GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Pseudomonas simiae WCS417

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate GFF25 PS417_00130 SulP family inorganic anion transporter

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__WCS417:GFF25
          Length = 530

 Score =  209 bits (532), Expect = 2e-58
 Identities = 156/511 (30%), Positives = 258/511 (50%), Gaps = 53/511 (10%)

Query: 20  WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79
           W  + T A   RD + G++  ++A+P ++A A+ +G+ P+YGLY A +  ++  L G S 
Sbjct: 15  WLPRQTRASVGRDAMVGLSGAVLALPQSIAYALIAGLPPEYGLYAAIIPVLIACLWGSSW 74

Query: 80  FSVSGPTAAFVVILY--------PVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYI 131
             + GPTAA  ++LY        P SQ + +  +L+ T L+G+F  L+G+ RFG L+ ++
Sbjct: 75  HLICGPTAAISIVLYASVSPLAVPGSQDY-ITLILLLTFLAGVFQWLLGMLRFGALVNFV 133

Query: 132 PVSVTLGFTSGIGITIGTMQIKDFLGLQM---AHVPEHYLQKV---GALFMALPTINVGD 185
             SV LGFT G  + I   Q+ + LGL +   A    + L  +   G    A   + +G 
Sbjct: 134 SHSVVLGFTLGAAVVIALGQLPNLLGLDLPSQATAINNLLTLIHHSGEWDPASVILGLGT 193

Query: 186 AAIGIVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGS 245
             +G +   ++  WP L       L AL  G  V  +   + GHVA + S          
Sbjct: 194 LLVGALLKYLVPRWPTL-------LIALTLGSLVTWLWPAMFGHVALVSSF--------- 237

Query: 246 QGNGIPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTG 305
               I +L P   LP DL         D I  LLP+A ++ MLG + SL  A  L   + 
Sbjct: 238 ----IGKLPPLSPLPMDL---------DVILRLLPSAVAVGMLGLVTSLSIARSLSVRSQ 284

Query: 306 TKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALL 365
               AN E+  QG  NI+  FF G  +  +  RS  +  AGA SP++ V  ++ V L  L
Sbjct: 285 QLLDANQEIRAQGFSNIVGGFFSGYLSAGSFTRSGLSYEAGACSPLAGVFSALWVALFAL 344

Query: 366 VLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVI 425
             A L++ +P+ +MAA +L+++W + +   +  L R +  + +++ L C++ T+L ++  
Sbjct: 345 FGAALIAHIPIPSMAASILLISWGLVDRRGIRALFRVSRAEFVVMSLTCVA-TLLLELQT 403

Query: 426 AISVGIVLASLLFMRRIARMTRLAPVVVDVPD-DVLVLRVIGPLFFAAAEGLFTDLESRL 484
           AI  G++ +   +++R ++     P V    D D  VLRV G +FF A+  L   L+S L
Sbjct: 404 AIYAGVLASLFFYLKRTSQ-----PRVQQWRDGDEDVLRVGGSIFFGASHYLQVRLQS-L 457

Query: 485 EGKRIVILKWDAVPVLDAGGLDAFQRFVKRL 515
           +GKR+VI +   +  +D  G++   +  +RL
Sbjct: 458 QGKRVVI-EAQQINFIDYSGVEMLHQEARRL 487


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: 635
Number of extensions: 41
Number of successful extensions: 3
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: 530
Length adjustment: 35
Effective length of query: 524
Effective length of database: 495
Effective search space:   259380
Effective search space used:   259380
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: 52 (24.6 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