RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7983
(184 letters)
>gnl|CDD|217409 pfam03178, CPSF_A, CPSF A subunit region. This family includes a
region that lies towards the C-terminus of the cleavage
and polyadenylation specificity factor (CPSF) A (160
kDa) subunit. CPSF is involved in mRNA polyadenylation
and binds the AAUAAA conserved sequence in pre-mRNA.
CPSF has also been found to be necessary for splicing of
single-intron pre-mRNAs. The function of the aligned
region is unknown but may be involved in RNA/DNA
binding.
Length = 318
Score = 59.9 bits (146), Expect = 4e-11
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 82 LVTQISPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDVKSDACEGFIDGDLIESFL 141
LV IS E Y L LQ++L + + ++ +RS+ +S + IDGDL+E FL
Sbjct: 260 LVPFISEEEYRRLQHLQQQLRDELPHLCGLDPRAFRSYY--SRSPPVKNVIDGDLLERFL 317
Query: 142 D 142
D
Sbjct: 318 D 318
>gnl|CDD|153118 cd07909, YciF, YciF bacterial stress response protein,
ferritin-like iron-binding domain. YciF is a bacterial
protein of unknown function that is up-regulated when
bacteria experience stress conditions, and is highly
conserved in a broad range of bacterial species. YciF
has a ferritin-like domain. Ferritin-like,
diiron-carboxylate proteins participate in a range of
functions including iron regulation, mono-oxygenation,
and reactive radical production. These proteins are
characterized by the fact that they catalyze
dioxygen-dependent oxidation-hydroxylation reactions
within diiron centers; one exception is manganese
catalase, which catalyzes peroxide-dependent
oxidation-reduction within a dimanganese center.
Diiron-carboxylate proteins are further characterized by
the presence of duplicate metal ligands, glutamates and
histidines (ExxH) and two additional glutamates within a
four-helix bundle. Outside of these conserved residues
there is little obvious homology. Members include
bacterioferritin, ferritin, rubrerythrin, aromatic and
alkene monooxygenase hydroxylases (AAMH), ribonucleotide
reductase R2 (RNRR2), acyl-ACP-desaturases
(Acyl_ACP_Desat), manganese (Mn) catalases,
demethoxyubiquinone hydroxylases (DMQH), DNA protecting
proteins (DPS), and ubiquinol oxidases (AOX), and the
aerobic cyclase system, Fe-containing subunit (ACSF).
Length = 147
Score = 27.5 bits (62), Expect = 2.4
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 8/62 (12%)
Query: 97 LQERLAQTIRSVGRIEHSFWRSFNTDVKSDACEGFIDG------DLIESFLDLNIKDMKS 150
+ L +T V R+E F S + C+ ++G +LIE D + D
Sbjct: 38 FESHLEETEGQVERLEQIF-ESLGEKPEGKKCKA-MEGLIKEAEELIEETGDSAVLDAAL 95
Query: 151 IA 152
IA
Sbjct: 96 IA 97
>gnl|CDD|183223 PRK11597, PRK11597, heat shock chaperone IbpB; Provisional.
Length = 142
Score = 27.8 bits (62), Expect = 2.5
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 10/46 (21%)
Query: 11 TLAFHLALATDSTFTFGTIDEIQKLHI---RTVPLGEAPRRIAYQE 53
TLA ++ + + +TF G LHI R P AP+RIA E
Sbjct: 98 TLAENMEV-SGATFVNGL------LHIDLIRNEPEAIAPQRIAISE 136
>gnl|CDD|202235 pfam02412, TSP_3, Thrombospondin type 3 repeat. The thrombospondin
repeat is a short aspartate rich repeat which binds to
calcium ions. The repeat was initially identified in
thrombospondin proteins that contained 7 of these
repeats. The repeat lacks defined secondary structure.
Length = 35
Score = 25.4 bits (56), Expect = 2.7
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 120 NTDVKSDACEGFIDGDLIESFLD 142
++D DAC+ D D + LD
Sbjct: 3 DSDGIGDACDNDFDNDGVPDLLD 25
>gnl|CDD|218128 pfam04523, Herpes_U30, Herpes virus tegument protein U30. This
family is named after the human herpesvirus protein, but
has been characterized in cytomegalovirus as UL47.
Cytomegalovirus UL47 is a component of the tegument,
which is a protein layer surrounding the viral capsid.
UL47 co-precipitates with UL48 and UL69 tegument
proteins, and the major capsid protein UL86. A
UL47-containing complex is thought to be involved in the
release of viral DNA from the disassembling virus
particle.
Length = 883
Score = 27.3 bits (61), Expect = 5.4
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 137 IESFLDLNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRI 183
+E FLD M ++ + LQI ++K+ ++ DI++I L R+
Sbjct: 301 VEQFLDKINDFMTTLGSYLQIA---CSSKKQLSLSDILEIKRRLLRL 344
>gnl|CDD|213558 TIGR00762, DegV, EDD domain protein, DegV family. This family of
proteins is related to DegV of Bacillus subtilis and
includes paralogous sets in several species (B.
subtilis, Deinococcus radiodurans, Mycoplasma
pneumoniae) that are closer in percent identity to each
than to most homologs from other species. This suggests
both recent paralogy and diversity of function. DegV
itself is encoded immediately downstream of DegU, a
transcriptional regulator of degradation, but is itself
uncharacterized. Crystallography suggested a
lipid-binding site, while comparison of the crystal
structure to dihydroxyacetone kinase and to a mannose
transporter EIIA domain suggests a conserved domain,
EDD, with phosphotransferase activity [Unknown
function, General].
Length = 275
Score = 26.7 bits (60), Expect = 7.0
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 16 LALATDSTFTFGTIDEIQKLHIRTVPL 42
+A+ TDST + I++ I VPL
Sbjct: 1 IAIVTDSTADL-PPELIEEYGITVVPL 26
>gnl|CDD|189781 pfam00948, Flavi_NS1, Flavivirus non-structural Protein NS1. The
NS1 protein is well conserved amongst the flaviviruses.
It contains 12 cysteines, and undergoes glycosylation in
a similar manner to other NS proteins. Mutational
analysis has strongly implied a role for NS1 in the
early stages of RNA replication.
Length = 355
Score = 26.6 bits (59), Expect = 8.8
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 105 IRSVGRIEHSFWRSFNTDVKSDACEGFID 133
IRSV R+EH+ WRS ++ + E +D
Sbjct: 56 IRSVTRLEHAMWRSIADELNAILSENEVD 84
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
0.320 0.135 0.375
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,281,427
Number of extensions: 850005
Number of successful extensions: 805
Number of sequences better than 10.0: 1
Number of HSP's gapped: 804
Number of HSP's successfully gapped: 14
Length of query: 184
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 93
Effective length of database: 6,901,388
Effective search space: 641829084
Effective search space used: 641829084
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 (21.8 bits)
S2: 56 (25.4 bits)