RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12005
         (188 letters)



>gnl|CDD|119367 cd01615, CIDE_N, CIDE_N domain, found at the N-terminus of the
          CIDE (cell death-inducing DFF45-like effector)
          proteins, as well as CAD nuclease (caspase-activated
          DNase/DNA fragmentation factor, DFF40) and its
          inhibitor, ICAD(DFF45). These proteins are associated
          with the chromatin condensation and DNA fragmentation
          events of apoptosis; the CIDE_N domain is thought to
          regulate the activity of ICAD/DFF45, and the CAD/DFF40
          and CIDE nucleases during apoptosis. The CIDE-N domain
          is also found in the FSP27/CIDE-C protein.
          Length = 78

 Score =  105 bits (264), Expect = 3e-30
 Identities = 40/75 (53%), Positives = 53/75 (70%), Gaps = 1/75 (1%)

Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRARLKLGMSS-VVKVVLDLDGTEVDEEEYFSTLEK 72
          P KV DS+R +K G+ A SL++L+++A  KL + S  V +VL+ DGTEVD+EEYF TL  
Sbjct: 4  PFKVCDSDRSRKKGVAASSLEELLSKACEKLKLPSAPVTLVLEEDGTEVDDEEYFQTLPD 63

Query: 73 NTSLMILSKNDKWTP 87
          NT LM+L    KWTP
Sbjct: 64 NTVLMLLEPGQKWTP 78


>gnl|CDD|119371 cd06538, CIDE_N_FSP27, CIDE_N domain of FSP27 proteins. The
          CIDE-N (cell death-inducing DFF45-like effector,
          N-terminal) domain is found in the FSP27/CIDE-C
          protein, which has been identified as a n adipocyte
          lipid droplet protein that negatively regulates
          lipolysis and promotes triglyceride accumulation. The
          CIDE protein family includes 3 members: CIDE-A, CIDE-B,
          and FSP27(CIDE-C). Based on sequence similarity with
          DFF40 and DFF45, CIDE proteins were initially
          characterized as mitochondrial activators of apoptosis.
          The CIDE-N domain of FSP27 is sufficient to increase
          apoptosis in vitro when overexpressed.
          Length = 79

 Score = 78.3 bits (193), Expect = 2e-19
 Identities = 32/76 (42%), Positives = 47/76 (61%)

Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRARLKLGMSSVVKVVLDLDGTEVDEEEYFSTLEKN 73
          P +V +++R  + GI+A SL+DL+N+    L +  +  +VLD DGT VD EE+F  L  N
Sbjct: 4  PFRVSNADRSLRKGIMADSLEDLLNKVLDALLLDCISSLVLDEDGTGVDTEEFFQALADN 63

Query: 74 TSLMILSKNDKWTPRS 89
          T  M+L K  KW P +
Sbjct: 64 TVFMVLGKGQKWKPPT 79


>gnl|CDD|128562 smart00266, CAD, Domains present in proteins implicated in
          post-mortem DNA fragmentation. 
          Length = 74

 Score = 76.2 bits (188), Expect = 8e-19
 Identities = 35/73 (47%), Positives = 48/73 (65%), Gaps = 1/73 (1%)

Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRARLKLGM-SSVVKVVLDLDGTEVDEEEYFSTLEK 72
          P KV D +R  + G+ A SL++L+++   KL +  S V +VL+ DGT VD+EEYF TL  
Sbjct: 2  PFKVRDHDRNVRKGVAASSLEELLSKVCDKLALPDSPVTLVLEEDGTIVDDEEYFQTLPD 61

Query: 73 NTSLMILSKNDKW 85
          NT LM L K +KW
Sbjct: 62 NTELMALEKGEKW 74


>gnl|CDD|202090 pfam02017, CIDE-N, CIDE-N domain.  This domain is found in CAD
          nuclease, and ICAD, the inhibitor of CAD nuclease. The
          two proteins interact through this domain.
          Length = 78

 Score = 72.8 bits (179), Expect = 2e-17
 Identities = 34/76 (44%), Positives = 48/76 (63%), Gaps = 3/76 (3%)

Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRA--RLKLGMSSVVKVVLDLDGTEVDEEEYFSTLE 71
          P KV D +R  K G+ A SL++L+++    L+L    +V +VL+ DGTEVD E+YF TL 
Sbjct: 4  PFKVRDHDRRIKKGVAASSLQELLSKVCDILQLPDG-LVTLVLEEDGTEVDTEDYFQTLP 62

Query: 72 KNTSLMILSKNDKWTP 87
           NT L+ L+   KW P
Sbjct: 63 DNTELVALTSGQKWAP 78


>gnl|CDD|119370 cd06537, CIDE_N_B, CIDE_N domain of CIDE-B proteins. The CIDE_N
          (cell death-inducing DFF45-like effector, N-terminal)
          domain is found at the N-terminus of the CIDE (cell
          death-inducing DFF45-like effector) proteins. These
          proteins are associated with the chromatin condensation
          and DNA fragmentation events of apoptosis; the CIDE_N
          domain is thought to regulate the activity of the
          CAD/DFF40,  ICAD/DFF45 and CIDE nucleases during
          apoptosis. The CIDE protein family includes 3 members:
          CIDE-A, CIDE-B, and FSP27(CIDE-C).  Based on sequence
          similarity with DFF40 and DFF45, CIDE proteins were
          initially characterized as mitochondrial activators of
          apoptosis. However, strong metabolic phenotypes of mice
          lacking CIDE-A and CIDE-B indicated that this family
          may play critical roles in energy balance.
          Length = 81

 Score = 65.7 bits (160), Expect = 1e-14
 Identities = 31/76 (40%), Positives = 49/76 (64%)

Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRARLKLGMSSVVKVVLDLDGTEVDEEEYFSTLEKN 73
          P +V D  R  + G+ A SL++L+ +A   L +S V+ +VL+ DGT VD E++F  LE +
Sbjct: 4  PFRVCDHKRTVRKGLTAASLQELLAKALETLLLSGVLTLVLEEDGTAVDSEDFFELLEDD 63

Query: 74 TSLMILSKNDKWTPRS 89
          T LM+L +   W+P+S
Sbjct: 64 TCLMVLEQGQSWSPKS 79


>gnl|CDD|119372 cd06539, CIDE_N_A, CIDE_N domain of CIDE-A proteins. The CIDE_N
          (cell death-inducing DFF45-like effector, N-terminal)
          domain is found at the N-terminus of the CIDE (cell
          death-inducing DFF45-like effector) proteins. These
          proteins are associated with the chromatin condensation
          and DNA fragmentation events of apoptosis; the CIDE_N
          domain is thought to regulate the activity of the
          CAD/DFF40, ICAD/DFF45, and CIDE nucleases during
          apoptosis. The CIDE protein family includes 3 members:
          CIDE-A, CIDE-B, and FSP27(CIDE-C).  Based on sequence
          similarity with DFF40 and DFF45, the CIDE proteins were
          initially characterized as mitochondrial activators of
          apoptosis. However, strong metabolic phenotypes of mice
          lacking CIDE-A and CIDE-B indicated that this family
          may play critical roles in energy balance.
          Length = 78

 Score = 65.4 bits (159), Expect = 1e-14
 Identities = 32/77 (41%), Positives = 50/77 (64%), Gaps = 1/77 (1%)

Query: 12 GLPCKVVDSNREKKIGIVALSLKDLMNRARLKLGMSS-VVKVVLDLDGTEVDEEEYFSTL 70
            P +V + +R  + G++A SL++L+++    L ++S +V +VL+ DGT VD EE+F TL
Sbjct: 2  ARPFRVSNHDRSSRRGVMASSLQELISKTLDALVITSGLVTLVLEEDGTVVDTEEFFQTL 61

Query: 71 EKNTSLMILSKNDKWTP 87
            NT  M+L K  KWTP
Sbjct: 62 GDNTHFMVLEKGQKWTP 78


>gnl|CDD|119369 cd06536, CIDE_N_ICAD, CIDE_N domain of ICAD. The CIDE_N  (cell
          death-inducing DFF45-like effector, N-terminal) domain
          is found at the N-terminus of the CAD nuclease
          (caspase-activated DNase/DNA fragmentation factor,
          DFF40) and its inhibitor, ICAD (DFF45). These proteins
          are associated with the chromatin condensation and DNA
          fragmentation events of apoptosis; the CIDE_N domain is
          thought to regulate the activity of the CAD/DFF40 and
          ICAD/DFF45 during apoptosis. In normal cells, DFF
          exists in the nucleus as a heterodimer composed of
          CAD/DFF40 as a latent nuclease and its chaperone and
          inhibitor subunit ICAD/DFF45. Apoptotic activation of
          caspase-3 results in the cleavage of DFF45/ICAD and
          release of active DFF40/CAD nuclease.
          Length = 80

 Score = 63.7 bits (155), Expect = 6e-14
 Identities = 31/77 (40%), Positives = 50/77 (64%), Gaps = 3/77 (3%)

Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRARLKLGM---SSVVKVVLDLDGTEVDEEEYFSTL 70
          PC V + +R+K+ G+ A SL++L  +A   LG    S+ + +VL  DGT V++E+YF  L
Sbjct: 4  PCVVCNVSRQKQHGVAASSLEELRIKACESLGFDSSSAPITLVLAEDGTIVEDEDYFLCL 63

Query: 71 EKNTSLMILSKNDKWTP 87
            NT  ++L++N+KW P
Sbjct: 64 PPNTKFVLLAENEKWAP 80


>gnl|CDD|119368 cd06535, CIDE_N_CAD, CIDE_N domain of CAD nuclease. The CIDE_N
          (cell death-inducing DFF45-like effector, N-terminal)
          domain is found at the N-terminus of CAD nuclease
          (caspase-activated DNase/DNA fragmentation factor,
          DFF40) and its inhibitor, ICAD(DFF45). These proteins
          are associated with the chromatin condensation and DNA
          fragmentation events of apoptosis; the CIDE_N domain is
          thought to regulate the activity of CAD/DFF40 and
          ICAD/DFF45 during apoptosis. In normal cells, DFF
          exists in the nucleus as a heterodimer composed of
          CAD/DFF40 as a latent nuclease and its chaperone and
          inhibitor subunit ICAD/DFF45. Apoptotic activation of
          caspase-3 results in the cleavage of DFF45/ICAD and the
          release of active DFF40/CAD nuclease.
          Length = 77

 Score = 46.6 bits (111), Expect = 1e-07
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRA--RLKLGMSSVVKVVLDLDGTEVDEEEYFSTLE 71
            K+   N  +K G+ A +LK+L+ +    L+L  +   ++ L  DGTEV  EEYF TL 
Sbjct: 4  CVKIRSLNSAQKYGVAAKNLKELLRKGCRLLQLPCAGS-RLCLYEDGTEV-TEEYFPTLP 61

Query: 72 KNTSLMILSKNDKW 85
           NT L++L+    W
Sbjct: 62 DNTELVLLTPGQSW 75


>gnl|CDD|216886 pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase.  This family
           includes RNA-dependent RNA polymerase proteins (RdRPs)
           from Luteovirus, Totivirus and Rotavirus.
          Length = 421

 Score = 30.1 bits (68), Expect = 0.62
 Identities = 17/96 (17%), Positives = 29/96 (30%), Gaps = 14/96 (14%)

Query: 97  LERNETNNDVTGFLTKIHGNNGVSILGGLELELLSDMDPESLTDIIP-------DKLFLD 149
           L   E    V         ++            L + +P      I         K   D
Sbjct: 116 LVEEELRKKVVLDAFDDFWSSRYLWCVNGSYHSLLEAEP----VKIDESPVRLVRKGLCD 171

Query: 150 QFKEVSSRYFSNKNHHSKETKSEKILHHRYVILFAV 185
               V  R F     H + + S+K+ H +  ++F+V
Sbjct: 172 ---PVPLRLFVKSEPHVRVSTSKKLEHGKTRLIFSV 204


>gnl|CDD|236302 PRK08578, PRK08578, preprotein translocase subunit SecF; Reviewed.
          Length = 292

 Score = 29.1 bits (66), Expect = 1.4
 Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 118 GVSILGGLELEL-LSDMDPESLTDIIPDKLFLDQFKEVSSRYF 159
           G+   GG E+ +  +D  P+ L   +  +  +D  K   + Y 
Sbjct: 45  GIDFTGGTEITIQTNDASPDELESALSGEPGVDVRKGSGNGYI 87


>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase.  The
           Era (E. coli Ras-like protein)-like family includes
           several distinct subfamilies (TrmE/ThdF, FeoB, YihA
           (EngB), Era, and EngA/YfgK) that generally show sequence
           conservation in the region between the Walker A and B
           motifs (G1 and G3 box motifs), to the exclusion of other
           GTPases. TrmE is ubiquitous in bacteria and is a
           widespread mitochondrial protein in eukaryotes, but is
           absent from archaea. The yeast member of TrmE family,
           MSS1, is involved in mitochondrial translation;
           bacterial members are often present in
           translation-related operons. FeoB represents an unusual
           adaptation of GTPases for high-affinity iron (II)
           transport. YihA (EngB) family of GTPases is typified by
           the E. coli YihA, which is an essential protein involved
           in cell division control. Era is characterized by a
           distinct derivative of the KH domain (the pseudo-KH
           domain) which is located C-terminal to the GTPase
           domain. EngA and its orthologs are composed of two
           GTPase domains and, since the sequences of the two
           domains are more similar to each other than to other
           GTPases, it is likely that an ancient gene duplication,
           rather than a fusion of evolutionarily distinct GTPases,
           gave rise to this family.
          Length = 161

 Score = 28.4 bits (64), Expect = 1.6
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 2/52 (3%)

Query: 39  RARLKLGMSSVVKVVLDLDGTEVDEEEYFSTLEKNT--SLMILSKNDKWTPR 88
            AR     + +V +V+D D T V+EE     L +     L++L+K D     
Sbjct: 69  EARQVADRADLVLLVVDSDLTPVEEEAKLGLLRERGKPVLLVLNKIDLVPES 120


>gnl|CDD|233088 TIGR00679, hpr-ser, Hpr(Ser) kinase/phosphatase.  Members of this
           family are the bifunctional enzyme, HPr
           kinase/phosphatase. All members of the seed alignment
           (n=57) have a gene tightly clustered with a gene for the
           phospocarrier protein HPr, its target [Regulatory
           functions, Protein interactions, Signal transduction,
           PTS].
          Length = 300

 Score = 27.8 bits (63), Expect = 3.0
 Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 2/41 (4%)

Query: 107 TGFLTKIHGNNGVSILGGLELELLSDMDPESLTDIIPDKLF 147
            G+    H    V I+G  EL  L  +D E   + + +KL 
Sbjct: 38  AGYFNYFH-PKRVQIIGNTELSYLESLDEEERKERL-EKLL 76


>gnl|CDD|215360 PLN02672, PLN02672, methionine S-methyltransferase.
          Length = 1082

 Score = 28.2 bits (63), Expect = 3.5
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 4/56 (7%)

Query: 105 DVTGFLTKIHGNN---GVSILGGLELELLSDMDPESLTDIIPDKLFLDQFKEVSSR 157
           D+   L+++  +N    V++LGGL  ELLS          + D + +D F      
Sbjct: 885 DLKSILSRLKSSNPSFAVALLGGLSTELLSGGHEFGFL-ALNDSVLIDAFHSAPGL 939


>gnl|CDD|181000 PRK07492, PRK07492, adenylosuccinate lyase; Provisional.
          Length = 435

 Score = 27.2 bits (61), Expect = 5.1
 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 7/31 (22%)

Query: 59  TEVDE-EEYFSTLEKNTSLM------ILSKN 82
           TEV E EE+FS  +K +S M      +L++N
Sbjct: 249 TEVLEAEEFFSPGQKGSSAMPHKRNPVLTEN 279


>gnl|CDD|240380 PTZ00362, PTZ00362, hypothetical protein; Provisional.
          Length = 479

 Score = 26.6 bits (59), Expect = 8.1
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 13  LPCKVVDSNREKKIGIVALSLKDLMNRARLK--LGMSSVVKVVLDLDGTEVDEEEYF 67
           LP K+      K   I    L++L+N    +  L    VVK ++D+   ++ E E F
Sbjct: 250 LPSKINSGYIYKNKIIAYDYLENLVNHILYQRALDELVVVKALVDIPYIDLSEIEGF 306


>gnl|CDD|221073 pfam11311, DUF3114, Protein of unknown function (DUF3114).  Some
           members in this family of proteins with unknown function
           are annotated as cytosolic proteins. This cannot be
           confirmed.
          Length = 252

 Score = 26.6 bits (59), Expect = 8.2
 Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 140 DIIPDKLFLDQFKEVSSRYFSNKNHHSKETKSEKILHH-RYVI 181
           D+ P   F   F ++    F   +  S+E++  K +H  RY+I
Sbjct: 53  DLAPHDPFWKDFAQLVQLAFP-GDDLSQESELAKRIHQFRYLI 94


>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
           catalytic domains.  Phosphoglycerate dehydrogenases
           (PGDHs) catalyze the initial step in the biosynthesis of
           L-serine from D-3-phosphoglycerate. PGDHs come in 3
           distinct structural forms, with this first group being
           related to 2-hydroxy acid dehydrogenases, sharing
           structural similarity to formate and glycerate
           dehydrogenases. PGDH in E. coli and Mycobacterium
           tuberculosis form tetramers, with subunits containing a
           Rossmann-fold NAD binding domain. Formate/glycerate and
           related dehydrogenases of the D-specific 2-hydroxyacid
           dehydrogenase superfamily include groups such as formate
           dehydrogenase, glycerate dehydrogenase, L-alanine
           dehydrogenase, and S-adenosylhomocysteine hydrolase.
           Despite often low sequence identity, these proteins
           typically have a characteristic arrangement of 2 similar
           subdomains of the alpha/beta Rossmann fold NAD+ binding
           form. The NAD+ binding domain is inserted within the
           linear sequence of the mostly N-terminal catalytic
           domain, which has a similar domain structure to the
           internal NAD binding domain. Structurally, these domains
           are connected by extended alpha helices and create a
           cleft in which NAD is bound, primarily to the C-terminal
           portion of the 2nd (internal) domain. Some related
           proteins have similar structural subdomain but with a
           tandem arrangement of the catalytic and NAD-binding
           subdomains in the linear sequence.
          Length = 304

 Score = 26.6 bits (60), Expect = 9.1
 Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 2/29 (6%)

Query: 118 GVSIL--GGLELELLSDMDPESLTDIIPD 144
           G+ +L   G+E+++   +  E L  II D
Sbjct: 12  GLELLREAGIEVDVAPGLSEEELLAIIAD 40


  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
   0.315    0.134    0.370 

Gapped
Lambda     K      H
   0.267   0.0720    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,407,906
Number of extensions: 862423
Number of successful extensions: 629
Number of sequences better than 10.0: 1
Number of HSP's gapped: 624
Number of HSP's successfully gapped: 28
Length of query: 188
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 97
Effective length of database: 6,901,388
Effective search space: 669434636
Effective search space used: 669434636
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: 42 (22.0 bits)
S2: 56 (25.4 bits)