RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12313
         (488 letters)



>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein.  The
           Ligand-gated Ion Channel (LIC) Family of
           Neurotransmitter Receptors TC 1.A.9)Members of the LIC
           family of ionotropic neurotransmitter receptors are
           found only in vertebrate and invertebrate animals. They
           exhibit receptor specificity for (1)acetylcholine, (2)
           serotonin, (3) glycine, (4) glutamate and (5)
           g-aminobutyric acid (GABA). All of these receptor
           channels are probably hetero- orhomopentameric. The best
           characterized are the nicotinic acetyl-choline receptors
           which are pentameric channels of a2bgd subunit
           composition. All subunits arehomologous. The three
           dimensional structures of the protein complex in both
           the open and closed configurations have been solved at
           0.9 nm resolution.The channel protein complexes of the
           LIC family preferentially transport cations or anions
           depending on the channel (e.g., the acetylcholine
           receptors are cationselective while glycine receptors
           are anion selective) [Transport and binding proteins,
           Cations and iron carrying compounds].
          Length = 459

 Score =  264 bits (677), Expect = 3e-83
 Identities = 106/295 (35%), Positives = 165/295 (55%), Gaps = 7/295 (2%)

Query: 176 VLNNLLKNYQSSEPPNHGKGEPTIIKTNMLIRSMGPISEIDMDYSMDCYFRQYWRDSRLS 235
           +L+ LLKNY +   P  G G P  +  N+ +RS+  + E +MDY+ + + RQ W D RL 
Sbjct: 34  LLDELLKNYDARVRPVFG-GPPVTVSFNLFLRSIMDVDEKNMDYTTNIWLRQEWTDERLQ 92

Query: 236 FMGPINNLSLSIKML--EKIWRPDTYILNGKQSYVHTITVPNKLLRINQDGDILYSMRLT 293
           +  P     +++     + IW PD +  N K +  H IT+ N L+RI+ +G +LYS R+T
Sbjct: 93  W-NPEEYPGVTLVRTPDDSIWVPDIFFYNEKDARFHGITMTNVLVRIHPNGSVLYSPRIT 151

Query: 294 IKANCPMSLRNFPMDTQSCPLILGSYAYPIEKLVYHWTPGKSISFVPGMAIS--QFDFIS 351
           +   CPM LRNFP D Q+C L   S+ Y    +   W    ++     + IS  +F+ + 
Sbjct: 152 LTLACPMDLRNFPFDVQNCSLKFESWGYTTNDIKLEWKEQGAVQVDDSLFISLPEFELLG 211

Query: 352 SP-KRNFTFKRREGEFSLLQVNFNLKRHRGYFVIQVYVPCVLIVVLSWVSFWIHREATSD 410
               R  T +   GE+  L  +F L+R   Y+++Q+Y+P +LIV+LSWVSFW+  +A+  
Sbjct: 212 VYGTRYCTSETNTGEYPCLTFSFVLRRRPLYYLLQLYIPSILIVILSWVSFWLPADASGA 271

Query: 411 RIGLGITTVLTLSTISLDSRTDLPKVRYATALDWFLLMSFFYCIATILEFAAVHY 465
           R+ LGITT+LT++T S   R  LP V Y  A+D +  +   +    +LE A V+Y
Sbjct: 272 RVSLGITTLLTMTTFSSGVRESLPAVSYVKAIDVYFAVCMAFVFLALLETAFVNY 326


>gnl|CDD|217293 pfam02931, Neur_chan_LBD, Neurotransmitter-gated ion-channel ligand
           binding domain.  This family is the extracellular ligand
           binding domain of these ion channels. This domain forms
           a pentameric arrangement in the known structure.
          Length = 215

 Score =  179 bits (457), Expect = 8e-54
 Identities = 60/215 (27%), Positives = 97/215 (45%), Gaps = 16/215 (7%)

Query: 176 VLNNLLKNYQSSEPPNHGKGEPTIIKTNMLIRSMGPISEIDMDYSMDCYFRQYWRDSRLS 235
           +L++LL+NY     P     +P  +   + +  +  + E + D + + + RQ W D RL+
Sbjct: 4   LLDDLLENYDKRVRPVKNGSDPVTVSVGLYLTQIIDVDEKNQDLTTNVWLRQQWTDERLA 63

Query: 236 F----MGPINNLSLSIKMLEKIWRPDTYILNGKQSYVHTITVPNKLLRINQDGDILYSMR 291
           +     G I +L L     +KIW+PD  + N K   +H IT PN  +R+  DG +L+S  
Sbjct: 64  WDPEDYGGITSLRLPS---DKIWKPDIVLYN-KADGIHDITTPNTNVRVYPDGTVLWSPP 119

Query: 292 LTIKANCPMSLRNFPMDTQSCPLILGSYAYPIEKLVYHWTPGKSISFVPGMAISQFDFIS 351
              K++CPM L  FP D Q+C L  GS+ Y  E++   W           + +S F    
Sbjct: 120 AIYKSSCPMDLTYFPFDQQNCSLKFGSWTYNGEEVDLRWKDDTPPILDEEIDLSDFTENG 179

Query: 352 -SPKRNFTFKRRE-------GEFSLLQVNFNLKRH 378
                +   KR E         +  +   F L+R 
Sbjct: 180 EWDIVDVPAKRNEYPYGCYSELYPDVTFYFVLRRK 214


>gnl|CDD|202474 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
           transmembrane region.  This family includes the four
           transmembrane helices that form the ion channel.
          Length = 228

 Score =  108 bits (273), Expect = 3e-27
 Identities = 33/107 (30%), Positives = 51/107 (47%), Gaps = 7/107 (6%)

Query: 386 VYVPCVLIVVLSWVSFWIHREATSDRIGLGITTVLTLSTISLDSRTDLPKVRYATALDWF 445
           + +PCVLI  LSW+ FW+  +A  +++ LGITT+LT++   L  R  LPK  Y   L   
Sbjct: 1   LIIPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIRESLPKTSYVVPLIGK 60

Query: 446 LLMSFFYCIATILEFAAVHYFTKLCYPGY-------PSGFIERLPVI 485
            L+   +     +E+A V        P            F+ +LP +
Sbjct: 61  YLVFTMFVFTASVEYAVVVLNVHHRSPSTHKMPEWVRKLFLRKLPRL 107


>gnl|CDD|184021 PRK13389, PRK13389, UTP--glucose-1-phosphate uridylyltransferase
           subunit GalU; Provisional.
          Length = 302

 Score = 33.3 bits (76), Expect = 0.21
 Identities = 15/35 (42%), Positives = 20/35 (57%)

Query: 70  INEEVNLKISSSNDTENELDHDFEADFLLEKHIKQ 104
           I E V +  SS N  EN  D  FE + +LEK +K+
Sbjct: 54  ITEIVLVTHSSKNSIENHFDTSFELEAMLEKRVKR 88


>gnl|CDD|183561 PRK12504, PRK12504, putative monovalent cation/H+ antiporter
           subunit B; Reviewed.
          Length = 178

 Score = 31.1 bits (71), Expect = 0.87
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 412 IGLGITTVLTLSTISLDSRTD 432
           +G GI+TVL L T++L  R D
Sbjct: 60  VGAGISTVLLLLTLALTGRPD 80


>gnl|CDD|220890 pfam10861, DUF2784, Protein of Unknown function (DUF2784).  This is
           a family of uncharacterized protein. The function is not
           known however it is conserved in Bacteria.
          Length = 114

 Score = 29.9 bits (68), Expect = 1.1
 Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 7/51 (13%)

Query: 440 TALDWFLLMSFF--YCIATILEFAAVHYFTKLCYPGYPSGFIER--LPVIG 486
            A+ W  L+ +    C  T LE        +    GYP GFIE   LP+I 
Sbjct: 38  PAIAWGALIEWLGIVCPLTPLE---NWLRRRAGEAGYPGGFIEHYLLPLIY 85


>gnl|CDD|218889 pfam06088, TLP-20, Nucleopolyhedrovirus telokin-like protein-20
           (TLP20).  This family consists of several
           Nucleopolyhedrovirus telokin-like protein-20 (TLP20)
           sequences. The function of this family is unknown but
           TLP20 is known to shares some antigenic similarities to
           the smooth muscle protein telokin although the amino
           acid sequence shows no homologies to telokin.
          Length = 162

 Score = 30.4 bits (69), Expect = 1.1
 Identities = 16/81 (19%), Positives = 27/81 (33%), Gaps = 20/81 (24%)

Query: 18  NYISDYNFTFNDTVDKPSENISAVYNISAVNNLTNLFYITSDVFRSHSLIFKI---NEEV 74
           +Y   YN   N               I+ +     LF I   V +    IFKI   N + 
Sbjct: 69  DYTVVYNLVSNS------------RRINVI-----LFNIKPTVLKKGGCIFKIVYWNSKK 111

Query: 75  NLKISSSNDTENELDHDFEAD 95
            +     + +  + + + E D
Sbjct: 112 FVSAPVPHHSSEDENDEDEED 132


>gnl|CDD|192997 pfam12349, Sterol-sensing, Sterol-sensing domain of SREBP
           cleavage-activation.  Sterol regulatory element-binding
           proteins (SREBPs) are membrane-bound transcription
           factors that promote lipid synthesis in animal cells.
           They are embedded in the membranes of the endoplasmic
           reticulum (ER) in a helical hairpin orientation and are
           released from the ER by a two-step proteolytic process.
           Proteolysis begins when the SREBPs are cleaved at
           Site-1, which is located at a leucine residue in the
           middle of the hydrophobic loop in the lumen of the ER.
           Upon proteolytic processing SREBP can activate the
           expression of genes involved in cholesterol biosynthesis
           and uptake. SCAP stimulates cleavage of SREBPs via
           fusion of the their two C-termini. This domain is the
           transmembrane region that traverses the membrane eight
           times and is the sterol-sensing domain of the cleavage
           protein. WD40 domains are found towards the C-terminus.
          Length = 153

 Score = 29.5 bits (67), Expect = 1.9
 Identities = 18/88 (20%), Positives = 39/88 (44%), Gaps = 19/88 (21%)

Query: 381 YFVIQVYVPCVLIVVLSWVSFWIHREAT-SDRIGLGITTV---LTLSTIS------LDSR 430
           + V+ V V  + ++V +       R     +RI   +  V   +TL++++      + + 
Sbjct: 44  FLVLAVGVDNMFLLVHAVQR--TPRSLDVEERIAEALGEVGPSITLTSLTELLAFLIGAL 101

Query: 431 TDLPKVR----YAT---ALDWFLLMSFF 451
           T +P V+    +A      D+ L ++FF
Sbjct: 102 TPMPAVQEFCLFAAVAVLFDFLLQITFF 129


>gnl|CDD|221230 pfam11800, RP-C_C, Replication protein C C-terminal region.
           Replication protein C is involved in the early stages of
           viral DNA replication.
          Length = 208

 Score = 29.9 bits (68), Expect = 2.5
 Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 3/38 (7%)

Query: 346 QFDFISSPK---RNFTFKRREGEFSLLQVNFNLKRHRG 380
           +   I+SP    R+ T +   GEFSL  +   L R RG
Sbjct: 169 RAGHINSPGGYLRDLTERAARGEFSLGPMLMALLRARG 206


>gnl|CDD|234776 PRK00478, scpA, segregation and condensation protein A/unknown
           domain fusion protein; Provisional.
          Length = 505

 Score = 29.1 bits (65), Expect = 5.4
 Identities = 32/148 (21%), Positives = 63/148 (42%), Gaps = 20/148 (13%)

Query: 38  ISAVYNISAVNNLTNLFYITSDVFRSHSLIFKINEEVNLKISSSNDTENELDHDFEADFL 97
           I+   N  A+  +T+   ITS++ R  +         +  + +  D E +L++D   +  
Sbjct: 202 INKHMNKKAIELITDYLVITSEILRIKA---------DNLLPNFED-ETKLEYDLNNNDE 251

Query: 98  LEKHIKQII-------SLVYFQVLYLHFVSTF---NVLSMFSVKLNNGYMKIMDDETKTH 147
            +K + +++       SL  F+ L L+ ++ F   N   +F +  N+  + + D      
Sbjct: 252 RDKIVARLVEYKRYSESLPSFEKLRLNRLAYFSKENDWDVFILTSNDQLVLLEDPLPNYV 311

Query: 148 WTNRLPKVSNHLKEKKKHDLMIGKNITL 175
              +L    N L EK K   +  KNI +
Sbjct: 312 SVLKLKHAMNKLFEKLKIKTLTNKNIVI 339


>gnl|CDD|165329 PHA03031, PHA03031, hypothetical protein; Provisional.
          Length = 449

 Score = 28.4 bits (63), Expect = 9.8
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 3/61 (4%)

Query: 18  NYISDYNFTFNDTVDKPSENISAVYNISAVNNLTNLFYITSDVFRSHSLIFKINEEVNLK 77
           +   + N T +D ++   E I  + NI     L  L   +    + H  I   N+E+++ 
Sbjct: 374 DEFKNINITHDDDIETSIEKIKKINNIELFKILNKLINKS---IKDHMQIISENKEIDIN 430

Query: 78  I 78
           I
Sbjct: 431 I 431


  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
   0.323    0.138    0.418 

Gapped
Lambda     K      H
   0.267   0.0789    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,604,193
Number of extensions: 2383262
Number of successful extensions: 1806
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1799
Number of HSP's successfully gapped: 30
Length of query: 488
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 387
Effective length of database: 6,457,848
Effective search space: 2499187176
Effective search space used: 2499187176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 61 (27.2 bits)