RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14149
         (217 letters)



>gnl|CDD|192488 pfam10228, DUF2228, Uncharacterized conserved protein (DUF2228).
           This is a family of conserved proteins of approximately
           700 residues found from worms to humans.
          Length = 253

 Score =  148 bits (375), Expect = 2e-44
 Identities = 78/217 (35%), Positives = 116/217 (53%), Gaps = 5/217 (2%)

Query: 1   TIIVSTGKDHLHFGYFRDCPDEAPVFIASNS-NRDCKINPVAPNIFIFINEKLNEKVKSA 59
           TIIV +    +H+GY+RD PD+ P  IA N   + C+   V  NIF  I   L +K K  
Sbjct: 40  TIIVGSHGTGVHYGYWRDSPDDKPPLIAFNDAKKGCEFTVVGENIFDAILLFLTKKSKEI 99

Query: 60  DLASSP-SKVSSLQQKLTDFAHGHKIDLDAPKLSSVVRARKAKTVCKGLSGVGIVVPYVK 118
                  S +  +Q+ LT++A    + L+    + V++ RK K V K     G+VVP   
Sbjct: 100 PFKKKKISALKKIQELLTEWAKELGLSLEQ--KTKVMKQRKKKVVTKTFHKGGLVVPVDN 157

Query: 119 KTELGYRPLQKSDKDLETLFRQYKDPSVDTRGKLKIKSILEEVSTWVTIAIDESDFGTGL 178
           KT++GYRPL +SD +L+ + +  ++ + D   + K    L+E+ T+V  A DE D+G GL
Sbjct: 158 KTDVGYRPLSESDANLKKILKTIEE-AEDKEERDKAFDELQELMTFVQFANDECDYGMGL 216

Query: 179 EFGLDLFGSGIEDLHSMTKCTLGVAYQYLYRNEFDTI 215
           E G+DLF SG +  H +    L  AY  L R +F  I
Sbjct: 217 ELGIDLFCSGSKYFHKVMLQLLPTAYNLLKRPQFAAI 253


>gnl|CDD|237735 PRK14503, PRK14503, mannosyl-3-phosphoglycerate synthase;
          Provisional.
          Length = 393

 Score = 30.1 bits (68), Expect = 0.79
 Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 8/47 (17%)

Query: 1  TIIVSTGKDHLHF--GYFRDCPDEAPVFIASNSNRDCKINPVAPNIF 45
           I+V    + L    G  +  P E P+ + SNS R        P+ F
Sbjct: 54 AIVVPVKNERLKLLEGVLKGIPHECPIIVVSNSKR------EPPDRF 94


>gnl|CDD|238103 cd00176, SPEC, Spectrin repeats, found in several proteins
          involved in cytoskeletal structure; family members
          include spectrin, alpha-actinin and dystrophin; the
          spectrin repeat forms a three helix bundle with the
          second helix interrupted by proline in some sequences;
          the repeats are independent folding units; tandem
          repeats are found in differing numbers and arrange in
          an antiparallel manner to form dimers; the repeats are
          defined by a characteristic tryptophan (W) residue in
          helix A and a leucine (L) at the carboxyl end of helix
          C and separated by a linker of 5 residues; two copies
          of the repeat are present here.
          Length = 213

 Score = 28.2 bits (63), Expect = 2.6
 Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 7/52 (13%)

Query: 48 INEKLNEKVKSADLASSPSKVSSLQQKLTDFAHGHKIDLDA--PKLSSVVRA 97
          ++EK  E + S D       V +L +K          +L A   ++ ++   
Sbjct: 16 LSEKE-ELLSSTDYGDDLESVEALLKKHEALEA----ELAAHEERVEALNEL 62


>gnl|CDD|240368 PTZ00339, PTZ00339, UDP-N-acetylglucosamine pyrophosphorylase;
          Provisional.
          Length = 482

 Score = 28.6 bits (64), Expect = 2.7
 Identities = 16/33 (48%), Positives = 18/33 (54%)

Query: 22 EAPVFIASNSNRDCKINPVAPNIFIFINEKLNE 54
          EAPV I  +S  +C I P   N FI I EK  E
Sbjct: 58 EAPVGIDIDSIHNCNIEPPNNNTFIDIYEKEKE 90


>gnl|CDD|162866 TIGR02460, osmo_MPGsynth, mannosyl-3-phosphoglycerate synthase.
          This family consists of examples of
          mannosyl-3-phosphoglycerate synthase (MPGS), which
          together mannosyl-3-phosphoglycerate phosphatase (MPGP)
          comprises a two-step pathway for mannosylglycerate
          biosynthesis. Mannosylglycerate is a compatible solute
          that tends to be restricted to extreme thermophiles of
          archaea and bacteria. Note that in Rhodothermus
          marinus, this pathway is one of two; the other is
          condensation of GDP-mannose with D-glycerate by
          mannosylglycerate synthase.
          Length = 381

 Score = 28.6 bits (64), Expect = 2.7
 Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 2/35 (5%)

Query: 2  IIVSTGKDHLHF--GYFRDCPDEAPVFIASNSNRD 34
          I+V    + LH   G     P E P+ + SNS R+
Sbjct: 54 IVVPVKNEKLHLLEGVLSGIPHECPIIVVSNSKRE 88


>gnl|CDD|235950 PRK07164, PRK07164, 5'-methylthioadenosine/S-adenosylhomocysteine
           nucleosidase; Provisional.
          Length = 218

 Score = 27.8 bits (62), Expect = 3.3
 Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 47  FINEKLNEKVKSADLASSPSKVSSLQQ--KLTDFAHGHKIDLDAPKLSSVVRARKAKTVC 104
           + N K+N+      L SS S +  L +   + DF      D++A  L+ V    K K  C
Sbjct: 120 YENNKINKNFNKIHLGSSNSFIFDLDKLKIIKDFIFVSFFDMEAFALAQVCFKNKVKFYC 179

Query: 105 -KGLS 108
            K +S
Sbjct: 180 IKYVS 184


>gnl|CDD|151938 pfam11501, Nsp1, Non structural protein Nsp1.  Nsp1 is the
           N-terminal cleavage product from the viral replicase
           that mediates RNA replication and processing. The
           specific function of the protein is unknown however the
           structure has been determined. The protein has a novel
           alpha/beta fold formed by a 6 stranded beta barrel with
           an alpha helix covering one end of the barrel and
           another helix alongside the barrel. Nsp1 could be
           involved in the degradation of mRNA.
          Length = 115

 Score = 27.3 bits (60), Expect = 3.6
 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 7/46 (15%)

Query: 80  HGHKIDLDAPKLSSVVRARKAKTVCKGLSGVGIVVPYVKKTELGYR 125
           HGHK+     ++  +   R   T+       G++VP+V +T + YR
Sbjct: 69  HGHKVVELVAEMDGIQYGRSGITL-------GVLVPHVGETPIAYR 107


>gnl|CDD|220527 pfam10026, DUF2268, Predicted Zn-dependent protease (DUF2268).
           This domain, found in various hypothetical bacterial
           proteins, as well as predicted zinc dependent proteases,
           has no known function.
          Length = 195

 Score = 27.2 bits (61), Expect = 4.8
 Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 9/50 (18%)

Query: 109 GVGIVVPYVKKTELGYRPLQKSDKDLETLFRQYKDPSVDTRGKLKIKSIL 158
           G   + P+              ++ LE L++Q   P++D +G  +    L
Sbjct: 110 GEEYLGPWTTPY---------DEEQLEHLWKQVIKPNLDLKGFSEHDPYL 150


>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF.  A
           previously described regulatory effect of HypF
           mutatation is attributable to loss of activity of a
           regulatory hydrogenase. A zinc finger-like region
           CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
           the regulatory hypothesis. However, more recent work
           (PUBMED:11375153) shows the direct effect is on the
           activity of expressed hydrogenases with nickel/iron
           centers, rather than on expression [Protein fate,
           Protein modification and repair].
          Length = 711

 Score = 27.8 bits (62), Expect = 6.0
 Identities = 20/98 (20%), Positives = 31/98 (31%), Gaps = 30/98 (30%)

Query: 94  VVRARKAKTVC------KGLSGVGIVVPYVKKTELGYRPLQKSDKDLETLFRQYKDPSVD 147
           +V  RK   +         L  +G+++PY         PL         L +    P V 
Sbjct: 243 IVLLRKKPDIKLAPNIAPNLPTIGVMLPYT--------PLH------HLLLQLLAFPLVM 288

Query: 148 TRGKLKIKSILEEVSTWVTIAIDESDFGTGLEFGLDLF 185
           T   L    +          AID ++    L+   D F
Sbjct: 289 TSANLPGLPM----------AIDNAEILDKLQGIADGF 316


>gnl|CDD|224750 COG1837, COG1837, Predicted RNA-binding protein (contains KH
           domain) [General function prediction only].
          Length = 76

 Score = 25.6 bits (57), Expect = 7.2
 Identities = 8/42 (19%), Positives = 16/42 (38%)

Query: 134 LETLFRQYKDPSVDTRGKLKIKSILEEVSTWVTIAIDESDFG 175
           +E L      P VD    +++     E +  + + +   D G
Sbjct: 1   MEELVEFIVKPLVDNPDDVRVDEEEGEKTVTIELRVAPEDMG 42


>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
           protein 40 (RBM40) and similar proteins.  This subfamily
           corresponds to the RRM2 of RBM40 and the RRM of RBM41.
           RBM40, also known as RNA-binding region-containing
           protein 3 (RNPC3) or U11/U12 small nuclear
           ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
           It serves as a bridging factor between the U11 and U12
           snRNPs. It contains two RNA recognition motifs (RRMs),
           also known as RBDs (RNA binding domains) or RNPs
           (ribonucleoprotein domains), connected by a linker that
           includes a proline-rich region. It binds to the
           U11-associated 59K protein via its RRM1 and employs the
           RRM2 to bind hairpin III of the U12 small nuclear RNA
           (snRNA). The proline-rich region might be involved in
           protein-protein interactions. RBM41 contains only one
           RRM. Its biological function remains unclear. .
          Length = 82

 Score = 25.2 bits (56), Expect = 9.4
 Identities = 6/26 (23%), Positives = 15/26 (57%)

Query: 130 SDKDLETLFRQYKDPSVDTRGKLKIK 155
           +++DL  +F ++ D S + +    I+
Sbjct: 14  TEEDLVYIFGRFVDSSSEEKNMFDIR 39


>gnl|CDD|215266 PLN02481, PLN02481, Omega-hydroxypalmitate O-feruloyl transferase.
          Length = 436

 Score = 26.9 bits (60), Expect = 9.7
 Identities = 44/151 (29%), Positives = 63/151 (41%), Gaps = 20/151 (13%)

Query: 45  FIFINEKLNEKVKSADLASSPSKVSSLQQKLTDF-------AHGHKIDLDAPKLSSV-VR 96
           F F  EKL EK+KS  L     K  S  + LT F       A     D     L +V  R
Sbjct: 239 FCFDPEKL-EKLKSMALEDGVIKKCSTFEALTAFVWRARTKALKMLPDQQTKLLFAVDGR 297

Query: 97  ARKAKTVCKGLSGVGIVVPYVKKT--ELGYRPLQKSDKDLETLFRQYKD----PSVD--- 147
           +R    + KG  G GIV+     T  EL   PL  +   ++   +   D     ++D   
Sbjct: 298 SRFNPPLPKGYFGNGIVLTNALTTAGELLENPLSHAVGLVQDAIKMVNDGYMRSAIDYFE 357

Query: 148 -TRGKLKIKSILEEVSTWVTIAIDESDFGTG 177
            TR +  + S L  ++TW  ++   +DFG G
Sbjct: 358 VTRARPSLASTLL-ITTWSRLSFHTTDFGWG 387


  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
   0.318    0.136    0.395 

Gapped
Lambda     K      H
   0.267   0.0710    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,991,560
Number of extensions: 1009454
Number of successful extensions: 687
Number of sequences better than 10.0: 1
Number of HSP's gapped: 684
Number of HSP's successfully gapped: 19
Length of query: 217
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 124
Effective length of database: 6,812,680
Effective search space: 844772320
Effective search space used: 844772320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.8 bits)