RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5744
(157 letters)
>gnl|CDD|128804 smart00531, TFIIE, Transcription initiation factor IIE.
Length = 147
Score = 121 bits (306), Expect = 4e-36
Identities = 45/113 (39%), Positives = 71/113 (62%)
Query: 31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQ 90
E L++D L+RN C+ E+D+ ELL ++K LR + L ++K+I+ + E + K
Sbjct: 1 GEAFLVLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTW 60
Query: 91 KVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLE 143
Y++INY T +++VKYKLD MRKR+E + D T+ + +KCP C +T LE
Sbjct: 61 YRYYWYINYDTLLDVVKYKLDKMRKRLEDKLEDETNNAYYKCPNCQSKYTFLE 113
>gnl|CDD|216839 pfam02002, TFIIE_alpha, TFIIE alpha subunit. The general
transcription factor TFIIE has an essential role in
eukaryotic transcription initiation together with RNA
polymerase II and other general factors. Human TFIIE
consists of two subunits TFIIE-alpha and TFIIE-beta, and
joins the pre-initiation complex after RNA polymerase II
and TFIIF. This family consists of the conserved amino
terminal region of eukaryotic TFIIE-alpha and proteins
from archaebacteria that are presumed to be TFIIE-alpha
subunits also Archaeoglobus fulgidus tfe.
Length = 105
Score = 81.6 bits (202), Expect = 5e-21
Identities = 36/103 (34%), Positives = 61/103 (59%), Gaps = 3/103 (2%)
Query: 24 VVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMET 83
VVRGF+ E L++D L+R + E+D+ ELL + LR + L + ++++ R R +
Sbjct: 6 VVRGFFGDEAVLVLDALLRKGEVTEEDLAELLGIDLNELRKLLYRLYDARLVKYRRRRD- 64
Query: 84 GLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATS 126
D Y++INY+ +N+VKYKLD MR+++E + T+
Sbjct: 65 --DETGWYRYYWYINYEKLLNVVKYKLDHMRQKLEKDLEFETN 105
>gnl|CDD|224589 COG1675, TFA1, Transcription initiation factor IIE, alpha subunit
[Transcription].
Length = 176
Score = 38.1 bits (89), Expect = 5e-04
Identities = 22/113 (19%), Positives = 54/113 (47%), Gaps = 3/113 (2%)
Query: 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNY 94
L++D L+ + ++++ ELL ++ +R + L D +I R + + +
Sbjct: 22 LVVDALLEKGELTDEELAELLGIKKNEVRRILYALYEDGLISYR---KKRDEESGWEEYT 78
Query: 95 YFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLL 147
++INY+ + ++K K + ++++ + T + + CP C ++ E L
Sbjct: 79 WYINYEKVLEVLKGKKRKILEKLKRKLEKETENNYYVCPNCHVKYSFDEAMEL 131
>gnl|CDD|218960 pfam06256, Nucleo_LEF-12, Nucleopolyhedrovirus LEF-12 protein.
This family consists of several Nucleopolyhedrovirus
late expression factor-12 (LEF-12) proteins. The
function of this family is unknown.
Length = 179
Score = 28.5 bits (64), Expect = 1.1
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 100 QTFVNIVKYKLDVMRKRMEMEERDATS 126
+++K LD M + E+ DA +
Sbjct: 13 ADIADMMKRTLDFMAEHGEITRADAAT 39
>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation
motif. This zinc-finger is the dimerisation motif for
LisH proteins, and is also a typical RING-type of plant
ubiquitin ligases.
Length = 55
Score = 25.8 bits (57), Expect = 2.6
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 126 SRSSFKCPRCLKTFTDLEPCLLVLWC 151
S F CP + TD E ++L C
Sbjct: 7 FHSIFVCPISKEVMTDEENPPVMLPC 32
>gnl|CDD|165478 PHA03212, PHA03212, serine/threonine kinase US3; Provisional.
Length = 391
Score = 27.7 bits (61), Expect = 2.6
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 51 ICELLKFERKMLRARISTLKNDKIIQTRLRME 82
IC++L ER +LRA I L ++II ++ E
Sbjct: 181 ICDILAIERSVLRA-IQYLHENRIIHRDIKAE 211
>gnl|CDD|224420 COG1503, eRF1, Peptide chain release factor 1 (eRF1)
[Translation, ribosomal structure and biogenesis].
Length = 411
Score = 27.7 bits (62), Expect = 2.8
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 60 KMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYY 95
LR ST N K TR + + ++ Q++ Y
Sbjct: 45 NRLRDEYSTASNIKSKVTRKNVLSAIESAMQRLKDY 80
>gnl|CDD|219299 pfam07112, DUF1368, Protein of unknown function (DUF1368). This
family consists of several proteins with seem to be
specific to red algae plasmids. Members of this family
are typically around 415 residues in length. The
function of this family is unknown.
Length = 404
Score = 27.6 bits (61), Expect = 3.0
Identities = 22/107 (20%), Positives = 39/107 (36%), Gaps = 9/107 (8%)
Query: 4 SDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLR 63
SD G + SL++LS++ + ++ + LL FER L
Sbjct: 216 SDNGSNRRKYINSLEKLSKVHLECRKQYIKFYLVYLKKPKHQFISFSG-NLLSFER--LS 272
Query: 64 ARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKL 110
T + + + M NY +N+ +FVN+ K+
Sbjct: 273 TAKLTTVSVILSSPLITMFESYC------NYSLVNWDSFVNLSNSKV 313
>gnl|CDD|235121 PRK03372, ppnK, inorganic polyphosphate/ATP-NAD kinase;
Provisional.
Length = 306
Score = 27.6 bits (62), Expect = 3.1
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 16 SLKQLSRLVVRGFYSIEDSLIIDMLVRN 43
L + VV Y +E+ + +D+ VR
Sbjct: 117 DLDEAVERVVDRDYRVEERMTLDVTVRV 144
>gnl|CDD|178669 PLN03122, PLN03122, Poly [ADP-ribose] polymerase; Provisional.
Length = 815
Score = 27.1 bits (60), Expect = 4.6
Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 4/68 (5%)
Query: 82 ETGLDGKAQKVNYYFINYQTFVNIVKYKLDV--MRKRMEMEERDATSRSSFKCPRC--LK 137
+ +G + ++ F ++ L + MR+ +E +D++ PRC
Sbjct: 47 DDSGNGNGKSAEDAVKEFEEFCKAIEEHLSIEQMREILEENGQDSSGSDDAVLPRCQDQL 106
Query: 138 TFTDLEPC 145
+ LE C
Sbjct: 107 FYGPLEKC 114
>gnl|CDD|233184 TIGR00917, 2A060601, Niemann-Pick C type protein family. The model
describes Niemann-Pick C type protein in eukaryotes. The
defective protein has been associated with Niemann-Pick
disease which is described in humans as autosomal
recessive lipidosis. It is characterized by the
lysosomal accumulation of unestrified cholesterol. It is
an integral membrane protein, which indicates that this
protein is most likely involved in cholesterol transport
or acts as some component of cholesterol homeostasis
[Transport and binding proteins, Other].
Length = 1204
Score = 26.7 bits (59), Expect = 6.9
Identities = 14/88 (15%), Positives = 27/88 (30%), Gaps = 17/88 (19%)
Query: 71 NDKIIQTRLRMETGLDGKAQKV-NYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSS 129
N + Q + + N V + + D +R +++
Sbjct: 17 NCPYNGPSKKPPDDGSSLIQSLCGFSHPNISGNVCCTETQFDTLRSNVQLA-------IP 69
Query: 130 F--KCPRCLKTFTDLEPCLLVLWCACPC 155
F +CP CL+ + L+C C
Sbjct: 70 FLVRCPACLRNLLN-------LFCELTC 90
>gnl|CDD|205590 pfam13412, HTH_24, Winged helix-turn-helix DNA-binding.
Length = 48
Score = 24.3 bits (54), Expect = 7.8
Identities = 10/44 (22%), Positives = 22/44 (50%)
Query: 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76
D I+ +L NP + + ++ E L + R+ L+ + +I+
Sbjct: 5 DLKILRLLQENPRISQRELAERLGLSLGTVNRRLKRLEEEGLIK 48
>gnl|CDD|240261 PTZ00085, PTZ00085, 40S ribosomal protein S28; Provisional.
Length = 73
Score = 24.7 bits (54), Expect = 9.7
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 40 LVRN---PCMKEDDICELLKFERKMLRAR 65
L+RN P +E DI L++ ER+ R R
Sbjct: 46 LIRNVKGPV-REGDILSLMETEREARRLR 73
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
0.325 0.138 0.414
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,559,068
Number of extensions: 671070
Number of successful extensions: 784
Number of sequences better than 10.0: 1
Number of HSP's gapped: 781
Number of HSP's successfully gapped: 27
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.0 bits)