RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13113
(286 letters)
>gnl|CDD|222071 pfam13359, DDE_4, DDE superfamily endonuclease. This family of
proteins are related to pfam00665 and are probably
endonucleases of the DDE superfamily. Transposase
proteins are necessary for efficient DNA transposition.
This domain is a member of the DDE superfamily, which
contain three carboxylate residues that are believed to
be responsible for coordinating metal ions needed for
catalysis. The catalytic activity of this enzyme
involves DNA cleavage at a specific site followed by a
strand transfer reaction.
Length = 155
Score = 133 bits (338), Expect = 5e-39
Identities = 50/160 (31%), Positives = 71/160 (44%), Gaps = 13/160 (8%)
Query: 92 IDGTHVPIELPSI--ENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQ 149
IDGT +PIE P E + Y K ++ V ++ P+ I V WPGS D RI +
Sbjct: 1 IDGTEIPIERPKSLEEQAQTYSGYKKHNTLKVLIVVDPDGRIIFVSVGWPGSVSDKRILE 60
Query: 150 NSRVYSRFDRREIRGLLLGDIGYAQNEFT-----FTPVRNPITPTPSQVAYNAAQIRTRN 204
NS + + + +L D G+ ++ P T +V +N R
Sbjct: 61 NSGLLEKLPPGDY---VLADRGFPLSDSLLAPPAKKPGGAQ--LTEEEVEFNRRIASARI 115
Query: 205 SVERLFGVLKRRFACLRKKLAN-QPTTCSHIITACAVLHN 243
VER+ G LK RF LR +L + TT I+ C LHN
Sbjct: 116 HVERVIGRLKGRFRILRGRLRISKLTTLDKIVLVCCALHN 155
>gnl|CDD|203098 pfam04827, Plant_tran, Plant transposon protein. This family
contains plant transposases which are putative members
of the PIF / Ping-Pong family.
Length = 205
Score = 43.4 bits (102), Expect = 3e-05
Identities = 47/186 (25%), Positives = 77/186 (41%), Gaps = 20/186 (10%)
Query: 77 QFSGIAGFPRVVVGCIDGTHVPIE-LPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVV 135
GFP ++ G +D H + P+ G++ R +I ++ + +L I+
Sbjct: 17 HIGESRGFPGML-GSLDCMHWKWKNCPTAWKGQYTRGDSKSPTIILEAVASYDLWIWHAF 75
Query: 136 ASWPGSTHDSRIFQNSRVYS----------RFDRREIR---GLLLGDIGYAQNEFTFTPV 182
PGS +D + S ++ R+ + G L D Y + +
Sbjct: 76 FGCPGSNNDINVLNQSPIFDDILQGTAPRVRYTVNGRQYNMGYYLADGIYPEWATFVKSI 135
Query: 183 RNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRK--KLANQPTTCSHIITACAV 240
R P A Q R VER FGVL+ RF + +L NQ + S+I+TAC +
Sbjct: 136 RLPQLEKHKLFAQQ--QEACRKDVERAFGVLQARFKIVATPARLWNQ-SDLSNIMTACII 192
Query: 241 LHNIAI 246
LHN+ +
Sbjct: 193 LHNMIV 198
>gnl|CDD|222263 pfam13613, DDE_4_2, DDE superfamily endonuclease. This family of
proteins are related to pfam00665 and are probably
endonucleases of the DDE superfamily. Transposase
proteins are necessary for efficient DNA transposition.
This domain is a member of the DDE superfamily, which
contain three carboxylate residues that are believed to
be responsible for coordinating metal ions needed for
catalysis. The catalytic activity of this enzyme
involves DNA cleavage at a specific site followed by a
strand transfer reaction.
Length = 95
Score = 30.7 bits (70), Expect = 0.23
Identities = 26/89 (29%), Positives = 36/89 (40%), Gaps = 15/89 (16%)
Query: 18 KLLAVL---RFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTA 74
+LL L R Y T I + + IS+ST R++ KV + L K P+ Q +
Sbjct: 18 QLLLTLVYLREYRT-YEHI-AASFG-ISESTANRIIHKVEDILIKSGP--FSLPK--QKS 70
Query: 75 KNQFSGIAGFPRVVVGCIDGTHVPIELPS 103
+ V ID T PIE P
Sbjct: 71 LRESEEE-----FEVVIIDATEQPIERPK 94
>gnl|CDD|240354 PTZ00310, PTZ00310, AMP deaminase; Provisional.
Length = 1453
Score = 32.5 bits (74), Expect = 0.31
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 10/76 (13%)
Query: 108 EHYRNRKHFYSINVQVIGGPNLEIYDVVASW-----PGSTHDSRIFQNSRVYSRFDRREI 162
E Y + Y+ N I G N++ +D +A W S H+ + Q RVY F + +
Sbjct: 958 EQYSRDRFTYAENRLSIYGINVKEWDDLAHWFDTHGMASKHNKWMIQVPRVYKVFRAQNV 1017
Query: 163 RGLLLGDIG-YAQNEF 177
+G G Y N F
Sbjct: 1018 ----IGSFGQYLDNIF 1029
>gnl|CDD|216602 pfam01609, DDE_Tnp_1, Transposase DDE domain. Transposase proteins
are necessary for efficient DNA transposition. This
domain is a member of the DDE superfamily, which contain
three carboxylate residues that are believed to be
responsible for coordinating metal ions needed for
catalysis. The catalytic activity of this enzyme
involves DNA cleavage at a specific site followed by a
strand transfer reaction. This family contains
transposases for IS4, IS421, IS5377, IS427, IS402,
IS1355, IS5, which was original isolated in
bacteriophage lambda.
Length = 194
Score = 30.3 bits (68), Expect = 0.75
Identities = 23/165 (13%), Positives = 41/165 (24%), Gaps = 36/165 (21%)
Query: 88 VVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDS-- 145
V ID T V Y+ K + ++ + V P + HD
Sbjct: 5 SVLIIDSTTVRTP-KDEAKERGYKGGKRRKGRKLHIVVDDTTGLPLSVVVTPANVHDRTA 63
Query: 146 -----RIFQNSRVYSRFDR----------------------------REIRGLLLGDIGY 172
+ + D +
Sbjct: 64 LKQLLDLLRPKGRLVLADAGYAGPELLDKLREKGVDFLIRLKKNQKLLKKAFRNYFAKVG 123
Query: 173 AQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRF 217
+++ ++ ++ YN R R +ER+F LKR F
Sbjct: 124 LKSKRYRVVLKREQKKRGFELRYNLLLYRLRWQIERVFKWLKRFF 168
>gnl|CDD|222244 pfam13586, DDE_Tnp_1_2, Transposase DDE domain. Transposase
proteins are necessary for efficient DNA transposition.
This domain is a member of the DDE superfamily, which
contain three carboxylate residues that are believed to
be responsible for coordinating metal ions needed for
catalysis.
Length = 86
Score = 26.9 bits (60), Expect = 3.8
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 201 RTRNSVERLFGVLK--RRFACLRKKLA 225
R +ER FG LK RR A +KLA
Sbjct: 43 PRRWVIERSFGWLKRFRRLATRYEKLA 69
>gnl|CDD|213338 cd05136, RasGAP_DAB2IP, Ras-GTPase Activating Domain of DAB2IP and
similar proteins. The DAB2IP family of Ras
GTPase-activating proteins includes DAB2IP, nGAP, and
Syn GAP. Disabled 2 interactive protein, (DAB2IP; also
known as ASK-interacting protein 1 (AIP1)), is a member
of the GTPase-activating proteins, down-regulates
Ras-mediated signal pathways, and mediates TNF-induced
activation of ASK1-JNK signaling pathways. The mechanism
by which TNF signaling is coupled to DAB2IP is not
known.
Length = 324
Score = 28.7 bits (65), Expect = 3.8
Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 204 NSVERLFGVLKRRFACLRKKLANQ--PTTCSHIITAC 238
+S L+ F+ R++L + +I+A
Sbjct: 152 SSHCVFPRELREVFSSWRERLEERGREDIADRLISAS 188
>gnl|CDD|226032 COG3501, VgrG, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 550
Score = 28.8 bits (65), Expect = 4.1
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 6/38 (15%)
Query: 142 THDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTF 179
+ RIFQ+ V EI +L + G A F
Sbjct: 110 RRNCRIFQDKSVP------EILETILQEHGIADFAFRL 141
>gnl|CDD|223162 COG0084, TatD, Mg-dependent DNase [DNA replication, recombination,
and repair].
Length = 256
Score = 28.3 bits (64), Expect = 4.6
Identities = 8/27 (29%), Positives = 13/27 (48%), Gaps = 7/27 (25%)
Query: 244 IAIARREAPPPENNELPVNVHIRDADD 270
+ +A+ LPV +H RDA +
Sbjct: 118 LELAKE-------LNLPVIIHTRDAHE 137
>gnl|CDD|234183 TIGR03361, VI_Rhs_Vgr, type VI secretion system Vgr family protein.
Members of this protein family belong to the Rhs
element Vgr protein family (see TIGR01646), but
furthermore all are found in genomes with type VI
secretion loci. However, members of this protein family,
although recognizably correlated to type VI secretion
according the partial phylogenetic profiling algorithm,
are often found far the type VI secretion locus.
Length = 513
Score = 28.3 bits (64), Expect = 4.8
Identities = 13/39 (33%), Positives = 16/39 (41%), Gaps = 6/39 (15%)
Query: 142 THDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFT 180
DSRIFQN V EI +L + G F +
Sbjct: 97 RRDSRIFQNKSV------PEIITEVLKEHGITDFRFRLS 129
>gnl|CDD|239062 cd02149, NfsB_like_nitroreductase, NAD(P)H:FMN oxidoreductase
family. This domain catalyzes the reduction of flavin,
nitrocompound, quinones and azo compounds using NADH or
NADPH as an electron donor. The enzyme is a homodimer,
and each monomer binds a FMN as co-factor. This family
includes FRase I in Vibrio fischeri, wihich reduces FMN
into FMNH2 as part of the bioluminescent reaction. The
family also includes oxygen-insensitive nitroreductases
that use NADH or NADPH as an electron donor in the ping
pong bi bi mechanism. This type of nitroreductase can be
used in cancer chemotherapy to activate a range of
prodrugs.
Length = 157
Score = 27.5 bits (62), Expect = 5.1
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 7/30 (23%)
Query: 220 LRKKLA-----NQP--TTCSHIITACAVLH 242
L+ +LA NQP T SH++ A
Sbjct: 55 LKARLAPAAWFNQPQVTDASHLVVFLARTD 84
>gnl|CDD|232780 TIGR00010, TIGR00010, hydrolase, TatD family. PSI-BLAST, starting
with a urease alpha subunit, finds a large superfamily
of proteins, including a number of different enzymes
that act as hydrolases at C-N bonds other than peptide
bonds (EC 3.5.-.-), many uncharacterized proteins, and
the members of this family. Several genomes have
multiple paralogs related to this family. However, a set
of 17 proteins can be found, one each from 17 of the
first 20 genomes, such that each member forms a
bidirectional best hit across genomes with all other
members of the set. This core set (and one other
near-perfect member), but not the other paralogs, form
the seed for this model. Additionally, members of the
seed alignment and all trusted hits, but not all
paralogs, have a conserved motif DxHxH near the amino
end. The member from E. coli was recently shown to have
DNase activity [Unknown function, Enzymes of unknown
specificity].
Length = 252
Score = 27.2 bits (61), Expect = 8.6
Identities = 8/29 (27%), Positives = 13/29 (44%), Gaps = 7/29 (24%)
Query: 242 HNIAIARREAPPPENNELPVNVHIRDADD 270
+ +A LPV +H RDA++
Sbjct: 112 AQLQLAEE-------LNLPVIIHARDAEE 133
>gnl|CDD|222777 PHA00144, PHA00144, major head protein.
Length = 438
Score = 27.5 bits (61), Expect = 9.1
Identities = 23/111 (20%), Positives = 44/111 (39%), Gaps = 7/111 (6%)
Query: 100 ELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPG-STHDSRIFQNSRVYSRFD 158
+P+++ H RNR++FY +Q + S S I + D
Sbjct: 116 AIPNVKTLFHTRNRQNFYKQTIQ-----RDSLKTAFVSDGNFDEFLSSIITSIYSSDEVD 170
Query: 159 RREIRGLLLGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERL 209
E LL+ D Y++ F + +PIT T ++ + R + +++
Sbjct: 171 EYEYMKLLI-DNYYSKGLFKTVKISDPITSTGAKDFVTEFLKKLRATAKKM 220
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related
protein 7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S),
an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3'
-UUU-OH) of 7SK RNA. LARP7 is a stable component of the
7SK small nuclear ribonucleoprotein (7SK snRNP). It
intimately associates with all the nuclear 7SK and is
required for 7SK stability. LARP7 also acts as a
negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. It plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. LARP7 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), at
the N-terminal region, which mediates binding to the
U-rich 3' terminus of 7SK RNA. LARP7 also carries
another putative RRM domain at its C-terminus. .
Length = 80
Score = 25.8 bits (57), Expect = 9.8
Identities = 6/29 (20%), Positives = 9/29 (31%)
Query: 54 SEELAKCHQQWIHFPEDLQTAKNQFSGIA 82
EE K + + PE +F
Sbjct: 51 PEEAQKACKHLNNPPETATDKPGKFPKTV 79
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
0.322 0.137 0.418
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,086,440
Number of extensions: 1446771
Number of successful extensions: 1068
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1060
Number of HSP's successfully gapped: 20
Length of query: 286
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 190
Effective length of database: 6,679,618
Effective search space: 1269127420
Effective search space used: 1269127420
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 (21.9 bits)
S2: 58 (26.1 bits)