RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18159
(294 letters)
>gnl|CDD|227357 COG5024, COG5024, Cyclin [Cell division and chromosome
partitioning].
Length = 440
Score = 139 bits (353), Expect = 2e-38
Identities = 84/297 (28%), Positives = 135/297 (45%), Gaps = 24/297 (8%)
Query: 13 TNSNNKKAESQNSRKTVL---KSKQTT-----VSEKKEKSLIEHFDKEIQLEDKPKVTGP 64
+ +N++A + L Q T + L + + E
Sbjct: 90 SGESNERARIPRLSECNLDSILFIQMTLNEDSYEPMIDYILKKDENSLSPYELDENQLAL 149
Query: 65 PSD----------VDDFDKETWEDPLQVSCYAMHIFEYLKSREAEF-QIKDYLPFQSSTE 113
D D EDPL V YA IFEYL E +YL QS
Sbjct: 150 DEKQAESKRESQSWQDLDATDQEDPLMVPEYASDIFEYLLKLELIDLPNPNYLIKQS--- 206
Query: 114 KGNINAEMRSVLVDWMVEVQETFELNHETLYLAVKLVDLYLGKVVCSRLNLQLLGATAIF 173
MRS+LVDW+VEV F L ETL+LA+ ++D +L V S QL+G +A+F
Sbjct: 207 --LYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALF 264
Query: 174 VSSKFDDRIPPQLSDLEYICSHTYSIQDLKDMEIKLVTAIGFDLGIPLSYRFLRRYARCN 233
++SK+++ P + DL Y ++ D+ E ++ + F++ P FLRR ++ +
Sbjct: 265 IASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKAS 324
Query: 234 RIQLPLLTLARYILELSLMEYSLIRESDSKLACASLYLAQKMNKLTPWNKTLEYYSE 290
+ T A++ E+S ++Y I+ S S A A++YL++K+ W++TL +YS
Sbjct: 325 DYDIFSRTPAKFSSEISPVDYKFIQISPSWCAAAAMYLSRKILSQNQWDRTLIHYSG 381
>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain. Cyclins regulate
cyclin dependent kinases (CDKs). Human cyclin-O is a
Uracil-DNA glycosylase that is related to other cyclins.
Cyclins contain two domains of similar all-alpha fold,
of which this family corresponds with the N-terminal
domain.
Length = 127
Score = 127 bits (322), Expect = 6e-37
Identities = 49/131 (37%), Positives = 81/131 (61%), Gaps = 6/131 (4%)
Query: 89 IFEYLKSREAEFQI-KDYLPFQSSTEKGNINAEMRSVLVDWMVEVQETFELNHETLYLAV 147
I+ YL+ E E + DYL Q +IN +MR++L+DW+VEV E F+L ETLYLAV
Sbjct: 2 IYAYLRELEEEDRPPPDYLDQQ-----PDINPKMRAILIDWLVEVHEEFKLLPETLYLAV 56
Query: 148 KLVDLYLGKVVCSRLNLQLLGATAIFVSSKFDDRIPPQLSDLEYICSHTYSIQDLKDMEI 207
+D +L K R LQL+G T + +++K+++ PP + D YI + Y+ +++ ME+
Sbjct: 57 NYLDRFLSKQPVPRTKLQLVGVTCLLIAAKYEEIYPPSVEDFVYITDNAYTKEEILRMEL 116
Query: 208 KLVTAIGFDLG 218
+++ + +DL
Sbjct: 117 LILSTLNWDLS 127
>gnl|CDD|217307 pfam02984, Cyclin_C, Cyclin, C-terminal domain. Cyclins regulate
cyclin dependent kinases (CDKs). Human CCNO is a
Uracil-DNA glycosylase that is related to other cyclins.
Cyclins contain two domains of similar all-alpha fold,
of which this family corresponds with the C-terminal
domain.
Length = 117
Score = 85.8 bits (213), Expect = 5e-21
Identities = 33/77 (42%), Positives = 48/77 (62%), Gaps = 3/77 (3%)
Query: 220 PLSYRFLRRYARCNRIQLPLLTLARYILELSLMEYSLIRESDSKLACASLYLAQKMNKLT 279
P FLRR+++ L TLA+Y+LELSL++Y ++ S +A A++YLA+K
Sbjct: 1 PTPLSFLRRFSKAADYDLETRTLAKYLLELSLLDYDFLKYPPSLIAAAAVYLARKTLGSP 60
Query: 280 PWNKTLEY---YSEEKL 293
PW +TLE+ YSEE L
Sbjct: 61 PWTETLEHYTGYSEEDL 77
>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold. Protein binding domain
functioning in cell-cycle and transcription control.
Present in cyclins, TFIIB and Retinoblastoma (RB).The
cyclins consist of 8 classes of cell cycle regulators
that regulate cyclin dependent kinases (CDKs). TFIIB is
a transcription factor that binds the TATA box. Cyclins,
TFIIB and RB contain 2 copies of the domain.
Length = 88
Score = 72.7 bits (179), Expect = 2e-16
Identities = 27/90 (30%), Positives = 50/90 (55%), Gaps = 2/90 (2%)
Query: 121 MRSVLVDWMVEVQETFELNHETLYLAVKLVDLYLGKVVCSRLNLQLLGATAIFVSSKFDD 180
MR +D++ V + L+ ETL LAV L+D +L + L+ A A+++++K ++
Sbjct: 1 MRPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEE 60
Query: 181 RIPPQLSDLEYICSHTYSIQDLKDMEIKLV 210
IPP L DL ++ + +++ ME L+
Sbjct: 61 -IPPWLKDLVHVT-GYATEEEILRMEKLLL 88
Score = 63.4 bits (155), Expect = 4e-13
Identities = 27/72 (37%), Positives = 42/72 (58%)
Query: 218 GIPLSYRFLRRYARCNRIQLPLLTLARYILELSLMEYSLIRESDSKLACASLYLAQKMNK 277
P FLRR A+ + LTLA +L+ L++YS++ S S +A A+LYLA K+ +
Sbjct: 1 MRPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEE 60
Query: 278 LTPWNKTLEYYS 289
+ PW K L + +
Sbjct: 61 IPPWLKDLVHVT 72
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and
Retinoblastoma. A helical domain present in cyclins and
TFIIB (twice) and Retinoblastoma (once). A protein
recognition domain functioning in cell-cycle and
transcription control.
Length = 83
Score = 67.6 bits (166), Expect = 1e-14
Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 127 DWMVEVQETFELNHETLYLAVKLVDLYLGKVVCSRLNLQLLGATAIFVSSKFDDRIPPQL 186
D++ V + L+ ETL LAV L+D +L + + L+ A A++++SK ++ P
Sbjct: 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTK 60
Query: 187 SDLEYICSHTYSIQDLKDMEIKLV 210
+ Y + ++ +++ ME L+
Sbjct: 61 ELVHY--TGYFTEEEILRMERLLL 82
Score = 63.0 bits (154), Expect = 5e-13
Identities = 24/66 (36%), Positives = 36/66 (54%)
Query: 224 RFLRRYARCNRIQLPLLTLARYILELSLMEYSLIRESDSKLACASLYLAQKMNKLTPWNK 283
FLRR + + L LA +L+ L +Y ++ S S +A A+LYLA K + PW K
Sbjct: 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTK 60
Query: 284 TLEYYS 289
L +Y+
Sbjct: 61 ELVHYT 66
>gnl|CDD|225417 COG2862, COG2862, Predicted membrane protein [Function unknown].
Length = 169
Score = 30.7 bits (70), Expect = 0.45
Identities = 29/93 (31%), Positives = 38/93 (40%), Gaps = 13/93 (13%)
Query: 136 FELNHETLYLAV-KLVDLYLGKVVCSRLNLQLLGATAIFVSSKFDDRIPPQLSDLEYICS 194
F++ L LA LVDL L V L + G +FVS K D + S L
Sbjct: 49 FDMGENDLILAALSLVDLLL---VAGLLVMVSFGGYELFVS-KLDIAEEDKPSWLG---- 100
Query: 195 HTYSIQDLKDMEIKLVTAIGFDLGIPLSYRFLR 227
I DL D++ KL +I + L FL
Sbjct: 101 ----IVDLSDLKQKLAASIVAISSVHLLKVFLN 129
>gnl|CDD|176546 cd08604, GDPD_SHV3_repeat_2, Glycerophosphodiester
phosphodiesterase domain repeat 2 of
glycerophosphodiester phosphodiesterase-like protein
SHV3 and SHV3-like proteins. This subfamily corresponds
to the glycerophosphodiester phosphodiesterase domain
(GDPD) repeat 2 present in glycerophosphodiester
phosphodiesterase (GP-GDE)-like protein SHV3 and
SHV3-like proteins (SVLs), which may play important an
role in cell wall organization. The prototype of this
family is a glycosylphosphatidylinositol (GPI) anchored
protein SHV3 encoded by shaven3 (shv3) gene from
Arabidopsis thaliana. Members in this family show
sequence homology to bacterial GP-GDEs (EC 3.1.4.46)
that catalyze the hydrolysis of various
glycerophosphodiesters, and produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols. Both, SHV3 and SVLs, have two tandemly
repeated GDPD domains whose biochemical functions remain
unclear. The residues essential for interactions with
the substrates and calcium ions in bacterial GP-GDEs are
not conserved in SHV3 and SVLs, which suggests that the
function of GDPD domains in these proteins might be
distinct from those in typical bacterial GP-GDEs. In
addition, the two tandem repeats show low sequence
similarity to each other, suggesting they have different
biochemical function. Most of the members of this family
are Arabidopsis-specific gene products. To date, SHV3
orthologues are only found in Physcomitrella patens.
This CD includes domain II (the second GDPD domain of
SHV3 and SVLs), which is necessary for SHV3 function.
Length = 300
Score = 30.4 bits (69), Expect = 0.94
Identities = 20/63 (31%), Positives = 26/63 (41%), Gaps = 11/63 (17%)
Query: 9 SMNLTNSNNKKAESQNSRKTVLKSKQTTVSEKKEKSLIEHFD---KEIQLEDKPKVTGPP 65
S+NL NS + ++ TTV E S I FD EIQ KP ++ P
Sbjct: 49 SINLINSTT-------VATSKFSNRATTVPEIGSTSGIFTFDLTWSEIQ-TLKPAISNPY 100
Query: 66 SDV 68
S
Sbjct: 101 SVT 103
>gnl|CDD|217507 pfam03350, UPF0114, Uncharacterized protein family, UPF0114.
Length = 124
Score = 29.5 bits (67), Expect = 1.0
Identities = 29/96 (30%), Positives = 43/96 (44%), Gaps = 16/96 (16%)
Query: 135 TFELNHETLYLAV-KLVDLYLGKVVCSRLNLQLLGATAIFVSSKFDDRIPPQLSDLEYIC 193
F ++ L LAV +L+DL+L + L + G +FVS K D P L +
Sbjct: 43 VFTIDETDLILAVLELIDLFLIGTL---LLIVGFGGYELFVS-KLDIAEHPDLPEW---- 94
Query: 194 SHTYSIQDLKDMEIKLVTAIGFDLGIPLSYRFLRRY 229
I L D++ KL I + I LS FL+ +
Sbjct: 95 ---LGIVSLDDLKQKLAGVI---VVI-LSVHFLKVF 123
>gnl|CDD|217862 pfam04051, TRAPP, Transport protein particle (TRAPP) component.
TRAPP plays a key role in the targeting and/or fusion of
ER-to-Golgi transport vesicles with their acceptor
compartment. TRAPP is a large multimeric protein that
contains at least 10 subunits. This family contains many
TRAPP family proteins. The Bet3 subunit is one of the
better characterized TRAPP proteins and has a dimeric
structure with hydrophobic channels. The channel
entrances are located on a putative membrane-interacting
surface that is distinctively flat, wide and decorated
with positively charged residues. Bet3 is proposed to
localise TRAPP to the Golgi.
Length = 148
Score = 29.1 bits (66), Expect = 1.6
Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 7/53 (13%)
Query: 196 TYSIQDLKDMEIKLVTAIGFDLGIPLSYRFLRR--YARCNRIQLPLLTLARYI 246
+Y ++D++D+ +L +G+++G L R L R RC + L + ++I
Sbjct: 11 SYLLRDVEDVNARL-EKMGYNIGQRLIERLLARSGSKRCTDL----LEVLKFI 58
>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 29.3 bits (66), Expect = 2.8
Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 11/82 (13%)
Query: 18 KKAESQNSRK-TVLKSKQTTVSEKKEKSLIEHFDKEIQLEDKPKV----------TGPPS 66
+K ++ SR SK + + + S D + +L V PP
Sbjct: 643 RKPKTPPSRAPPASLSKPASSPDASQTSASFDLDPDFELATHQSVPEAALASGSAPAPPP 702
Query: 67 DVDDFDKETWEDPLQVSCYAMH 88
D +D+ WE+ +V+
Sbjct: 703 VPDPYDRPPWEEAPEVASANDG 724
>gnl|CDD|237827 PRK14832, PRK14832, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 253
Score = 27.3 bits (60), Expect = 9.0
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 71 FDKETWEDPLQVSCYAMHIFEYLKSRE 97
F E W+ P++ + M +FE L RE
Sbjct: 71 FSTENWQRPIEEVDFLMLLFERLLRRE 97
>gnl|CDD|165265 PHA02956, PHA02956, hypothetical protein; Provisional.
Length = 189
Score = 26.8 bits (59), Expect = 9.8
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 149 LVDLYLGKVVCSRLNL-QLLGATAIFVSSKFDDRIPPQLSDLEYICSHTYSIQDLKDMEI 207
++D GK++C + + L I D I +L + I +H +Q LKD+ I
Sbjct: 110 IIDSSSGKIICEGIGIIDKLRLHGI-------DFIKDKLFSEDEIINHLVGVQKLKDICI 162
Query: 208 KLV 210
K++
Sbjct: 163 KMI 165
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
0.317 0.133 0.377
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,426,430
Number of extensions: 1360892
Number of successful extensions: 1148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1145
Number of HSP's successfully gapped: 28
Length of query: 294
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 198
Effective length of database: 6,679,618
Effective search space: 1322564364
Effective search space used: 1322564364
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 (21.7 bits)
S2: 59 (26.4 bits)