RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14289
         (297 letters)



>gnl|CDD|220160 pfam09271, LAG1-DNAbind, LAG1, DNA binding.  Members of this family
           are found in various eukaryotic hypothetical proteins
           and in the DNA-binding protein LAG-1. They adopt a beta
           sandwich structure, with nine strands in two
           beta-sheets, in a Greek-key topology, and allow for DNA
           binding. This domain is also known as RHR-N
           (Rel-homology region) as it related to Rel domain
           proteins.
          Length = 138

 Score =  212 bits (541), Expect = 9e-70
 Identities = 90/138 (65%), Positives = 106/138 (76%), Gaps = 5/138 (3%)

Query: 99  VIVILHAKVAQKSYGNEKRFFCPPPCIYLYGEGWRLRQEQLLREGESEQAAQLCAFIGIG 158
            + ILHAKVAQKSYGNEKRF CPPPC+YL G GWRL+ + L   G S+QA ++  +IGIG
Sbjct: 1   TVSILHAKVAQKSYGNEKRFLCPPPCVYLIGPGWRLKPQPLQPNGISDQATEISPYIGIG 60

Query: 159 NSDQ---DMQQLDLNNGKQYCAA--KTLYISDSDKRKHFMLSVKMFYGSGHDIGVFTSKR 213
            S+Q   +MQ+L+ +  K Y  A  KTLYISDSDKRKHF L V+MF GSG D+G F SKR
Sbjct: 61  GSEQQQAEMQKLNFDGQKVYGTAALKTLYISDSDKRKHFRLLVRMFLGSGQDLGTFPSKR 120

Query: 214 IKVISKPSKKKQSLKNAD 231
           IKVISKPSKK+QSLKNAD
Sbjct: 121 IKVISKPSKKRQSLKNAD 138


>gnl|CDD|117815 pfam09270, BTD, Beta-trefoil DNA-binding domain.  Members of this
           family of DNA binding domains adopt a beta-trefoil fold,
           that is, a capped beta-barrel with internal pseudo
           threefold symmetry. In the DNA-binding protein LAG-1, it
           also is the site of mutually exclusive interactions with
           NotchIC (and the viral protein EBNA2) and co-repressors
           (SMRT/N-Cor and CIR).
          Length = 152

 Score =  106 bits (266), Expect = 2e-28
 Identities = 53/63 (84%), Positives = 58/63 (92%)

Query: 232 LCIASGTKVALFNRLRSQTVSTRYLHVENGNFHASSTQWGAFTIHLLDDDESESEEFSVR 291
           LCIASG+KVALFNRLRSQTVSTRYLHVENG FHASS QWGAFTIHLLDDD +ES+EF VR
Sbjct: 1   LCIASGSKVALFNRLRSQTVSTRYLHVENGAFHASSAQWGAFTIHLLDDDRNESDEFDVR 60

Query: 292 DWF 294
           + +
Sbjct: 61  EGY 63


>gnl|CDD|183111 PRK11382, frlB, fructoselysine-6-P-deglycase; Provisional.
          Length = 340

 Score = 34.2 bits (78), Expect = 0.072
 Identities = 16/43 (37%), Positives = 25/43 (58%)

Query: 67  EGWVPHSLHYRNDDQRLTREAMERYLRDRSDMVIVILHAKVAQ 109
           E  VP      ND+ R T E    +++ R+D VIVI +A+++Q
Sbjct: 256 EPGVPFLFLLGNDESRHTTERAINFVKQRTDNVIVIDYAEISQ 298


>gnl|CDD|152159 pfam11723, Aromatic_hydrox, Homotrimeric ring hydroxylase.  This
           domain is found on aromatic hydroxylating enzymes such
           as 2-oxo-1,2-dihydroquinoline 8-monooxygenase from
           Pseudomonas putida and carbazole 1,9a-dioxygenase from
           Janthinobacterium. These enzymes are homotrimers and are
           distantly related to the typical oxygenase. This domain
           is found C terminal to the Rieske domain which binds an
           iron-sulphur cluster.
          Length = 240

 Score = 32.8 bits (75), Expect = 0.15
 Identities = 19/90 (21%), Positives = 32/90 (35%), Gaps = 19/90 (21%)

Query: 43  YLP--SKLTRYFAMI--VCDPSQNKVHYEG-----WVPHSLHYRNDDQRLTREAMERYLR 93
           Y+P       YF ++  V    +    +E      W   +L+  NDD    RE+M+ +  
Sbjct: 149 YVPIDENTHEYFQLLGRVVATEEEAKSFEDEFEEKWREAALNGFNDDDIWARESMQPFYA 208

Query: 94  D----------RSDMVIVILHAKVAQKSYG 113
           D            D  IV      ++ + G
Sbjct: 209 DDRGWSEEQLFEPDAAIVAWRKLASEHARG 238


>gnl|CDD|183484 PRK12379, PRK12379, propionate/acetate kinase; Provisional.
          Length = 396

 Score = 30.9 bits (70), Expect = 0.93
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 6/64 (9%)

Query: 122 PPCIYLYGEGWRLRQEQLLR----EGESEQ--AAQLCAFIGIGNSDQDMQQLDLNNGKQY 175
            P  YLYG  W   +E  +R     G S +  + +  + + +   D  +    L NG   
Sbjct: 151 APEAYLYGLPWEYYEELGVRRYGFHGTSHRYVSQRAHSLLNLDEDDSGLVVAHLGNGASI 210

Query: 176 CAAK 179
           CA +
Sbjct: 211 CAVR 214


>gnl|CDD|233729 TIGR02103, pullul_strch, alpha-1,6-glucosidases, pullulanase-type. 
           Members of this protein family include secreted (or
           membrane-anchored) pullulanases of Gram-negative
           bacteria and pullulanase-type starch debranching enzymes
           of plants. Both enzymes hydrolyze alpha-1,6 glycosidic
           linkages. Pullulan is an unusual, industrially important
           polysaccharide in which short alpha-1,4 chains
           (maltotriose) are connected in alpha-1,6 linkages.
           Enzymes that cleave alpha-1,6 linkages in pullulan and
           release maltotriose are called pullulanases although
           pullulan itself may not be the natural substrate. This
           family is closely homologous to, but architecturally
           different from, the Gram-positive pullulanases of
           Gram-positive bacteria (TIGR02102) [Energy metabolism,
           Biosynthesis and degradation of polysaccharides].
          Length = 898

 Score = 30.6 bits (69), Expect = 1.1
 Identities = 16/37 (43%), Positives = 17/37 (45%), Gaps = 3/37 (8%)

Query: 123 PCIYLYGEGWRLRQEQLLREGESEQAAQL-CAFIGIG 158
           P IY YGEGW   +    R      A QL  A  GIG
Sbjct: 518 PEIYFYGEGWDFGEVANNRRF--INATQLNLAGTGIG 552


>gnl|CDD|130264 TIGR01196, edd, 6-phosphogluconate dehydratase.  A close homolog,
           designated MocB (mannityl opine catabolism), is found in
           a mannopine catabolism region of a plasmid of
           Agrobacterium tumefaciens. However, it is not essential
           for mannopine catabolism, branches within the cluster of
           6-phosphogluconate dehydratases (with a short branch
           length) in a tree rooted by the presence of other
           dehydyatases. It may represent an authentic
           6-phosphogluconate dehydratase, redundant with the
           chromosomal copy shown to exist in plasmid-cured
           strains. This model includes mocB above the trusted
           cutoff, although the designation is somewhat tenuous
           [Energy metabolism, Entner-Doudoroff].
          Length = 601

 Score = 29.4 bits (66), Expect = 2.9
 Identities = 16/41 (39%), Positives = 20/41 (48%)

Query: 127 LYGEGWRLRQEQLLREGESEQAAQLCAFIGIGNSDQDMQQL 167
           L+ EG   R+E L  E  S  A   C F G  NS+Q M + 
Sbjct: 195 LFAEGKVGREELLKSEMASYHAPGTCTFYGTANSNQMMMEF 235


>gnl|CDD|221053 pfam11271, DUF3068, Protein of unknown function (DUF3068).  Some
           members in this family of proteins with unknown function
           are annotated as membrane proteins however this cannot
           be confirmed.
          Length = 300

 Score = 27.8 bits (62), Expect = 6.8
 Identities = 9/24 (37%), Positives = 11/24 (45%)

Query: 85  REAMERYLRDRSDMVIVILHAKVA 108
            E   RYLRD     +V+L A   
Sbjct: 232 EEQQRRYLRDGVGKEVVVLDATFT 255


>gnl|CDD|238664 cd01368, KISc_KIF23_like, Kinesin motor domain, KIF23-like
           subgroup. Members of this group may play a role in
           mitosis. This catalytic (head) domain has ATPase
           activity and belongs to the larger group of P-loop
           NTPases. Kinesins are microtubule-dependent molecular
           motors that play important roles in intracellular
           transport and in cell division. In most kinesins, the
           motor domain is found at the N-terminus (N-type). N-type
           kinesins are (+) end-directed motors, i.e. they
           transport cargo towards the (+) end of the microtubule.
           Kinesin motor domains hydrolyze ATP at a rate of about
           80 per second, and move along the microtubule at a speed
           of about 6400 Angstroms per second. To achieve that,
           kinesin head groups work in pairs. Upon replacing ADP
           with ATP, a kinesin motor domain increases its affinity
           for microtubule binding and locks in place. Also, the
           neck linker binds to the motor domain, which repositions
           the other head domain through the coiled-coil domain
           close to a second tubulin dimer, about 80 Angstroms
           along the microtubule. Meanwhile, ATP hydrolysis takes
           place, and when the second head domain binds to the
           microtubule, the first domain again replaces ADP with
           ATP, triggering a conformational change that pulls the
           first domain forward.
          Length = 345

 Score = 27.7 bits (62), Expect = 8.1
 Identities = 13/39 (33%), Positives = 14/39 (35%), Gaps = 11/39 (28%)

Query: 29  RNQTHKSAPRKHIHYLPSKLTRYF----------AMIVC 57
            NQ   S   K + Y  SKLT  F           MIV 
Sbjct: 286 ENQLSGSTN-KMVPYRDSKLTHLFQNYFDGEGKARMIVN 323


>gnl|CDD|181189 PRK07986, PRK07986, adenosylmethionine--8-amino-7-oxononanoate
           transaminase; Validated.
          Length = 428

 Score = 27.7 bits (62), Expect = 8.2
 Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 3/24 (12%)

Query: 53  AMIVCDPSQNKVH--YEGWVPHSL 74
           AM VCDP  N +H  Y+G++P +L
Sbjct: 151 AMSVCDP-DNSMHSLYKGYLPENL 173


  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
   0.320    0.134    0.408 

Gapped
Lambda     K      H
   0.267   0.0664    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,849,773
Number of extensions: 1367136
Number of successful extensions: 1154
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1152
Number of HSP's successfully gapped: 19
Length of query: 297
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 201
Effective length of database: 6,679,618
Effective search space: 1342603218
Effective search space used: 1342603218
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.6 bits)