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)