RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780219|ref|YP_003064632.1| hypothetical protein CLIBASIA_00520 [Candidatus Liberibacter asiaticus str. psy62] (117 letters) >gnl|CDD|132738 cd06940, NR_LBD_REV_ERB, The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily. The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, REV-ERB receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 189 Score = 27.8 bits (62), Expect = 0.66 Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 1/32 (3%) Query: 66 LRNLHNAISKMESELKELLSDILLKRHPDEID 97 L N+ N + ++ L L ++ K HP+E Sbjct: 131 LENV-NLVEALQETLIRALRTLIAKNHPNEPS 161 >gnl|CDD|36166 KOG0948, KOG0948, KOG0948, Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]. Length = 1041 Score = 27.2 bits (60), Expect = 1.0 Identities = 11/71 (15%), Positives = 31/71 (43%), Gaps = 1/71 (1%) Query: 48 LFKTYPDTMDKINTVQTALRNLHNAISKMESELKELLS-DILLKRHPDEIDKINPIKNSA 106 + P + I+ + + + + +++ L L + + R PD I ++P+K+ Sbjct: 724 EMEVVPVLLTLIDAISSIRLYIPKDLRSVDARLSVLKAVQEVKSRFPDGIPLLDPVKDMN 783 Query: 107 NEISKLKEDLS 117 + + K+ + Sbjct: 784 IKDVEFKKLVK 794 >gnl|CDD|147117 pfam04799, Fzo_mitofusin, fzo-like conserved region. Family of putative transmembrane GTPase. The fzo protein is a mediator of mitochondrial fusion. This conserved region is also found in the human mitofusin protein. Length = 171 Score = 26.2 bits (58), Expect = 2.1 Identities = 12/61 (19%), Positives = 29/61 (47%), Gaps = 1/61 (1%) Query: 30 FKQMKYESQESKKSLSDALFKTYPDTMDKINTVQTALRNLHNAISKMESELKELLSDILL 89 F ++ + + K L + + + ++ T+Q+ + L N + +E+EL++ L Sbjct: 111 FARLCQQVDVTSKDLEEEI-AELTKEIQRLETIQSRSKLLRNKANLLENELEDFTKTFLT 169 Query: 90 K 90 K Sbjct: 170 K 170 >gnl|CDD|39803 KOG4603, KOG4603, KOG4603, TBP-1 interacting protein [Signal transduction mechanisms]. Length = 201 Score = 25.8 bits (56), Expect = 2.5 Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 1/58 (1%) Query: 58 KINTVQTALRNLHNAISKMESELKELLSDILLKRHPDEIDKINP-IKNSANEISKLKE 114 KI + +++L S +E+E+KEL S + + +EI ++ + + +K Sbjct: 87 KIVALTEKVQSLQQTCSYVEAEIKELSSALTTEEMQEEIQELKKEVAGYRERLKNIKA 144 >gnl|CDD|37854 KOG2643, KOG2643, KOG2643, Ca2+ binding protein, contains EF-hand motifs [Inorganic ion transport and metabolism]. Length = 489 Score = 26.1 bits (57), Expect = 2.6 Identities = 16/58 (27%), Positives = 26/58 (44%) Query: 15 LLGSCDDNPKDPIVQFKQMKYESQESKKSLSDALFKTYPDTMDKINTVQTALRNLHNA 72 LL N K K++K + ++ K +S FK + ++ +N ALR H A Sbjct: 344 LLAYAGVNSKKKHKYLKRVKEKFKDDGKGISLQEFKAFFRFLNNLNDFDIALRFYHMA 401 >gnl|CDD|37353 KOG2142, KOG2142, KOG2142, Molybdenum cofactor sulfurase [Coenzyme transport and metabolism]. Length = 728 Score = 25.8 bits (56), Expect = 2.8 Identities = 22/92 (23%), Positives = 32/92 (34%), Gaps = 9/92 (9%) Query: 19 CDDNPKDPIVQFKQMKYESQESKKSLSDALFKTYPDTMDKINTVQTALRNLHNAISKMES 78 C DN P+ + Q + + + +T P + + Q N Sbjct: 400 CGDNDGQPVSGYMQTPADVGAYLSAQVSDVLETDPLMKSPVFSEQEDSDN---------G 450 Query: 79 ELKELLSDILLKRHPDEIDKINPIKNSANEIS 110 LL + LKRH D PIK +A EI Sbjct: 451 IATPLLERVQLKRHFDAAVASYPIKCAAFEIE 482 >gnl|CDD|36320 KOG1104, KOG1104, KOG1104, Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]. Length = 759 Score = 25.7 bits (56), Expect = 3.4 Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 8/63 (12%) Query: 55 TMDKINTVQTALRNLHNAISKMESELKELLSDILLKRHPDEIDKINP--IKNSANEISKL 112 M T LH+A++K+ L +I +E+ + K+ + L Sbjct: 623 EMVNEFTRLYLWEILHSALNKLNKHLNRSQKNI------EEVTEKLETAEKSEIDLEDDL 676 Query: 113 KED 115 + Sbjct: 677 SAE 679 >gnl|CDD|36435 KOG1221, KOG1221, KOG1221, Acyl-CoA reductase [Lipid transport and metabolism]. Length = 467 Score = 25.6 bits (56), Expect = 3.6 Identities = 10/33 (30%), Positives = 22/33 (66%) Query: 70 HNAISKMESELKELLSDILLKRHPDEIDKINPI 102 A ++ +ELK+ L ++L ++ P+ ++K+ PI Sbjct: 52 KAAQERLRTELKDPLFEVLKEKKPEALEKVVPI 84 >gnl|CDD|37387 KOG2176, KOG2176, KOG2176, Exocyst complex, subunit SEC15 [Intracellular trafficking, secretion, and vesicular transport]. Length = 800 Score = 24.5 bits (53), Expect = 6.7 Identities = 10/72 (13%), Positives = 33/72 (45%) Query: 19 CDDNPKDPIVQFKQMKYESQESKKSLSDALFKTYPDTMDKINTVQTALRNLHNAISKMES 78 + K + + + + + L + ++ + D++D++ V+ + L + +S Sbjct: 42 DGNQHKPVMEKLENRIRNHDKEIEKLCNFHYQDFIDSIDELLKVRGDAQKLKSQVSDTNR 101 Query: 79 ELKELLSDILLK 90 L+E ++++K Sbjct: 102 RLQESGKELIVK 113 >gnl|CDD|153125 cd02434, Nodulin-21_like_3, Nodulin-21 and CCC1-related protein family. Nodulin-21_like_3: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter. . Length = 225 Score = 24.2 bits (53), Expect = 7.9 Identities = 8/38 (21%), Positives = 16/38 (42%), Gaps = 1/38 (2%) Query: 18 SCDDNPKDPIVQFKQMKYESQESKKSLSDALFKTYPDT 55 + + K +V+ +K S+E + + L K Y Sbjct: 77 NYPEGEKSEMVEIYSLKGLSEEVADQVVELLSK-YRKL 113 >gnl|CDD|113812 pfam05055, DUF677, Protein of unknown function (DUF677). This family consists of AT14A like proteins from Arabidopsis thaliana. At14a has a small domain that has sequence similarities to integrins from fungi, insects and humans. Transcripts of At14a are found in all Arabidopsis tissues and localizes partly to the plasma membrane. Length = 336 Score = 24.4 bits (53), Expect = 8.1 Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 10/71 (14%) Query: 25 DPIVQFKQMKYESQESKKSLSDALFKTYPDTMDKINTVQTALRNLHNAISKMESELKELL 84 I++ K+ +E+Q+ SL + F++ T+D T++ + +E +LL Sbjct: 49 KVIIESKEDVWENQD-LFSLVNVYFESTKKTLDFCETLENCVER---------AERSQLL 98 Query: 85 SDILLKRHPDE 95 + + E Sbjct: 99 IREAVAQFEKE 109 >gnl|CDD|145980 pfam03122, Herpes_MCP, Herpes virus major capsid protein. This family represents the major capsid protein (MCP) of herpes viruses. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces. Length = 1352 Score = 24.1 bits (53), Expect = 9.0 Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 4/34 (11%) Query: 48 LFKTYPDT-MDK---INTVQTALRNLHNAISKME 77 L +T+ DT +DK I +QT RNL N + +E Sbjct: 129 LSETFEDTLLDKLLNIRAIQTLARNLQNGLDALE 162 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 0.315 0.132 0.361 Gapped Lambda K H 0.267 0.0790 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,332,712 Number of extensions: 57908 Number of successful extensions: 158 Number of sequences better than 10.0: 1 Number of HSP's gapped: 158 Number of HSP's successfully gapped: 38 Length of query: 117 Length of database: 6,263,737 Length adjustment: 81 Effective length of query: 36 Effective length of database: 4,513,408 Effective search space: 162482688 Effective search space used: 162482688 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: 42 (22.0 bits) S2: 51 (23.3 bits)