RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16643
         (165 letters)



>gnl|CDD|217928 pfam04148, Erv26, Transmembrane adaptor Erv26.  Erv26 is an
           integral membrane protein that is packed into COPII
           vesicles and cycles between the ER and Golgi
           compartments. It directs pro-alkaline phosphatase into
           endoplasmic reticulum-derived COPII transport vesicles.
          Length = 207

 Score =  146 bits (371), Expect = 4e-45
 Identities = 62/153 (40%), Positives = 89/153 (58%), Gaps = 15/153 (9%)

Query: 27  VTAGLYYLAELVEEYSVLAKKVIQWLIIITLLIYAGFFCFEDLPTILLICGVLAQVLHLI 86
           + +GLYYL+ELVEE++V AK+ +  LI   + IY     F+  P  L +  + +  ++L 
Sbjct: 23  IASGLYYLSELVEEHTVPAKRFLTRLIYFIIGIYILLLIFDGFPFTLTLFSIFSHCVYLS 82

Query: 87  IIQNFPYVSLTSPAFIAAVVLIVVNHYYAMSYF---------------QSNYHSFAEVMA 131
            ++ FP++SLTSP F+ + VL+V+NHY    +F               Q N   F EV +
Sbjct: 83  NLKTFPFISLTSPTFLLSCVLVVINHYLWFRHFSDVEIPPSFRPDYVPQRNRPPFTEVAS 142

Query: 132 FFTLCLWLVPFSLLVSLSANDMVLPTVAETRPL 164
           +F LC+WLVPF+L VSLSAND VLPT  E    
Sbjct: 143 YFGLCVWLVPFALFVSLSANDNVLPTTNEPSSS 175


>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
           membrane/ATP-binding component; Reviewed.
          Length = 588

 Score = 28.7 bits (65), Expect = 1.4
 Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 10/67 (14%)

Query: 46  KKVIQWLIIITLLIYAGFFCFEDLPTILLIC--GVLAQVLHLIIIQNFPYVSLTSPAFIA 103
            K  +  + +++L+  GF     L  +LLI    +LA +L  +II+N P  +L  P FI 
Sbjct: 17  SKPAKRWLNLSILL--GF-----LSGLLLIAQAWLLATILQALIIENIPREALLPP-FIL 68

Query: 104 AVVLIVV 110
            ++L V+
Sbjct: 69  LILLFVL 75


>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
           This model represents a set of proteins with extensive
           C-terminal homology to the ATP-dependent protease La,
           product of the lon gene of E. coli. The model is based
           on a seed alignment containing only archaeal members,
           but several bacterial proteins match the model well.
           Because several species, including Thermotoga maritima
           and Treponema pallidum, contain both a close homolog of
           the lon protease and nearly full-length homolog of the
           members of this family, we suggest there may also be a
           functional division between the two families. Members of
           this family from Pyrococcus horikoshii and Pyrococcus
           abyssi each contain a predicted intein [Protein fate,
           Degradation of proteins, peptides, and glycopeptides].
          Length = 608

 Score = 27.9 bits (62), Expect = 2.6
 Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 5/68 (7%)

Query: 27  VTAGLYYLAELVEEYSVLAKKVIQ---WLIIITLLIYAGFFCFEDLPTILLICGVLAQVL 83
           V AG     E+VE+Y   A K       L+ +   I    +  ++LP   L+  V+A  L
Sbjct: 86  VPAGEG--REIVEDYKKKAFKQPSSRNLLLFMIGFIVLSEYFLKNLPPNYLLAAVIAAAL 143

Query: 84  HLIIIQNF 91
            L+I   F
Sbjct: 144 ILLIFGFF 151


>gnl|CDD|145936 pfam03052, Adeno_52K, Adenoviral protein L1 52/55-kDa.  The
           adenoviral protein L1 52/55-kDa is expressed in both the
           early and late stages of infection which suggests that
           it could play multiple roles in the viral life cycle.
           The L1 52/55 kDa protein interacts with the viral IVa2
           protein and is required for DNA packaging. L1 53/55-kDa
           is required to mediate stable association between the
           viral DNA and empty capsid.
          Length = 198

 Score = 27.1 bits (60), Expect = 3.6
 Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 7/48 (14%)

Query: 1   AGLYYLAELVEEYSVLAKKVIQWLI-------IVTAGLYYLAELVEEY 41
           A L+   E  E Y V  +      +        +  GLYYL + ++ Y
Sbjct: 84  AELHRAYEQTEVYEVSFQDTFNNHVRTLLWRPELPLGLYYLWDFLQAY 131


>gnl|CDD|233476 TIGR01574, miaB-methiolase, tRNA-N(6)-(isopentenyl)adenosine-37
          thiotransferase enzyme MiaB.  This model represents
          homologs of the MiaB enzyme responsible for the
          modification of the isopentenylated adenine-37 base of
          most bacterial and eukaryotic tRNAs that read codons
          beginning with uracil (all except tRNA(I,V) Ser).
          Adenine-37 is next to the anticodon on the 3' side in
          these tRNA's, and lack of modification at this site
          leads to an increased spontaneous mutation frequency.
          Isopentenylated A-37 is modified by methylthiolation at
          position 2, either by MiaB alone or in concert with a
          separate methylase yet to be discovered (MiaC?). MiaB
          contains a 4Fe-4S cluster which is labile under
          oxidizing conditions. Additionally, the sequence is
          homologous (via PSI-BLAST searches) to the biotin
          synthetase, BioB, which utilizes both an iron-sulfur
          cluster and S-adenosym methionine (SAM) to generate a
          radical which is responsible for initiating the
          insertion of sulfur into the substrate. It is
          reasonable to surmise that the methyl group of SAM
          becomes the methyl group of the product, but this has
          not been shown, and the possibility of a separate
          methylase exists. This equivalog is a member of a
          subfamily (TIGR00089) which contains several other
          hypothetical equivalogs which are all probably enzymes
          with similar function acting on different substrates.
          These enzymes contain a TRAM domain (pfam01938) which
          is believed to be responsible for binding to tRNAs.
          Hits to this model span all major groups of bacteria
          and eukaryotes, but not archaea, which are known to
          lack this particular tRNA modification. The enzyme from
          Thermotoga maritima has been cloned, expressed,
          spectroscopically characterized and shown to complement
          the E. coli MiaB enzyme [Protein synthesis, tRNA and
          rRNA base modification].
          Length = 438

 Score = 27.5 bits (61), Expect = 3.9
 Identities = 10/23 (43%), Positives = 13/23 (56%)

Query: 72 ILLICGVLAQVLHLIIIQNFPYV 94
          I+ +CG +A  L   I Q  PYV
Sbjct: 74 IIGVCGCMASHLGNEIFQRAPYV 96


>gnl|CDD|190565 pfam03208, PRA1, PRA1 family protein.  This family includes the
           PRA1 (Prenylated rab acceptor) protein which is a Rab
           guanine dissociation inhibitor (GDI) displacement
           factor. This family also includes the glutamate
           transporter EAAC1 interacting protein GTRAP3-18.
          Length = 153

 Score = 26.1 bits (58), Expect = 8.2
 Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 2/32 (6%)

Query: 117 SYFQSNYHSFAEVMAFFTLCLWLVPFSLLVSL 148
            YFQ+NY     V+A   L L   P SL+V L
Sbjct: 39  LYFQTNY--AIVVLAVLLLSLLTNPLSLIVLL 68


>gnl|CDD|218288 pfam04842, DUF639, Plant protein of unknown function (DUF639).
           Plant protein of unknown function.
          Length = 682

 Score = 26.4 bits (58), Expect = 8.7
 Identities = 11/22 (50%), Positives = 15/22 (68%)

Query: 139 LVPFSLLVSLSANDMVLPTVAE 160
           L+ FSLL  +   D+VL T+AE
Sbjct: 366 LLIFSLLEQVPGGDIVLETLAE 387


  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
   0.331    0.143    0.432 

Gapped
Lambda     K      H
   0.267   0.0765    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,780,440
Number of extensions: 855446
Number of successful extensions: 1481
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1461
Number of HSP's successfully gapped: 144
Length of query: 165
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 75
Effective length of database: 6,945,742
Effective search space: 520930650
Effective search space used: 520930650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 55 (24.9 bits)