RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy672
(314 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 = 150 bits (380), Expect = 5e-45
Identities = 51/158 (32%), Positives = 72/158 (45%), Gaps = 11/158 (6%)
Query: 117 VDCTHVPIQLPS--VENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFT 174
+D T +PI+ P E + + K +L V ++ P+ I V GWPGSV D RI
Sbjct: 1 IDGTEIPIERPKSLEEQAQTYSGYKKHNTLKVLIVVDPDGRIIFVSVGWPGSVSDKRILE 60
Query: 175 NSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLL-----NPTTPQEQRYNKAHIKTRNSV 229
NS + + G+ +L D G+ + L P T +E +N+ R V
Sbjct: 61 NSGLLEKLPPGDY---VLADRGFPLSDSLLAPPAKKPGGAQLTEEEVEFNRRIASARIHV 117
Query: 230 ERLFGIWKRRFACLRRKLANSPVT-CTHIVTACAVLHN 266
ER+ G K RF LR +L S +T IV C LHN
Sbjct: 118 ERVIGRLKGRFRILRGRLRISKLTTLDKIVLVCCALHN 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 = 58.1 bits (140), Expect = 4e-10
Identities = 43/181 (23%), Positives = 76/181 (41%), Gaps = 15/181 (8%)
Query: 110 FPGVVGCVDCTHVPIQ-LPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVH 168
FPG++G +DC H + P+ G+ R + ++ ++ + +L IW G PGS +
Sbjct: 24 FPGMLGSLDCMHWKWKNCPTAWKGQYTRGDSKSPTIILEAVASYDLWIWHAFFGCPGSNN 83
Query: 169 DSRIFTNSRVCHRFERGE-------VRGI------LLGDSGYAQNTFLYTPLLNPTTPQE 215
D + S + +G V G L D Y + + P +
Sbjct: 84 DINVLNQSPIFDDILQGTAPRVRYTVNGRQYNMGYYLADGIYPEWATFVKSIRLPQLEKH 143
Query: 216 QRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTH-IVTACAVLHNIAVQTRQE 274
+ + + R VER FG+ + RF + + I+TAC +LHN+ V+ ++
Sbjct: 144 KLFAQQQEACRKDVERAFGVLQARFKIVATPARLWNQSDLSNIMTACIILHNMIVEDERD 203
Query: 275 L 275
L
Sbjct: 204 L 204
>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 = 35.0 bits (81), Expect = 0.007
Identities = 19/93 (20%), Positives = 33/93 (35%), Gaps = 12/93 (12%)
Query: 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKF--PE 95
K +LL + + S G+S+ T R++ +V L ++ F P+
Sbjct: 12 KLSLEDQLLLTLVYLREYRTYEHIAASFGISESTANRIIHKVEDILIKS----GPFSLPK 67
Query: 96 QLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPS 128
Q + V +D T PI+ P
Sbjct: 68 QKSLR---ESEEEF---EVVIIDATEQPIERPK 94
>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is
present in several RNA-processing factors such as Pcf11
and Nrd1. Pcf11 is a conserved and essential subunit of
the yeast cleavage factor IA, which is required for
polyadenylation-dependent 3'-RNA processing and
transcription termination. Nrd1 is implicated in
polyadenylation-independent 3'-RNA processing. CID binds
tightly to the carboxy-terminal domain (CTD) of RNA
polymerase (Pol) II. During transcription, Pol II
synthesizes eukaryotic messenger RNA. Transcription is
coupled to RNA processing through the CTD, which
consists of up to 52 repeats of the sequence Tyr 1-Ser
2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight
alpha-helices in a right-handed superhelical
arrangement, which closely resembles that of the VHS
domains and ARM (Armadillo) repeat proteins, except for
its two amino-terminal helices.
Length = 114
Score = 33.3 bits (77), Expect = 0.039
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 218 YNKAHIKTRNSVERLFGIWKRRF 240
Y K KTR +ERL IW+ RF
Sbjct: 88 YEKVDEKTRKKLERLLNIWEERF 110
>gnl|CDD|218279 pfam04818, CTD_bind, RNA polymerase II-binding domain. This domain
binds to the phosphorylated C-terminal domain (CTD) of
RNA polymerase II.
Length = 64
Score = 29.5 bits (67), Expect = 0.36
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 218 YNKAHIKTRNSVERLFGIWKRR 239
Y + + + + RL IW+ R
Sbjct: 39 YKEGDEEVKKKIRRLLNIWEER 60
>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 = 30.7 bits (69), Expect = 0.76
Identities = 29/172 (16%), Positives = 43/172 (25%), Gaps = 48/172 (27%)
Query: 111 PGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQ-VIGGPNLEIWDVVSGWPGSVHD 169
V +D T V ++ K + V+ VV P +VHD
Sbjct: 3 GPSVLIIDSTTVRTP-KDEAKERGYKGGKRRKGRKLHIVVDDTTGLPLSVVVT-PANVHD 60
Query: 170 SRIFTNSRVCHRFERGEVRGILLGDSGYAQ----------NTFLYTPL------------ 207
++ ++L D+GYA L
Sbjct: 61 RTALK--QLLDLLRPKGR--LVLADAGYAGPELLDKLREKGVDFLIRLKKNQKLLKKAFR 116
Query: 208 -------------------LNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRF 240
E RYN + R +ER+F KR F
Sbjct: 117 NYFAKVGLKSKRYRVVLKREQKKRGFELRYNLLLYRLRWQIERVFKWLKRFF 168
>gnl|CDD|172486 PRK13984, PRK13984, putative oxidoreductase; Provisional.
Length = 604
Score = 29.0 bits (65), Expect = 3.5
Identities = 13/27 (48%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 271 TRQELPA-EDEVEEEVEEDVVVNDGVG 296
T +E+PA +E+EE +EE VV+ G G
Sbjct: 458 TFEEMPADMEEIEEGLEEGVVIYPGWG 484
>gnl|CDD|233313 TIGR01210, TIGR01210, TIGR01210 family protein. This family of
exclusively archaeal proteins has no characterized close
homologs. Several rounds of PSI-BLAST with a stringent
cutoff of 1e-8 shows apparent similarity of the central
region of this family to the central regions of the
oxygen-independent coproporphyrinogen III dehydrogenase
HemN and to other enzymes [Hypothetical proteins,
Conserved].
Length = 313
Score = 28.2 bits (63), Expect = 5.5
Identities = 16/50 (32%), Positives = 24/50 (48%)
Query: 264 LHNIAVQTRQELPAEDEVEEEVEEDVVVNDGVGRNGAGAVIRRAFINEHF 313
L + V++R E E+++EE + V V VG A IR IN+
Sbjct: 103 LKEVVVESRPEFIDEEKLEELRKIGVNVEVAVGLETANDRIREKSINKGS 152
>gnl|CDD|221608 pfam12501, DUF3708, Phosphate ATP-binding cassette transporter.
This domain family is found in bacteria, and is
typically between 143 and 173 amino acids in length. The
family is found in association with pfam00528. There is
a single completely conserved residue P that may be
functionally important.
Length = 127
Score = 27.1 bits (61), Expect = 7.0
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 270 QTRQELPAEDEVEEEVEEDVVVND 293
LPAE + E E +V++D
Sbjct: 70 LVLASLPAEVQALEGSERSLVLSD 93
>gnl|CDD|234846 PRK00844, glgC, glucose-1-phosphate adenylyltransferase;
Provisional.
Length = 407
Score = 27.9 bits (63), Expect = 7.4
Identities = 17/33 (51%), Positives = 23/33 (69%), Gaps = 2/33 (6%)
Query: 281 VEEEVE-EDVVVNDGVGRNGAGAVIRRAFINEH 312
VE E ED V+ DGV R G GAV+RRA ++++
Sbjct: 340 VESGAEVEDSVLMDGV-RIGRGAVVRRAILDKN 371
>gnl|CDD|224297 COG1379, COG1379, PHP family phosphoesterase with a Zn ribbon
[General function prediction only].
Length = 403
Score = 27.8 bits (62), Expect = 8.9
Identities = 9/36 (25%), Positives = 16/36 (44%)
Query: 121 HVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEI 156
H + LPS+ E +S N++ G P + +
Sbjct: 84 HHLLILPSLSAAEELSEWLSKYSKNIETEGRPRVYL 119
>gnl|CDD|183921 PRK13255, PRK13255, thiopurine S-methyltransferase; Reviewed.
Length = 218
Score = 27.1 bits (61), Expect = 9.5
Identities = 8/24 (33%), Positives = 10/24 (41%)
Query: 40 PPMTRLLAVIQFYATGNFQIFTGD 63
P TR + Y G I+ GD
Sbjct: 82 TPQTRQSGEFEHYQAGEITIYCGD 105
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
0.321 0.137 0.417
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: 16,236,797
Number of extensions: 1543743
Number of successful extensions: 1251
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1243
Number of HSP's successfully gapped: 13
Length of query: 314
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 217
Effective length of database: 6,635,264
Effective search space: 1439852288
Effective search space used: 1439852288
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: 59 (26.5 bits)