RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy7564
         (115 letters)



>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain.
          Cadherins are glycoproteins involved in Ca2+-mediated
          cell-cell adhesion. The cadherin repeat domains occur
          as tandem repeats in the extracellular regions, which
          are thought to mediate cell-cell contact when bound to
          calcium. They play numerous roles in cell fate,
          signalling, proliferation, differentiation, and
          migration; members include E-, N-, P-, T-, VE-, CNR-,
          proto-, and FAT-family cadherin, desmocollin, and
          desmoglein, a large variety of domain architectures
          with varying repeat copy numbers. Cadherin-repeat
          containing proteins exist as monomers, homodimers, or
          heterodimers.
          Length = 98

 Score = 56.6 bits (137), Expect = 7e-12
 Identities = 24/65 (36%), Positives = 33/65 (50%), Gaps = 7/65 (10%)

Query: 2  SHPVQLFAILKPALHPPYGVLLTKKPLDYEATRIYNLSVTATNMAG--AKAVCSVIVHIL 59
           +   LF+I      P  G + T KPLD E    Y L+VTAT+  G    +  +V + +L
Sbjct: 39 GNEDGLFSI-----DPSTGEITTAKPLDREEQSSYTLTVTATDGGGPPLSSTATVTITVL 93

Query: 60 DRNDN 64
          D NDN
Sbjct: 94 DVNDN 98



 Score = 32.3 bits (74), Expect = 0.012
 Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 7/38 (18%)

Query: 73  YTGYVSEAAPIGALVLTNTSLPLVIRAEDKDSETNALL 110
           Y   V E AP G +VLT       + A D DS  N  +
Sbjct: 2   YEVSVPENAPPGTVVLT-------VSATDPDSGENGEV 32


>gnl|CDD|214520 smart00112, CA, Cadherin repeats.  Cadherins are glycoproteins
          involved in Ca2+-mediated cell-cell adhesion. Cadherin
          domains occur as repeats in the extracellular regions
          which are thought to mediate cell-cell contact when
          bound to calcium.
          Length = 81

 Score = 55.8 bits (135), Expect = 1e-11
 Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 2/49 (4%)

Query: 20 GVLLTKKPLDYEATRIYNLSVTATNMAG--AKAVCSVIVHILDRNDNTP 66
          G + T KPLD E    Y L+V AT+  G    +  +V + +LD NDN P
Sbjct: 33 GEITTTKPLDREEQPEYTLTVEATDGGGPPLSSTATVTITVLDVNDNAP 81


>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain. 
          Length = 92

 Score = 39.6 bits (93), Expect = 3e-05
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)

Query: 20 GVLLTKKPLDYEATRIYNLSVTATNMA--GAKAVCSVIVHIL 59
          G L T KPLD E+   Y L+V AT+       +  +V + +L
Sbjct: 51 GDLSTTKPLDRESIGEYELTVLATDSGGPPLSSTTTVTITVL 92



 Score = 26.1 bits (58), Expect = 2.6
 Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 7/36 (19%)

Query: 73  YTGYVSEAAPIGALVLTNTSLPLVIRAEDKDSETNA 108
           Y+  V E AP+G  VLT       + A D D   N 
Sbjct: 1   YSASVPENAPVGTEVLT-------VTATDADLGPNG 29


>gnl|CDD|233661 TIGR01971, NuoI, NADH-quinone oxidoreductase, chain I.  This model
           represents the I subunit (one of 14: A->N) of the
           NADH-quinone oxidoreductase complex I which generally
           couples NADH and ubiquinone oxidation/reduction in
           bacteria and mammalian mitochondria, but may act on
           NADPH and/or plastoquinone in cyanobacteria and plant
           chloroplasts. This model excludes "I" subunits from the
           closely related F420H2 dehydrogenase and formate
           hydrogenlyase complexes [Energy metabolism, Electron
           transport].
          Length = 122

 Score = 28.9 bits (65), Expect = 0.34
 Identities = 15/51 (29%), Positives = 20/51 (39%), Gaps = 10/51 (19%)

Query: 50  AVC-----SVIVHILDRNDNTPYFTQLNYT-----GYVSEAAPIGALVLTN 90
           AVC      V+    +       F Q+N+      G   EA P  A+VLT 
Sbjct: 53  AVCPADAIRVVPAEGEDGKRRLKFYQINFGRCIFCGLCEEACPTDAIVLTP 103


>gnl|CDD|206635 cd00031, CA_like, Cadherin repeat-like domain.  Cadherins are
          glycoproteins involved in Ca2+-mediated cell-cell
          adhesion. The cadherin repeat domains occur as tandem
          repeats in the extracellular regions, which are thought
          to mediate cell-cell contact when bound to calcium.
          They play numerous roles in cell fate, signalling,
          proliferation, differentiation, and migration; members
          include E-, N-, P-, T-, VE-, CNR-, proto-, and
          FAT-family cadherin, desmocollin, and desmoglein, a
          large variety of domain architectures with varying
          repeat copy numbers. Cadherin-repeat containing
          proteins exist as monomers, homodimers, or
          heterodimers. This family also includes the
          cadherin-like repeats of extracellular
          alpha-dystroglycan.
          Length = 98

 Score = 27.7 bits (61), Expect = 0.80
 Identities = 15/63 (23%), Positives = 24/63 (38%), Gaps = 7/63 (11%)

Query: 4  PVQLFAILKPALHPPYGVLLTKKPLDYEATRIYNLSVTATNMAGAKAVCSVIVHI--LDR 61
                       P  G+L   + LD E   ++ +SV+A ++       S +  I   D 
Sbjct: 41 LPSWLHW-----EPHSGILEGLEKLDREDKGVHYISVSAASLGANVPQTSSVFSIEVYDE 95

Query: 62 NDN 64
          NDN
Sbjct: 96 NDN 98


>gnl|CDD|214795 smart00736, CADG, Dystroglycan-type cadherin-like domains.
          Cadherin-homologous domains present in metazoan
          dystroglycans and alpha/epsilon sarcoglycans, yeast
          Axl2p and in a very large protein from magnetotactic
          bacteria. Likely to bind calcium ions.
          Length = 97

 Score = 27.3 bits (61), Expect = 1.0
 Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 27 PLDYEATRIYNLSVTATNMAGAKAVCSVIVHILDRNDN 64
          P + +     +L VTAT+ +GA A  +  + +++ ND 
Sbjct: 61 PTNSDVGS-LSLKVTATDSSGASASDTFTITVVNTNDA 97


>gnl|CDD|221138 pfam11573, Med23, Mediator complex subunit 23.  Med23 is one of the
           subunits of the Tail portion of the Mediator complex
           that regulates RNA polymerase II activity. Med23 is
           required for heat-shock-specific gene expression, and
           has been shown to mediate transcriptional activation of
           E1A in mice.
          Length = 1341

 Score = 27.5 bits (61), Expect = 1.9
 Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 2/41 (4%)

Query: 31  EATRIYNLSVTATNMAGAKAVCSVIVHILDRNDN--TPYFT 69
           E    +  SV+   +    AV  VI+HI DRN N    YFT
Sbjct: 149 EKALRFPYSVSPEIVPQLLAVEEVILHIFDRNANLLPAYFT 189


>gnl|CDD|177537 PHA03134, PHA03134, thymidine kinase; Provisional.
          Length = 340

 Score = 26.3 bits (58), Expect = 3.6
 Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 3/53 (5%)

Query: 7   LFAILK-PALHPPYGVLLTKKP--LDYEATRIYNLSVTATNMAGAKAVCSVIV 56
           LFA  K   L    GVLL      LD    ++ NL V   +++G    C+  V
Sbjct: 255 LFAAFKARELLDDRGVLLEVHAWALDALMLKLRNLEVFTLDLSGTPRQCAAAV 307


>gnl|CDD|217328 pfam03031, NIF, NLI interacting factor-like phosphatase.  This
          family contains a number of NLI interacting factor
          isoforms and also an N-terminal regions of RNA
          polymerase II CTC phosphatase and FCP1 serine
          phosphatase. This region has been identified as the
          minimal phosphatase domain.
          Length = 153

 Score = 25.7 bits (57), Expect = 5.8
 Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 12/73 (16%)

Query: 15 LHPPYGVLLTKKP-LDY---EATRIYNLSV-TATNMAGAKAVCS-------VIVHILDRN 62
          L+  +GV + K+P LD    E ++ Y + + TA++   A  V            H L R 
Sbjct: 26 LNFNHGVYVKKRPGLDEFLQELSKYYEIVIFTASSKEYADPVLDKLDPKKKYFKHRLYRE 85

Query: 63 DNTPYFTQLNYTG 75
            T Y   L+  G
Sbjct: 86 SCTFYVKDLSLLG 98


>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter.  This
            model describes the photoreceptor protein (rim protein)
            in eukaryotes. It is the member of ABC transporter
            superfamily. Rim protein is a membrane glycoprotein which
            is localized in the photoreceptor outer segment discs.
            Mutation/s in its genetic loci is implicated in the
            recessive Stargardt's disease [Transport and binding
            proteins, Other].
          Length = 2272

 Score = 26.1 bits (57), Expect = 5.9
 Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 5/51 (9%)

Query: 9    AILKPALH-----PPYGVLLTKKPLDYEATRIYNLSVTATNMAGAKAVCSV 54
            AIL+ +L        YG+ +  +PL+    ++  ++V  T++    A+C +
Sbjct: 1637 AILRASLPKDRDPEEYGITVISQPLNLTKEQLSEITVLTTSVDAVVAICVI 1687


>gnl|CDD|224786 COG1874, LacA, Beta-galactosidase [Carbohydrate transport and
           metabolism].
          Length = 673

 Score = 25.8 bits (57), Expect = 6.0
 Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 2/38 (5%)

Query: 25  KKPLDYEATRIYNLSVTATNMAGAKAVCSVIVHILDRN 62
            + +   A   Y   +TATN+ G   +    V ILDR+
Sbjct: 638 FQTVTLPA--EYTDLITATNLLGGLTLKPYEVRILDRS 673


>gnl|CDD|182833 PRK10913, PRK10913, dipeptide transporter; Provisional.
          Length = 300

 Score = 25.5 bits (56), Expect = 7.0
 Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 3/42 (7%)

Query: 18  PYGVLLTKKPLDYEATRIYNLSVTATNMAGAKAVCSVIVHIL 59
           P+ V LT+  +  E  R Y   VTA+ +AGA A+  + ++IL
Sbjct: 174 PHYVRLTRAAVLVEVNRDY---VTASRVAGAGAMRQMFINIL 212


>gnl|CDD|222887 PHA02581, 9, baseplate wedge tail fiber connector; Provisional.
          Length = 284

 Score = 25.4 bits (56), Expect = 7.1
 Identities = 11/33 (33%), Positives = 16/33 (48%)

Query: 38  LSVTATNMAGAKAVCSVIVHILDRNDNTPYFTQ 70
           L VTA N  G     +  + ++D N N  Y T+
Sbjct: 202 LLVTAENADGTVTKTAETLLLIDNNANKVYSTE 234


  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
   0.316    0.132    0.378 

Gapped
Lambda     K      H
   0.267   0.0713    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,611,943
Number of extensions: 458918
Number of successful extensions: 404
Number of sequences better than 10.0: 1
Number of HSP's gapped: 400
Number of HSP's successfully gapped: 25
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
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 (21.6 bits)
S2: 53 (24.2 bits)