RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7686
(243 letters)
>gnl|CDD|202203 pfam02319, E2F_TDP, E2F/DP family winged-helix DNA-binding
domain. This family contains the transcription factor
E2F and its dimerisation partners TDP1 and TDP2, which
stimulate E2F-dependent transcription. E2F binds to DNA
as a homodimer or as a heterodimer in association with
TDP1/2, the heterodimer having increased binding
efficiency. The crystal structure of an E2F4-DP2-DNA
complex shows that the DNA-binding domains of the E2F
and DP proteins both have a fold related to the
winged-helix DNA-binding motif. Recognition of the
central c/gGCGCg/c sequence of the consensus
DNA-binding site is symmetric, and amino acids that
contact these bases are conserved among all known E2F
and DP proteins.
Length = 67
Score = 108 bits (271), Expect = 1e-30
Identities = 45/66 (68%), Positives = 54/66 (81%)
Query: 9 RFEKSLGLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68
R EKSLGLLT KF+ L +++P+G+ L AA+ L+VKQKRRIYDITNVLEGIGLIEK +K
Sbjct: 1 RKEKSLGLLTQKFLKLCEKSPDGITDLNEAAKELDVKQKRRIYDITNVLEGIGLIEKKSK 60
Query: 69 NIIRWK 74
N IRW
Sbjct: 61 NEIRWI 66
>gnl|CDD|182613 PRK10644, PRK10644, arginine:agmatin antiporter; Provisional.
Length = 445
Score = 33.2 bits (76), Expect = 0.12
Identities = 9/26 (34%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 132 CYI-PTDVILGMFPDSSLMCLKAPYG 156
CY+ + I+GM P+++L +P+G
Sbjct: 238 CYVLSSTAIMGMIPNAALRVSASPFG 263
>gnl|CDD|237861 PRK14947, PRK14947, DNA polymerase III subunit beta; Provisional.
Length = 384
Score = 32.0 bits (73), Expect = 0.26
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 20 KFVSLLQQAPEGVLHLKYAAE--NLEVKQKRRIY 51
FV L+++ P G + LK A NL ++Q RR Y
Sbjct: 73 AFVDLVRKLPPGEITLKLDASSGNLLIEQGRRKY 106
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 31.1 bits (71), Expect = 0.51
Identities = 21/104 (20%), Positives = 45/104 (43%), Gaps = 22/104 (21%)
Query: 49 RIYDITNVLEGIG-LIEKNN---------KNIIR---WKALKNKNEEEYDLEQSKLIELR 95
I I ++++ I LI ++N KN + W L + +E+ D Q + L
Sbjct: 362 LIESINDIIDAINELIREHNEKIDNLKKEKNKAKKKLWLHLVAELKEDIDAYQKEKKGLE 421
Query: 96 DEISDM-------RNHEAVIDEHIRKCQQSLRNIQE--EEVNRK 130
I+ + +++ I++ ++ L NI+ +E+N+
Sbjct: 422 KAINSLEKEIKQLEAEIKALEKEIKELEKQLTNIEPTADEINKL 465
>gnl|CDD|184793 PRK14696, tynA, tyramine oxidase; Provisional.
Length = 721
Score = 30.2 bits (68), Expect = 1.1
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRR----IYDITNVLEGIGLIEKNNKNIIRWK 74
T+F + + P+ +A EN V Q R+ + D +V+E + ++ N ++ W+
Sbjct: 115 TRFTEISLKEPDKEAVWAFALENKPVDQPRKADVIMLDGKHVIEAV--VDLQNNKVLSWQ 172
Query: 75 ALK 77
+K
Sbjct: 173 PIK 175
>gnl|CDD|204385 pfam10039, DUF2275, Predicted integral membrane protein (DUF2275).
This domain, found in various hypothetical bacterial
proteins and in the RNA polymerase sigma factor, has no
known function.
Length = 209
Score = 29.1 bits (65), Expect = 1.9
Identities = 8/62 (12%), Positives = 14/62 (22%), Gaps = 1/62 (1%)
Query: 164 ISTDENKIKLHVKSSHPEEPVNILLLDTEPKKEKPQTRGRKR-KWSEDRRLIVVPNPPSR 222
+ N + E L + P TR +DR ++
Sbjct: 133 MPDAFNFEIEETYAGAHEPLEFALAFAKINARIAPFTRTHAFPGELDDRPAALLVARAKD 192
Query: 223 KD 224
Sbjct: 193 PP 194
>gnl|CDD|218681 pfam05667, DUF812, Protein of unknown function (DUF812). This
family consists of several eukaryotic proteins of
unknown function.
Length = 536
Score = 29.3 bits (66), Expect = 2.0
Identities = 10/58 (17%), Positives = 25/58 (43%), Gaps = 1/58 (1%)
Query: 75 ALKNKNEEEYDLEQSK-LIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRKQ 131
+ EE+ E+ L L+++I ++ + + I+ ++ + EE +Q
Sbjct: 255 PAEMDTEEDRTKEREAELEALQEQIDELESSIEEVLSEIKALASKIKQVNEELTTVRQ 312
>gnl|CDD|214371 CHL00122, secA, preprotein translocase subunit SecA; Validated.
Length = 870
Score = 29.2 bits (66), Expect = 2.2
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 3/62 (4%)
Query: 41 NLEVKQKRRIYDITNVL---EGIGLIEKNNKNIIRWKALKNKNEEEYDLEQSKLIELRDE 97
N E K K+ +YD+ E I I +N NI+ K D E K++ E
Sbjct: 495 NPEFKLKKELYDLLLSYKSNEKISTISQNFLNILNSLKNDLKFLSLSDFENLKILNEASE 554
Query: 98 IS 99
IS
Sbjct: 555 IS 556
>gnl|CDD|236943 PRK11638, PRK11638, lipopolysaccharide biosynthesis protein WzzE;
Provisional.
Length = 342
Score = 28.9 bits (65), Expect = 2.4
Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 105 EAVIDEHIRKCQQSLRNIQEEEVNRKQCYIPTDVILGMFPDSSLMCLKAP 154
+A+ D + +Q+L+ +++ ++R Q +P + + PDS L L P
Sbjct: 211 KAIYDREVNSVEQALKIAEQQGISRSQTDVPAEEL----PDSELFLLGRP 256
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 29.1 bits (65), Expect = 2.5
Identities = 18/97 (18%), Positives = 43/97 (44%)
Query: 45 KQKRRIYDITNVLEGIGLIEKNNKNIIRWKALKNKNEEEYDLEQSKLIELRDEISDMRNH 104
K K I + +L I II+ ++ K+ +Y ++S+ +L ++I ++ +
Sbjct: 302 KYKNDIENKKQILSNIDAEINKYHAIIKKLSVLQKDYNDYIKKKSRYDDLNNQILELEGY 361
Query: 105 EAVIDEHIRKCQQSLRNIQEEEVNRKQCYIPTDVILG 141
E + +++ + + I+E N ++ IL
Sbjct: 362 EMDYNSYLKSIESLKKKIEEYSKNIERMSAFISEILK 398
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 28.3 bits (64), Expect = 2.7
Identities = 11/58 (18%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 76 LKNKNEEEYDLEQSKLIELRDEISDMRNHE-AVIDEHIRKCQQSLRNIQEEEVNRKQC 132
LK + + ++ +L + EIS + ++++ + K + L++I E R+
Sbjct: 132 LKGRGTDSEEVIARRLENAKKEISHADEFDYVIVNDDLEKALEELKSIILAERLRRDI 189
>gnl|CDD|131106 TIGR02051, MerR, Hg(II)-responsive transcriptional regulator. This
model represents the mercury (II) responsive
transcriptional activator of the mer organomercurial
resistance operon. This protein is a member of the MerR
family of transcriptional activators (pfam00376) and
contains a distinctive pattern of cysteine residues in
its metal binding loop, Cys-X(8)-Cys-Pro, as well as a
conserved and critical cysteine at the N-terminal end of
the dimerization helix [Cellular processes,
Detoxification, Regulatory functions, DNA interactions].
Length = 124
Score = 27.7 bits (62), Expect = 2.7
Identities = 9/36 (25%), Positives = 21/36 (58%)
Query: 81 EEEYDLEQSKLIELRDEISDMRNHEAVIDEHIRKCQ 116
E Y+L KL ++ +++D+ E +++E + +C
Sbjct: 75 REMYELASRKLKSVQAKMADLLRIERLLEELLEQCP 110
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 28.2 bits (64), Expect = 4.2
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 60 IGLIEKNNKNIIRWKALKNKNEEEYDLEQSKLIELRDEISDMRN-HEAVIDEHIRKCQQS 118
I E+ K I+ + +E +++ L+E ++EI +RN E + E + Q+
Sbjct: 33 IKEAEEEAKRIL-----EEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKL 87
Query: 119 LRNIQ--EEEVNRKQ 131
+ + EE ++RK
Sbjct: 88 EKRLLQKEENLDRKL 102
>gnl|CDD|224296 COG1378, COG1378, Predicted transcriptional regulators
[Transcription].
Length = 247
Score = 27.8 bits (62), Expect = 4.8
Identities = 14/72 (19%), Positives = 29/72 (40%), Gaps = 6/72 (8%)
Query: 39 AENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKALK-----NKNEEEYDLEQSKLIE 93
+E V + + +YD+ LE GL+E +++A+ + +EE +L
Sbjct: 37 SEASGVPRPK-VYDVLRSLEKKGLVEVIEGRPKKYRAVPPEELIERIKEELQELLRELES 95
Query: 94 LRDEISDMRNHE 105
+E+
Sbjct: 96 ELEELERELARR 107
>gnl|CDD|145416 pfam02252, PA28_beta, Proteasome activator pa28 beta subunit. PA28
activator complex (also known as 11s regulator of 20S
proteasome) is a ring shaped hexameric structure of
alternating alpha and beta subunits. This family
represents the beta subunit. The activator complex binds
to the 20S proteasome ana simulates peptidase activity
in and ATP-independent manner.
Length = 150
Score = 26.8 bits (60), Expect = 7.1
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 74 KALKNKNEEEY-----DLEQSKLIELRDEISDMRNHEAVIDEHIRK 114
KA K + E+Y +L++ + IELR + ++RN+ AV+ + I K
Sbjct: 88 KAAKYPHVEDYREAVHELDEKEYIELRLIVLEIRNNYAVLHDIIIK 133
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 27.1 bits (61), Expect = 9.3
Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 11/72 (15%)
Query: 30 EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKALKNKNEEEYDLEQS 89
E AA+ E+ +K VLE + K K + + K E +
Sbjct: 202 EDENDDSLAADESELPEK--------VLEKFKALAKQYKK---LRKAQEKKVEGRLAQHK 250
Query: 90 KLIELRDEISDM 101
K +LR+++ +
Sbjct: 251 KYAKLREKLKEE 262
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 27.3 bits (61), Expect = 10.0
Identities = 23/107 (21%), Positives = 42/107 (39%), Gaps = 11/107 (10%)
Query: 30 EGVLHLKYAAENLEVKQK--RRIYDITNVLEGIG-LIEKNNKNIIRW--------KALKN 78
EG LK K+ R++ + LE + I + K + K +K+
Sbjct: 224 EGYELLKEKEALERQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKD 283
Query: 79 KNEEEYDLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125
EEE + K+ EL EI+ + A + + ++ L ++ E
Sbjct: 284 LGEEEQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAE 330
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
0.316 0.135 0.390
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,515,986
Number of extensions: 1198195
Number of successful extensions: 1405
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1393
Number of HSP's successfully gapped: 73
Length of query: 243
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 149
Effective length of database: 6,768,326
Effective search space: 1008480574
Effective search space used: 1008480574
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: 41 (21.6 bits)
S2: 58 (26.1 bits)