEA   +  LR AP  D++V++ C  LTVLFDMV
Sbjct: 364 LLLAPLLGLVPMSALAALLFVVAWNMSEARHFLHTLRSAPPGDVLVLVTCFGLTVLFDMV 423

Query: 425 IAISVGIVLASLLFMRRIARMTRL-------APVVVDVPDDVLVLRVIGPLFFAAAEGLF 477
           +A++VGI LA+ LF+RR+A +T         A     VPD V +  V GPLFFAAAE   
Sbjct: 424 LAVAVGIGLAAALFIRRMALLTSADRVRQEGAATTTRVPDSVALYDVNGPLFFAAAEKAL 483

Query: 478 TDLESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRLPE-GCELRVCNVEFQPLRTMAR 536
           + L       R  I+    VP +DA  +   +  +  + + G  L    +  + +  + R
Sbjct: 484 STLRMVDPEVRTAIVDMHDVPSMDATAIVTLRSIIDEMQQHGVALIFVGLPTRIIAKLRR 543

Query: 537 AGIQPIPGRLAFFPNRRAAMADL 559
           AGI+  PGRL +  +   A+A +
Sbjct: 544 AGIRKQPGRLGYCSSLDTALATI 566


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: 783
Number of extensions: 46
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: 574
Length adjustment: 36
Effective length of query: 523
Effective length of database: 538
Effective search space:   281374
Effective search space used:   281374
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 24 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