RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= 537021.9.peg.1140_1
         (90 letters)



>gnl|CDD|112562 pfam03753, HHV6-IE, Human herpesvirus 6 immediate early protein.
           The proteins in this family are poorly characterized,
           but an investigation has indicated that the immediate
           early protein is required the down-regulation of MHC
           class I expression in dendritic cells. Human herpesvirus
           6 immediate early protein is also referred to as U90.
          Length = 993

 Score = 29.3 bits (65), Expect = 0.25
 Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 17/72 (23%)

Query: 17  EFCTNSNS-KQDCLISQFKLFEKHYREQQ-------KGVNEI---------LDILKSVKW 59
            FC  +N  KQD L  + ++ EK+ +  Q       K +N+I         L I  + K 
Sbjct: 187 AFCIKTNKLKQDLLECKNEIIEKNSKNMQTMQDFAIKQMNQIFMDMCDKTFLKIHFNCKN 246

Query: 60  LFSALKNIAIAV 71
           L  A KN+  AV
Sbjct: 247 LIEAAKNLGAAV 258


>gnl|CDD|32865 COG3051, CitF, Citrate lyase, alpha subunit [Energy production and
           conversion].
          Length = 513

 Score = 28.0 bits (62), Expect = 0.64
 Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 5/40 (12%)

Query: 36  FEKHYREQQKGVNEILDILKSVKWLFSALKNIAIAVTSLT 75
           F   +R     VN ++D++  +       KN+ +A +SL+
Sbjct: 70  FHHAFRGGDLVVNMVMDVIAKM-----GFKNLTLASSSLS 104


>gnl|CDD|144408 pfam00798, Arena_glycoprot, Arenavirus glycoprotein. 
          Length = 473

 Score = 27.3 bits (61), Expect = 0.96
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 66 NIAIAVTSLTAIIYGLLNI 84
          NIA+   SL AII G++N+
Sbjct: 20 NIALIAVSLIAIIKGVVNL 38


>gnl|CDD|34224 COG4586, COG4586, ABC-type uncharacterized transport system, ATPase
           component [General function prediction only].
          Length = 325

 Score = 24.8 bits (54), Expect = 4.7
 Identities = 8/28 (28%), Positives = 14/28 (50%)

Query: 37  EKHYREQQKGVNEILDILKSVKWLFSAL 64
           +  + E+   + EILD+   +KW    L
Sbjct: 130 DDEFAERLDFLTEILDLEGFLKWPVRKL 157


>gnl|CDD|132904 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit
          of Bacterial RNA polymerase.  The bacterial alpha
          subunit of RNA polymerase (RNAP) consists of two
          independently folded domains: an amino-terminal domain
          (alphaNTD) and a carboxy-terminal domain (alphaCTD).
          AlphaCTD is not required for RNAP assembly but
          interacts with transcription activators. AlphaNTD is
          essential in vivo and in vitro for RNAP assembly and
          basal transcription. It is similar to the eukaryotic
          RPB3/AC40/archaeal D subunit, and contains two
          subdomains: one subdomain is similar the eukaryotic
          Rpb11/AC19/archaeal L subunit which is involved in
          dimerization; and the other is an inserted beta sheet
          subdomain. The alphaNTDs of plant plastid RNAP (PEP)
          are also included in this subfamily. PEP is largely
          responsible for the transcription of photosynthetic
          genes and is closely related to the multi-subunit
          bacterial RNAP, which is a large multi-subunit complex
          responsible for the synthesis of all bacterial RNAs.
          The bacterial RNAP core enzyme consists of four
          subunits (beta', beta, alpha and omega). All residues
          in the alpha subunit that is involved in dimerization
          or in the interaction with other subunits are located
          within alphaNTD.
          Length = 215

 Score = 24.0 bits (53), Expect = 8.6
 Identities = 13/43 (30%), Positives = 17/43 (39%), Gaps = 8/43 (18%)

Query: 45 KGVNE-ILDILKSVKWLFSALKNIAIAVTSLTAIIYGLLNIKG 86
           GV E +L+IL +       LK I     S        L +KG
Sbjct: 59 PGVREDVLEILLN-------LKEIVFKSDSEDEPQVLRLKVKG 94


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.323    0.136    0.400 

Gapped
Lambda     K      H
   0.267   0.0714    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,034,605
Number of extensions: 43136
Number of successful extensions: 145
Number of sequences better than 10.0: 1
Number of HSP's gapped: 145
Number of HSP's successfully gapped: 15
Length of query: 90
Length of database: 6,263,737
Length adjustment: 59
Effective length of query: 31
Effective length of database: 4,988,806
Effective search space: 154652986
Effective search space used: 154652986
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 (22.0 bits)
S2: 51 (23.5 bits)