RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11553
         (146 letters)



>gnl|CDD|216025 pfam00617, RasGEF, RasGEF domain.  Guanine nucleotide exchange
           factor for Ras-like small GTPases.
          Length = 185

 Score =  161 bits (410), Expect = 1e-51
 Identities = 56/138 (40%), Positives = 85/138 (61%), Gaps = 1/138 (0%)

Query: 2   SSYELVYHTVGRHRFQQITANLDVFLRRFNEIQYWVITEILLVTSLNKRVQILRKMIKLA 61
              EL+    G+   +  + N++ F+ RFN++  WV TEIL    L KR ++++K IK+A
Sbjct: 24  DPRELLDSAWGKKDSKL-SPNIEAFISRFNQLSRWVATEILSEEDLKKRAKVIKKFIKIA 82

Query: 62  AYCKEYRNINALFAVLMGLSNVAVSRLSLTWDKLPSKSKKTYTELEALIDPSKNHRAYRQ 121
            +C+E  N N+L A++ GL++  +SRL  TW+ +  K KK   ELE L+ PSKN + YR+
Sbjct: 83  QHCRELNNFNSLMAIISGLNSSPISRLKKTWELVSKKYKKLLEELEELMSPSKNFKNYRE 142

Query: 122 AVSKLQSPVIPFMPLLLK 139
           A+ K   P IPF+ L LK
Sbjct: 143 ALKKANPPCIPFLGLYLK 160


>gnl|CDD|214539 smart00147, RasGEF, Guanine nucleotide exchange factor for Ras-like
           small GTPases. 
          Length = 242

 Score =  150 bits (381), Expect = 2e-46
 Identities = 60/137 (43%), Positives = 88/137 (64%), Gaps = 2/137 (1%)

Query: 5   ELVYHTVGRHRFQ-QITANLDVFLRRFNEIQYWVITEILLVTSLNKRVQILRKMIKLAAY 63
           EL+    G+   +     NL+ F+RRFNE+  WV TEIL  T+   R ++L K I++A +
Sbjct: 28  ELLGSVWGKRSKKSPSPLNLEAFIRRFNEVSNWVATEILKQTTPKDRAELLSKFIQVAKH 87

Query: 64  CKEYRNINALFAVLMGLSNVAVSRLSLTWDKLPSKSKKTYTELEALIDPSKNHRAYRQAV 123
           C+E  N N+L A++  LS+  +SRL  TW+KLPSK KK + ELE L+ P +N++ YR+A+
Sbjct: 88  CRELNNFNSLMAIVSALSSSPISRLKKTWEKLPSKYKKLFEELEELLSPERNYKNYREAL 147

Query: 124 SKL-QSPVIPFMPLLLK 139
           S     P IPF+ +LLK
Sbjct: 148 SSCNLPPCIPFLGVLLK 164


>gnl|CDD|238087 cd00155, RasGEF, Guanine nucleotide exchange factor for Ras-like
           small GTPases. Small GTP-binding proteins of the Ras
           superfamily function as molecular switches in
           fundamental events such as signal transduction,
           cytoskeleton dynamics and intracellular trafficking.
           Guanine-nucleotide-exchange factors (GEFs) positively
           regulate these GTP-binding proteins in response to a
           variety of signals. GEFs catalyze the dissociation of
           GDP from the inactive GTP-binding proteins. GTP can then
           bind and induce structural changes that allow
           interaction with effectors.
          Length = 237

 Score =  140 bits (355), Expect = 1e-42
 Identities = 54/142 (38%), Positives = 88/142 (61%), Gaps = 3/142 (2%)

Query: 1   MSSYELVYHTVG-RHRFQQITANLDVFLRRFNEIQYWVITEILLVTSLNKRVQILRKMIK 59
           +  +EL+      + +   ++ NL+ F+ RFN +  WV +EILL T+  KR ++L K I+
Sbjct: 24  IEPFELLGSLWSKKDKNIHLSPNLERFIERFNNLSNWVASEILLCTNPKKRARLLSKFIQ 83

Query: 60  LAAYCKEYRNINALFAVLMGLSNVAVSRLSLTWDKLPSKSKKTYTELEALIDPSKNHRAY 119
           +A +C+E  N N+L A++  LS+  +SRL  TW+ L SK KK + ELE L+DPS+N + Y
Sbjct: 84  VAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEVLSSKLKKLFEELEELVDPSRNFKNY 143

Query: 120 RQAVSKL--QSPVIPFMPLLLK 139
           R+ +  +    P +PF+ + LK
Sbjct: 144 RKLLKSVGPNPPCVPFLGVYLK 165


>gnl|CDD|236400 PRK09188, PRK09188, serine/threonine protein kinase; Provisional.
          Length = 365

 Score = 29.0 bits (65), Expect = 0.92
 Identities = 9/31 (29%), Positives = 13/31 (41%)

Query: 7  VYHTVGRHRFQQITANLDVFLRRFNEIQYWV 37
          V+ TV R  F           RR +E+ +W 
Sbjct: 30 VFSTVERGYFAGDPGTARAVRRRVSEVPWWS 60


>gnl|CDD|224131 COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope
          biogenesis, outer membrane].
          Length = 291

 Score = 28.3 bits (64), Expect = 1.4
 Identities = 12/26 (46%), Positives = 13/26 (50%), Gaps = 7/26 (26%)

Query: 33 IQYWV-------ITEILLVTSLNKRV 51
          IQY V       I EIL+VT   KR 
Sbjct: 38 IQYIVEEAVAAGIEEILIVTGRGKRA 63


>gnl|CDD|216082 pfam00723, Glyco_hydro_15, Glycosyl hydrolases family 15.  In
           higher organisms this family is represented by
           phosphorylase kinase subunits.
          Length = 416

 Score = 27.4 bits (61), Expect = 3.3
 Identities = 14/72 (19%), Positives = 22/72 (30%), Gaps = 3/72 (4%)

Query: 4   YELVYHTVGRHRFQQITANLDVFLRRFNEIQYWVITEILLVTSLNKRVQILRKMIKLAAY 63
           Y+ +YH  GR R+         F  +                S+   V+        A  
Sbjct: 320 YDELYHWAGRGRWTLTRYARG-FFEKLVSSTVGTPYSSSTFISIPLAVKEYADGFVKA-- 376

Query: 64  CKEYRNINALFA 75
            +EY N   L +
Sbjct: 377 VEEYANSLGLLS 388


>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 558

 Score = 27.2 bits (61), Expect = 3.6
 Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 79  GLSNVAVSRLSLTWD-KLPSKSKKT-YTELEALI 110
           GL +++++R  L W   +P    K  Y   +ALI
Sbjct: 228 GLKDLSITRTDLDWGIPVPGDPGKVIYVWFDALI 261


>gnl|CDD|233673 TIGR01991, HscA, Fe-S protein assembly chaperone HscA.  The Heat
           Shock Cognate proteins HscA and HscB act together as
           chaperones. HscA resembles DnaK but belongs in a
           separate clade. The apparent function is to aid assembly
           of iron-sulfur cluster proteins. Homologs from Buchnera
           and Wolbachia are clearly in the same clade but are
           highly derived and score lower than some examples of
           DnaK [Protein fate, Protein folding and stabilization].
          Length = 599

 Score = 26.8 bits (60), Expect = 4.6
 Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 14/77 (18%)

Query: 36  WVITEILLVTSLNKRVQILRKMIKLAAYCKEYRNINALFAVLMGLSNVAVSRLSLTWDKL 95
           W++ ++ +   LN   +  R +++ A   KE             L++     +  T D  
Sbjct: 228 WILKQLGISADLNP--EDQRLLLQAARAAKEA------------LTDAESVEVDFTLDGK 273

Query: 96  PSKSKKTYTELEALIDP 112
             K K T  E EALI P
Sbjct: 274 DFKGKLTRDEFEALIQP 290


>gnl|CDD|133021 cd02541, UGPase_prokaryotic, Prokaryotic UGPase catalyses the
          synthesis of UDP-glucose.  Prokaryotic UDP-Glucose
          Pyrophosphorylase (UGPase) catalyzes a reversible
          production of UDP-Glucose  and pyrophosphate (PPi) from
          glucose-1-phosphate and UTP.  UDP-glucose plays pivotal
          roles in galactose utilization, in glycogen synthesis,
          and in the synthesis of the carbohydrate moieties of
          glycolipids , glycoproteins , and proteoglycans. UGPase
          is found in both prokaryotes and eukaryotes, although
          prokaryotic and eukaryotic forms of UGPase catalyze the
          same reaction, they share low sequence similarity.
          Length = 267

 Score = 26.7 bits (60), Expect = 4.8
 Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 7/25 (28%)

Query: 33 IQYWV-------ITEILLVTSLNKR 50
          IQY V       I +I++VT   KR
Sbjct: 34 IQYIVEEAVAAGIEDIIIVTGRGKR 58


>gnl|CDD|220129 pfam09159, Ydc2-catalyt, Mitochondrial resolvase Ydc2 / RNA
           splicing MRS1.  Members of this family adopt a secondary
           structure consisting of two beta sheets and one alpha
           helix, arranged as a beta-alpha-beta motif. Each beta
           sheet has five strands, arranged in a 32145 order, with
           the second strand being antiparallel to the rest.
           Mitochondrial resolvase Ydc2 is capable of resolving
           Holliday junctions and cleaves DNA after 5'-CT-3' and
           5'-TT-3' sequences. This family also contains the
           mitochondrial RNA-splicing protein MRS1 which is
           involved in the excision of group I introns.
          Length = 254

 Score = 26.6 bits (59), Expect = 5.2
 Identities = 12/53 (22%), Positives = 17/53 (32%)

Query: 78  MGLSNVAVSRLSLTWDKLPSKSKKTYTELEALIDPSKNHRAYRQAVSKLQSPV 130
           MG+ N A  +L     K P++S  T      L    K       A  +     
Sbjct: 6   MGIKNFAFCKLKGPSMKAPTRSLPTLNAWLKLNLDEKIGADDAPATDEKSKIS 58


>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
          Length = 648

 Score = 26.3 bits (59), Expect = 8.0
 Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 2/34 (5%)

Query: 79  GLSNVAVSRLSLTWD-KLPSKSKK-TYTELEALI 110
           GL ++++SR S  W   +P   K   Y  ++AL+
Sbjct: 200 GLEDLSISRTSFDWGIPVPFDPKHVVYVWIDALL 233


>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
           recombination, and repair].
          Length = 342

 Score = 25.8 bits (57), Expect = 9.3
 Identities = 7/33 (21%), Positives = 13/33 (39%)

Query: 91  TWDKLPSKSKKTYTELEALIDPSKNHRAYRQAV 123
                P   K+ +   E L+ P +    + QA+
Sbjct: 157 GDIGKPKTKKELWELAEQLLTPDRRPGDFNQAM 189


>gnl|CDD|214485 smart00044, CYCc, Adenylyl- / guanylyl cyclase, catalytic domain.
           Present in two copies in mammalian adenylyl cyclases.
          Eubacterial homologues are known. Two residues (Asn,
          Arg) are thought to be involved in catalysis. These
          cyclases have important roles in a diverse range of
          cellular processes.
          Length = 194

 Score = 25.7 bits (57), Expect = 9.5
 Identities = 10/37 (27%), Positives = 14/37 (37%)

Query: 39 TEILLVTSLNKRVQILRKMIKLAAYCKEYRNINALFA 75
          T+ LL   L   V    K        + Y N+  LF+
Sbjct: 6  TDRLLDQLLPASVAEQLKRGGSPVPAESYDNVTILFS 42


  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
   0.324    0.134    0.393 

Gapped
Lambda     K      H
   0.267   0.0763    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,371,755
Number of extensions: 645942
Number of successful extensions: 760
Number of sequences better than 10.0: 1
Number of HSP's gapped: 758
Number of HSP's successfully gapped: 30
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.5 bits)