RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy816
         (138 letters)



>gnl|CDD|238020 cd00063, FN3, Fibronectin type 3 domain; One of three types of
           internal repeats found in the plasma protein
           fibronectin. Its tenth fibronectin type III repeat
           contains an RGD cell recognition sequence in a flexible
           loop between 2 strands. Approximately 2% of all animal
           proteins contain the FN3 repeat; including extracellular
           and intracellular proteins, membrane spanning cytokine
           receptors, growth hormone receptors, tyrosine
           phosphatase receptors, and adhesion molecules. FN3-like
           domains are also found in bacterial glycosyl hydrolases.
          Length = 93

 Score = 30.2 bits (68), Expect = 0.13
 Identities = 25/102 (24%), Positives = 39/102 (38%), Gaps = 12/102 (11%)

Query: 27  PAAPKLRVQLADAGKG-IQLTWSLDTTSDMAAIESYQLYAYQENKNVPVNSSLWKNIGKL 85
           P+ P   +++ D     + L+W+     D   I  Y +  Y+E       S  WK +   
Sbjct: 1   PSPPT-NLRVTDVTSTSVTLSWT-PPEDDGGPITGYVVE-YRE-----KGSGDWKEVEV- 51

Query: 86  EALPLPMACTLTQFTAGHTYHFLVRAIDVYKRYSAFSNPGTI 127
                  + TLT    G  Y F VRA++     S  S   T+
Sbjct: 52  -TPGSETSYTLTGLKPGTEYEFRVRAVNGGGE-SPPSESVTV 91


>gnl|CDD|215438 PLN02818, PLN02818, tocopherol cyclase.
          Length = 403

 Score = 28.5 bits (64), Expect = 1.1
 Identities = 20/58 (34%), Positives = 25/58 (43%), Gaps = 20/58 (34%)

Query: 11  PTPSVSNVVGAMYEMVPA-----APKLRVQL----ADAGKGIQLTWSLDTTSDMAAIE 59
           PT  V         + P      A KL++QL     D  KG  +   LD TS MAA+E
Sbjct: 323 PTTDVG--------LAPFCRDTFAGKLKLQLWERSWDGSKGKLI---LDATSSMAAVE 369


>gnl|CDD|223004 PHA03173, PHA03173, UL37 tegument protein; Provisional.
          Length = 1028

 Score = 28.5 bits (64), Expect = 1.3
 Identities = 24/66 (36%), Positives = 32/66 (48%), Gaps = 8/66 (12%)

Query: 1   MPAKVRAPVPPTPSVSNVV--GAMYEMVPAAPKLRVQLAD-AGKGIQLTWSLDTTSDMAA 57
           +P +VR PVPP PSVSN +   +MY     A  LR +L D A +   L  S+     + A
Sbjct: 688 LPPEVRPPVPPRPSVSNSLFLASMY-----ATALRGRLQDLAARTDALVDSIADAIVLLA 742

Query: 58  IESYQL 63
                L
Sbjct: 743 SHMLTL 748


>gnl|CDD|238291 cd00525, AE_Prim_S_like, AE_Prim_S_like: primase domain similar to
           that found in the small subunit of archaeal and
           eukaryotic (A/E) DNA primases. The replication
           machineries of A/Es are distinct from that of bacteria.
           Primases are DNA-dependent RNA polymerases which
           synthesis the short RNA primers required for DNA
           replication. In eukaryotes, this small catalytically
           active primase subunit (p50) and a larger primase
           subunit (p60), referred to jointly as the core primase,
           associate with the B subunit and the DNA polymerase
           alpha subunit in a complex, called Pol alpha-pri. In
           addition to its catalytic role in replication,
           eukaryotic DNA primase may play a role in coupling
           replication to DNA damage repair and in checkpoint
           control during S phase. Pfu41 and Pfu46 comprise the
           primase complex of the archaea Pyrococcus furiosus;
           these proteins have sequence identity to the eukaryotic
           p50 and p60 primase proteins respectively. Pfu41
           preferentially uses dNTPs as substrate. Pfu46 regulates
           the primase activity of Pfu41. Also found in this group
           is the primase-polymerase (primpol) domain of replicases
           from archaeal plasmids including the ORF904 protein of
           pRN1 from Sulfolobus islandicus (pRN1 primpol). The pRN1
           primpol domain exhibits DNA polymerase and primase
           activities; a cluster of active site residues (three
           acidic residues, and a histidine) is required for both
           these activities. The pRN1 primpol primase activity
           prefers dNTPs to rNTPs; however incorporation of dNTPs
           requires rNTP as cofactor. This group also includes the
           Pol domain of bacterial LigD proteins such Mycobacterium
           tuberculosis (Mt)LigD. MtLigD contains an N-terminal Pol
           domain, a central phosphoesterase module, and a
           C-terminal ligase domain. LigD Pol plays a role in
           non-homologous end joining (NHEJ)-mediated repair of DNA
           double-strand breaks (DSB) in vivo, perhaps by filling
           in short 5'-overhangs with ribonucleotides; the filled
           in termini would be sealed by the associated LigD ligase
           domain. The MtLigD Pol domain is stimulated by
           manganese, is error-prone, and prefers adding rNTPs to
           dNTPs in vitro.
          Length = 136

 Score = 27.3 bits (61), Expect = 1.7
 Identities = 13/54 (24%), Positives = 17/54 (31%), Gaps = 6/54 (11%)

Query: 86  EALPLPMACTLTQFTAGHTYHFLVRAIDV----YKRYSAFSNPGTIHLRTPATV 135
           E L      TL   +     H  VR ID+      R      P ++H R     
Sbjct: 81  ELLDEDGLNTLVVTSGSRGLHVYVRLIDIRVNARGRLLVA--PPSVHPRPGGPP 132


>gnl|CDD|200951 pfam00041, fn3, Fibronectin type III domain. 
          Length = 84

 Score = 26.2 bits (58), Expect = 2.8
 Identities = 13/71 (18%), Positives = 23/71 (32%), Gaps = 10/71 (14%)

Query: 43  IQLTWSLDTTSDMAAIESYQLYAYQENKNVPVNSSLWKNIGKLEALPLPMACTLTQFTAG 102
           + L+WS    +    I  Y++     N            +          + TLT    G
Sbjct: 16  LTLSWSPPPGN--GPITGYEVEYRPVNGGEEWK---EITVPGTT-----TSYTLTGLKPG 65

Query: 103 HTYHFLVRAID 113
             Y   V+A++
Sbjct: 66  TEYEVRVQAVN 76


>gnl|CDD|215621 PLN03188, PLN03188, kinesin-12 family protein; Provisional.
          Length = 1320

 Score = 26.4 bits (58), Expect = 7.0
 Identities = 8/16 (50%), Positives = 12/16 (75%)

Query: 2  PAKVRAPVPPTPSVSN 17
           AK+++P+PP P  SN
Sbjct: 64 SAKLKSPLPPRPPSSN 79


>gnl|CDD|235893 PRK06939, PRK06939, 2-amino-3-ketobutyrate coenzyme A ligase;
           Provisional.
          Length = 397

 Score = 25.9 bits (58), Expect = 8.8
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 97  TQFTAGHTYHFLVRAIDVYKR 117
           TQ +A HT   L RAID +++
Sbjct: 369 TQMSAAHTKEQLDRAIDAFEK 389


  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    0.130    0.388 

Gapped
Lambda     K      H
   0.267   0.0591    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,981,217
Number of extensions: 584203
Number of successful extensions: 451
Number of sequences better than 10.0: 1
Number of HSP's gapped: 451
Number of HSP's successfully gapped: 12
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
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: 54 (24.9 bits)