RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5
         (128 letters)



>gnl|CDD|148567 pfam07019, Rab5ip, Rab5-interacting protein (Rab5ip).  This
          family consists of several Rab5-interacting protein
          (RIP5 or Rab5ip) sequences. The ras-related GTPase rab5
          is rate-limiting for homotypic early endosome fusion.
          Rab5ip represents a novel rab5 interacting protein that
          may function on endocytic vesicles as a receptor for
          rab5-GDP and participate in the activation of rab5.
          Length = 81

 Score = 69.5 bits (171), Expect = 6e-17
 Identities = 27/74 (36%), Positives = 45/74 (60%)

Query: 14 DVIYWARQILGIILGIVWGFIPLRGFIGLALFALTNAGLLYLYIVNYQCVDEDEYGGTFE 73
          DV+YW RQ++ ++ G++ G + L GF+G   + L + G  YLY      +DE+ +GG +E
Sbjct: 1  DVLYWVRQVISLLAGVIAGILGLTGFLGFIFYFLISLGTSYLYYAKVGKIDEEYFGGRWE 60

Query: 74 MAKEGFMTSFAAFL 87
          +  EG +T  A F+
Sbjct: 61 LFTEGLLTGLATFV 74


>gnl|CDD|234179 TIGR03355, VI_chp_2, type VI secretion protein, EvpB/VC_A0108
           family.  Work by Mougous, et al. (2006), describes
           IAHP-related loci as a type VI secretion system
           (PMID:16763151). This protein family is associated with
           type VI secretion loci, although not treated explicitly
           by Mougous, et al [Protein fate, Protein and peptide
           secretion and trafficking, Cellular processes,
           Pathogenesis].
          Length = 473

 Score = 27.3 bits (61), Expect = 2.9
 Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 10/31 (32%)

Query: 98  FEMAKEGFM-------TSFAAFLVSFSHQSV 121
           FE+A+ GF+       + +AAF   FS QSV
Sbjct: 324 FELAELGFIPLVHRKNSDYAAF---FSAQSV 351


>gnl|CDD|224188 COG1269, NtpI, Archaeal/vacuolar-type H+-ATPase subunit I [Energy
           production and conversion].
          Length = 660

 Score = 26.9 bits (60), Expect = 3.1
 Identities = 13/54 (24%), Positives = 22/54 (40%)

Query: 10  DEFLDVIYWARQILGIILGIVWGFIPLRGFIGLALFALTNAGLLYLYIVNYQCV 63
              L  + W   ILG++L I+     +   +G+        G+L L +V    V
Sbjct: 489 GAILPQLLWLLIILGLLLLILGYKWSVPELLGMVGAMFGAFGILGLLVVGLILV 542


>gnl|CDD|234039 TIGR02866, CoxB, cytochrome c oxidase, subunit II.  Cytochrome c
          oxidase is the terminal electron acceptor of
          mitochondria (and one of several possible acceptors in
          prokaryotes) in the electron transport chain of aerobic
          respiration. The enzyme couples the oxidation of
          reduced cytochrome c with the reduction of molecular
          oxygen to water. This process results in the pumping of
          four protons across the membrane which are used in the
          proton gradient powered synthesis of ATP. The oxidase
          contains two heme a cofactors and three copper atoms as
          well as other bound ions [Energy metabolism, Electron
          transport].
          Length = 199

 Score = 26.2 bits (58), Expect = 5.3
 Identities = 16/32 (50%), Positives = 17/32 (53%), Gaps = 2/32 (6%)

Query: 24 GIILGIVWGFIPLRGFIGLALFALTNAGLLYL 55
             L  VW  IPL   +GL  FA T  GLLYL
Sbjct: 53 NRRLEYVWTVIPLIIVVGL--FAATAKGLLYL 82


>gnl|CDD|223961 COG1030, NfeD, Membrane-bound serine protease (ClpP class)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 436

 Score = 26.2 bits (58), Expect = 5.5
 Identities = 16/39 (41%), Positives = 19/39 (48%)

Query: 22  ILGIILGIVWGFIPLRGFIGLALFALTNAGLLYLYIVNY 60
           ILG IL +   F+P  G IGL    L   GLL L+    
Sbjct: 289 ILGAILIVAEAFVPGFGVIGLLGIILFIIGLLLLFPSGT 327


>gnl|CDD|215482 PLN02892, PLN02892, isocitrate lyase.
          Length = 570

 Score = 25.9 bits (57), Expect = 6.8
 Identities = 12/24 (50%), Positives = 12/24 (50%)

Query: 27  LGIVWGFIPLRGFIGLALFALTNA 50
           LG  W FI L GF   AL   T A
Sbjct: 462 LGYCWQFITLAGFHANALVVDTFA 485


>gnl|CDD|114045 pfam05297, Herpes_LMP1, Herpesvirus latent membrane protein 1
          (LMP1).  This family consists of several latent
          membrane protein 1 or LMP1s mostly from Epstein-Barr
          virus. LMP1 of EBV is a 62-65 kDa plasma membrane
          protein possessing six membrane spanning regions, a
          short cytoplasmic N-terminus and a long cytoplasmic
          carboxy tail of 200 amino acids. EBV latent membrane
          protein 1 (LMP1) is essential for EBV-mediated
          transformation and has been associated with several
          cases of malignancies. EBV-like viruses in Cynomolgus
          monkeys (Macaca fascicularis) have been associated with
          high lymphoma rates in immunosuppressed monkeys.
          Length = 382

 Score = 25.8 bits (56), Expect = 7.3
 Identities = 14/24 (58%), Positives = 15/24 (62%)

Query: 35 PLRGFIGLALFALTNAGLLYLYIV 58
          PL   IGLAL  L  A L +LYIV
Sbjct: 20 PLSSSIGLALLLLLLALLFWLYIV 43


  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
   0.330    0.146    0.451 

Gapped
Lambda     K      H
   0.267   0.0770    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,001,467
Number of extensions: 661394
Number of successful extensions: 1239
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1235
Number of HSP's successfully gapped: 103
Length of query: 128
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 42
Effective length of database: 7,123,158
Effective search space: 299172636
Effective search space used: 299172636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.1 bits)