RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

Searching..................................................done

Query= psy10759
         (162 letters)



>gnl|CDD|217924 pfam04142, Nuc_sug_transp, Nucleotide-sugar transporter.  This
           family of membrane proteins transport nucleotide sugars
           from the cytoplasm into golgi vesicles. Human SLC35A1
           transports CMP-sialic acid, SLC35A2 transports
           UDP-galactose and SLC35A3 transports UDP-GlcNAc.
          Length = 238

 Score =  119 bits (301), Expect = 4e-34
 Identities = 52/145 (35%), Positives = 89/145 (61%), Gaps = 1/145 (0%)

Query: 16  FSLGVLLFGIVLIQIDESASESISRKSDNGNQLIGFGQVILASVSSGFTSVYLERIYKAD 75
            SL +L  G+ ++Q+D+ +SE+ S++    N  +G   V+ A  +SGF  VY E+I K  
Sbjct: 75  ASLLLLFLGVAIVQLDQKSSETNSKRGAEQNPGLGLSAVLAACFTSGFAGVYFEKILK-G 133

Query: 76  GDDTLLIKNLQLSLLSIPISMINVLLQDSDTVSQHGLFFGYDGLVLTDVLFNALGGLIIS 135
            + ++ I+N+QL    I  +++   L D   +S+ G FFGY   V   VL  A+GGL+++
Sbjct: 134 SNTSIWIRNIQLYFFGIFFALLTCWLYDGSAISEKGFFFGYTAFVWAVVLLQAVGGLVVA 193

Query: 136 LVLKHHDNITKIFSTSVSIVVTFVL 160
           +V+K+ DNI K F+TS++I+++ V 
Sbjct: 194 VVVKYADNILKGFATSLAIILSTVA 218


>gnl|CDD|129885 TIGR00803, nst, UDP-galactose transporter.  The 10-12 TMS
           Nucleotide Sugar Transporters (TC
           2.A.7.10)Nucleotide-sugar transporters (NSTs) are found
           in the Golgi apparatus and the endoplasmic reticulum of
           eukaryotic cells. Members of the family have been
           sequenced from yeast, protozoans and animals. Animals
           such as C. elegans possess many of these transporters.
           Humans have at least two closely related isoforms of the
           UDP-galactose:UMP exchange transporter.NSTs generally
           appear to function by antiport mechanisms, exchanging a
           nucleotide-sugar for a nucleotide. Thus, CMP-sialic acid
           is exchanged for CMP; GDP-mannose is preferentially
           exchanged for GMP, and UDP-galactose and
           UDP-N-acetylglucosamine are exchanged for UMP (or
           possibly UDP). Other nucleotide sugars (e.g.,
           GDP-fucose, UDP-xylose, UDP-glucose,
           UDP-N-acetylgalactosamine, etc.) may also be transported
           in exchange for various nucleotides, but their
           transporters have not been molecularly characterized.
           Each compound appears to be translocated by its own
           transport protein. Transport allows the compound,
           synthesized in the cytoplasm, to be exported to the
           lumen of the Golgi apparatus or the endoplasmic
           reticulum where it is used for the synthesis of
           glycoproteins and glycolipids.
          Length = 222

 Score = 67.8 bits (166), Expect = 2e-14
 Identities = 53/153 (34%), Positives = 84/153 (54%), Gaps = 5/153 (3%)

Query: 8   GSKSLKKVFSLGVLLFGIVLIQIDESASESISRKSDNGNQLIGFGQVILASVSSGFTSVY 67
            S    + FSL +L  G+ ++Q+ +S+++++      GN ++G   V+ A +SSGF  VY
Sbjct: 48  ASLGDDQWFSLKLLKLGVAIVQMVQSSAKTLMF----GNPVVGLSAVLSALLSSGFAGVY 103

Query: 68  LERIYKADGDDTLLIKNLQLSLLSIPISMINVLLQDSDTVSQHGLFFGYDGLVLTDVLFN 127
            E+I K DGD     +NLQL L  +  +   +L  D   +S  G F GY   V    L N
Sbjct: 104 FEKILK-DGDTMFWSRNLQLPLFGLFSTFSVLLWSDGTLISNFGFFIGYPTAVWIVGLLN 162

Query: 128 ALGGLIISLVLKHHDNITKIFSTSVSIVVTFVL 160
             GGL I  V+++ DN TK F T++SI+++ + 
Sbjct: 163 VGGGLCIGGVVRYADNTTKSFVTALSIILSTLA 195


>gnl|CDD|219846 pfam08449, UAA, UAA transporter family.  This family includes
           transporters with a specificity for
           UDP-N-acetylglucosamine.
          Length = 303

 Score = 31.0 bits (71), Expect = 0.19
 Identities = 30/145 (20%), Positives = 60/145 (41%), Gaps = 17/145 (11%)

Query: 17  SLGVLLFGIVLIQIDESASESISRKSDNGNQLIGFGQVILASVSSGFTSVYLERIYKA-- 74
           +LGV++F +       SA +S + K    +  +G   +  A +    T    E++YK   
Sbjct: 128 TLGVIIFTLA------SAKDSKNSKLTTFSDNVGIALLFGALLMDALTGNTQEKLYKKYG 181

Query: 75  -DGDDTLLIKNLQLSLLSIPISMINVLLQDSDTVSQHGLFFGYDGLVLTDVLFNALGGLI 133
               + +   +    LLS+P  ++ +L   +  +     F      VL  +L N+L   +
Sbjct: 182 KHSKEMMFYSH----LLSLPFFLLGLLDIRTGLLFSAESFCLRHPSVLFYLLLNSLTQYV 237

Query: 134 -ISLVLKHHDNITKIFSTSVSIVVT 157
               V      I++  + +V++V T
Sbjct: 238 GQFFVFYL---ISEFGALTVTLVTT 259


>gnl|CDD|227249 COG4912, COG4912, Predicted DNA alkylation repair enzyme [DNA
          replication, recombination, and repair].
          Length = 222

 Score = 30.1 bits (68), Expect = 0.40
 Identities = 12/56 (21%), Positives = 18/56 (32%), Gaps = 4/56 (7%)

Query: 30 IDESASESISRKSDNGNQLIGFGQVILASVSSGFTSVYLERIYKADGDDTLLIKNL 85
          IDE+    +S       +  G    I A+   G     L  + K    +     NL
Sbjct: 13 IDEALKILMSDYMKAQFKRHG----IRAAERKGIRKDDLRDLAKLIKKNHENALNL 64


>gnl|CDD|237896 PRK15066, PRK15066, inner membrane transport permease; Provisional.
          Length = 257

 Score = 28.3 bits (64), Expect = 1.6
 Identities = 18/42 (42%), Positives = 26/42 (61%), Gaps = 9/42 (21%)

Query: 119 LVLTDVLFNALGGLIISLVLKHHDNITKIFSTSVSIVVTFVL 160
           ++LT +LF +LGGLI ++  K  D+I        SI+ TFVL
Sbjct: 147 VLLTAILF-SLGGLINAVFAKSFDDI--------SIIPTFVL 179


>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
           synthase PfaA.  Members of the seed for this alignment
           are involved in omega-3 polyunsaturated fatty acid
           biosynthesis, such as the protein PfaA from the
           eicosapentaenoic acid biosynthesis operon in
           Photobacterium profundum strain SS9. PfaA is encoded
           together with PfaB, PfaC, and PfaD, and the functions of
           the individual polypeptides have not yet been described.
           More distant homologs of PfaA, also included with the
           reach of this model, appear to be involved in
           polyketide-like biosynthetic mechanisms of
           polyunsaturated fatty acid biosynthesis, an alternative
           to the more familiar iterated mechanism of chain
           extension and desaturation, and in most cases are
           encoded near genes for homologs of PfaB, PfaC, and/or
           PfaD.
          Length = 2582

 Score = 26.5 bits (58), Expect = 8.6
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 9/61 (14%)

Query: 49  IGFGQVILASVSSGFTSVYLERIYKADG----DDTLLIKNLQLSLL-----SIPISMINV 99
           +G GQ   +S+++      L++++KA G    D  +LIK  Q   +     S P S+ NV
Sbjct: 125 VGGGQKQSSSLNARLQYPVLKKVFKASGVEDEDSEMLIKKFQDQYIHWEENSFPGSLGNV 184

Query: 100 L 100
           +
Sbjct: 185 I 185


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.320    0.139    0.377 

Gapped
Lambda     K      H
   0.267   0.0761    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,954,366
Number of extensions: 741137
Number of successful extensions: 733
Number of sequences better than 10.0: 1
Number of HSP's gapped: 731
Number of HSP's successfully gapped: 38
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (24.9 bits)