RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4617
         (314 letters)



>gnl|CDD|144634 pfam01115, F_actin_cap_B, F-actin capping protein, beta subunit. 
          Length = 240

 Score =  416 bits (1072), Expect = e-148
 Identities = 170/272 (62%), Positives = 196/272 (72%), Gaps = 35/272 (12%)

Query: 11  QMDCALDLMRRLPPQQIEKNLSDLIDLVPGLCEDLLSSVDQPLKIARDKEMGKDYLLCDY 70
           ++D ALDL+RRLPP++IE+NL+DLIDL P L EDLLSSVDQPLKI +D E GKDYL CDY
Sbjct: 1   KLDAALDLLRRLPPKKIEENLNDLIDLAPDLTEDLLSSVDQPLKIKKDSETGKDYLCCDY 60

Query: 71  NRDGDSYRSPWSNVYDPPLE-DGSMPSERLRKLEIDANHAFDQYREMYFEGGVSSVYLWD 129
           NRDGDSYRSPWSN Y PPLE DG +PSERLRKLEI AN AFD YR++Y+EGGVSSVYLWD
Sbjct: 61  NRDGDSYRSPWSNKYFPPLEADGPVPSERLRKLEIKANEAFDVYRDLYYEGGVSSVYLWD 120

Query: 130 LDHGFAEIDANHAFDQYREMYFEGGVSSVYLWDLDHGFAGVILIKKAGDGSRKIQGCWDS 189
           LD                                + GFAGV+LIKKAGD    I G WDS
Sbjct: 121 LDD-------------------------------EDGFAGVVLIKKAGDSGEGISGSWDS 149

Query: 190 IHVVEVQEKPTGRNAHYKLTSTVMLWLQTNKIASGKMNLGGSLTRQIEMDAQVSDTS--P 247
           IHV EV E  +G  AHYKLTSTV+L L+T+   SG +NL GSLTRQ E D +VSD +   
Sbjct: 150 IHVFEVTETSSG-TAHYKLTSTVILELKTDSSKSGPLNLSGSLTRQKEKDLKVSDDNTTS 208

Query: 248 HIANIGRMVEEMENKIRNTLNEIYFGKTKDIV 279
           HI NIGR++E+MENK+RN L E+YFGKTKDIV
Sbjct: 209 HIVNIGRLIEDMENKMRNLLEEVYFGKTKDIV 240


>gnl|CDD|238860 cd01822, Lysophospholipase_L1_like, Lysophospholipase L1-like
          subgroup of SGNH-hydrolases. The best characterized
          member in this family is TesA, an E. coli periplasmic
          protein with thioesterase, esterase, arylesterase,
          protease and lysophospholipase activity.
          Length = 177

 Score = 33.3 bits (77), Expect = 0.096
 Identities = 8/22 (36%), Positives = 12/22 (54%)

Query: 17 DLMRRLPPQQIEKNLSDLIDLV 38
          D +R +PP Q   NL  +I+  
Sbjct: 76 DGLRGIPPDQTRANLRQMIETA 97


>gnl|CDD|204512 pfam10557, Cullin_Nedd8, Cullin protein neddylation domain.  This
          is the neddylation site of cullin proteins which are a
          family of structurally related proteins containing an
          evolutionarily conserved cullin domain. With the
          exception of APC2, each member of the cullin family is
          modified by Nedd8 and several cullins function in
          Ubiquitin-dependent proteolysis, a process in which the
          26S proteasome recognises and subsequently degrades a
          target protein tagged with K48-linked poly-ubiquitin
          chains. Cullins are molecular scaffolds responsible for
          assembling the ROC1/Rbx1 RING-based E3 ubiquitin
          ligases, of which several play a direct role in
          tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like
          protein, which was originally found to be conjugated to
          Cdc53, a cullin component of the SCF
          (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in
          Saccharomyces cerevisiae, and Nedd8 modification has
          now emerged as a regulatory pathway of fundamental
          importance for cell cycle control and for embryogenesis
          in metazoans. The only identified Nedd8 substrates are
          cullins. Neddylation results in covalent conjugation of
          a Nedd8 moiety onto a conserved cullin lysine residue.
          Length = 68

 Score = 28.3 bits (64), Expect = 1.0
 Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 2/36 (5%)

Query: 3  KCINYTELQMDCALDLMRRLPPQ--QIEKNLSDLID 36
          K +++ EL  +    L +R PP    I+K +  LI+
Sbjct: 21 KTLSHNELVAEVIEQLKKRFPPSVADIKKRIESLIE 56


>gnl|CDD|225975 COG3443, COG3443, Predicted periplasmic or secreted protein
           [General function prediction only].
          Length = 193

 Score = 29.7 bits (67), Expect = 1.6
 Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 8/58 (13%)

Query: 63  KDYLLCDYNRDGDSYRSPWSNVYDPPLEDGSMPSERLRKLEIDANHAFDQYREMYFEG 120
           KD  L D+  DGD     W +VY P L+DG++      K + D      +Y+  Y +G
Sbjct: 28  KDRTLSDW--DGD-----WQSVY-PYLQDGTLDPVFQYKAKRDGKKTAAEYKAYYRKG 77


>gnl|CDD|235550 PRK05660, PRK05660, HemN family oxidoreductase; Provisional.
          Length = 378

 Score = 29.1 bits (66), Expect = 3.2
 Identities = 14/27 (51%), Positives = 16/27 (59%), Gaps = 3/27 (11%)

Query: 16  LDLMRRLPPQQIEKNLSDL---IDLVP 39
           LDLM  LP Q +E+ L DL   I L P
Sbjct: 162 LDLMHGLPDQSLEEALDDLRQAIALNP 188


>gnl|CDD|130370 TIGR01303, IMP_DH_rel_1, IMP dehydrogenase family protein.  This
           model represents a family of proteins, often annotated
           as a putative IMP dehydrogenase, related to IMP
           dehydrogenase and GMP reductase and restricted to the
           high GC Gram-positive bacteria. All species in which a
           member is found so far (Corynebacterium glutamicum,
           Mycobacterium tuberculosis, Streptomyces coelicolor,
           etc.) also have IMP dehydrogenase as described by
           TIGRFAMs entry TIGR01302 [Unknown function, General].
          Length = 475

 Score = 28.3 bits (63), Expect = 5.3
 Identities = 27/88 (30%), Positives = 39/88 (44%), Gaps = 5/88 (5%)

Query: 76  SYRSPWSNVYD----PPLEDGSMPSERLRKLEIDANHAFDQYREMYFEGGVSSVYLW-DL 130
           +Y SP   + D    P  E   M S+R       A++AFD+ R+  FE G+S+  +  D 
Sbjct: 363 TYESPGDLMRDRDGRPYKESFGMASKRAVVARTGADNAFDRARKALFEEGISTSRMGLDP 422

Query: 131 DHGFAEIDANHAFDQYREMYFEGGVSSV 158
           D G  E   +H     R      G SS+
Sbjct: 423 DRGGVEDLIDHIISGVRSSCTYAGASSL 450


>gnl|CDD|235560 PRK05685, fliS, flagellar protein FliS; Validated.
          Length = 132

 Score = 27.2 bits (61), Expect = 5.7
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 21/74 (28%)

Query: 226 MNLGGSLTRQIEMDAQVSDTSPH-------------IANIGRMVEE--MENKIRNTLNEI 270
           M       +Q+ +++QVS  SPH             +A     +E+  +E K        
Sbjct: 3   MRNAYQAYQQVSVESQVSSASPHKLIQMLYEGALSFLAQAKLAIEQGDIEAKG------E 56

Query: 271 YFGKTKDIVNGLRS 284
           Y  K  +I+NGLR+
Sbjct: 57  YLSKAINIINGLRN 70


>gnl|CDD|217711 pfam03748, FliL, Flagellar basal body-associated protein FliL.
           This FliL protein controls the rotational direction of
           the flagella during chemotaxis. FliL is a cytoplasmic
           membrane protein associated with the basal body.
          Length = 99

 Score = 26.7 bits (60), Expect = 6.2
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 17/85 (20%)

Query: 227 NLGGSLTR---QIEMDAQVSDTSPHIANIGRMVEEMENKIRNTLNEIYFGKTKDIVNGLR 283
           NL         +I +  +V D  P  A     +EE    IR+ +  +   KT + ++   
Sbjct: 12  NLADDGRTRYLKIGIALEVDD--PKAAEE---LEEKMPLIRDAILLLLSSKTAEDLSTP- 65

Query: 284 SLQPLSVQQAQQALKQDLAAALQKR 308
                   + ++ LK++L   + + 
Sbjct: 66  --------EGKEKLKEELLERINEV 82


>gnl|CDD|132743 cd06945, NR_LBD_Nurr1_like, The ligand binding domain of Nurr1 and
           related nuclear receptor proteins, members of nuclear
           receptor superfamily.  The ligand binding domain of
           nuclear receptor Nurr1_like: This family of nuclear
           receptors, including Nurr1, Nerve growth
           factor-induced-B (NGFI-B) and DHR38 are involved in the
           embryo development. Nurr1 is a transcription factor that
           is expressed in the embryonic ventral midbrain and is
           critical for the development of dopamine (DA) neurons.
           Structural studies have shown that the ligand binding
           pocket of Nurr1 is filled by bulky hydrophobic residues,
           making it unable to bind to ligands. Therefore, it
           belongs to the class of orphan receptors. However, Nurr1
           forms heterodimers with RXR and can promote signaling
           via its partner, RXR. NGFI-B is an early immediate gene
           product of embryo development that is rapidly produced
           in response to a variety of cellular signals including
           nerve growth factor. It is involved in T-cell-mediated
           apoptosis, as well as neuronal differentiation and
           function. NGFI-B regulates transcription by binding to a
           specific DNA target upstream of its target genes and
           regulating the rate of tr anscriptional initiation.
           Another group of receptor in this family is DHR38.
           DHR38 is the Drosophila homolog to the vertebrate
           NGFI-B-type orphan receptor. It interacts with the USP
           component of the ecdysone receptor complex, suggesting
           that DHR38 might modulate ecdysone-triggered signals in
           the fly, in addition to the ECR/USP pathway. Nurr1_like
           proteins exhibit a modular structure that is
           characteristic for nuclear receptors; they have a
           central well conserved DNA binding domain (DBD), a
           variable N-terminal domain, a non-conserved hinge and a
           C-terminal ligand binding domain (LBD).
          Length = 239

 Score = 27.8 bits (62), Expect = 6.9
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 9/51 (17%)

Query: 254 RMVEEMENKIRNTLNE----IYFGKTK-----DIVNGLRSLQPLSVQQAQQ 295
           + VEE++NKI + L +     Y G+ K      ++  L  L+ LS +  Q+
Sbjct: 163 KKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQR 213


>gnl|CDD|214649 smart00404, PTPc_motif, Protein tyrosine phosphatase, catalytic
           domain motif. 
          Length = 105

 Score = 26.6 bits (59), Expect = 8.1
 Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 8/52 (15%)

Query: 249 IANIGR-----MVEEMENKIRNTLNEIYFGKTKDIVNGLRSLQPLSVQQAQQ 295
            A +GR      ++ +  ++     E+      D V  LRS +P  VQ  +Q
Sbjct: 47  SAGVGRTGTFVAIDILLQQLEAEAGEVDI---FDTVKELRSQRPGMVQTEEQ 95


>gnl|CDD|214469 smart00012, PTPc_DSPc, Protein tyrosine phosphatase, catalytic
           domain, undefined specificity.  Protein tyrosine
           phosphatases. Homologues detected by this profile and
           not by those of "PTPc" or "DSPc" are predicted to be
           protein phosphatases with a similar fold to DSPs and
           PTPs, yet with unpredicted specificities.
          Length = 105

 Score = 26.6 bits (59), Expect = 8.1
 Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 8/52 (15%)

Query: 249 IANIGR-----MVEEMENKIRNTLNEIYFGKTKDIVNGLRSLQPLSVQQAQQ 295
            A +GR      ++ +  ++     E+      D V  LRS +P  VQ  +Q
Sbjct: 47  SAGVGRTGTFVAIDILLQQLEAEAGEVDI---FDTVKELRSQRPGMVQTEEQ 95


>gnl|CDD|182521 PRK10528, PRK10528, multifunctional acyl-CoA thioesterase I and
           protease I and lysophospholipase L1; Provisional.
          Length = 191

 Score = 27.4 bits (61), Expect = 8.2
 Identities = 10/22 (45%), Positives = 13/22 (59%)

Query: 17  DLMRRLPPQQIEKNLSDLIDLV 38
           D +R  PPQQ E+ L  +I  V
Sbjct: 83  DGLRGFPPQQTEQTLRQIIQDV 104


>gnl|CDD|234709 PRK00275, glnD, PII uridylyl-transferase; Provisional.
          Length = 895

 Score = 28.1 bits (63), Expect = 8.5
 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 15/71 (21%)

Query: 249 IANIGRMVEEMENKIRN----TLNE----IYFGKTKDIVNGLRSLQPLSVQQAQQALKQD 300
           +A IGR+  E +  ++N    TL E    ++F    D  N     QPLS  Q    L+  
Sbjct: 828 LARIGRIFLEFDLSLQNAKIATLGERVEDVFF--ITDADN-----QPLSDPQLCSRLQDA 880

Query: 301 LAAALQKRNAK 311
           +   L  RN K
Sbjct: 881 ICEQLDARNEK 891


  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
   0.317    0.135    0.401 

Gapped
Lambda     K      H
   0.267   0.0705    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,128,010
Number of extensions: 1553738
Number of successful extensions: 1451
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1445
Number of HSP's successfully gapped: 18
Length of query: 314
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 217
Effective length of database: 6,635,264
Effective search space: 1439852288
Effective search space used: 1439852288
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: 59 (26.6 bits)