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)