RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15697
(332 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 = 121 bits (305), Expect = 1e-33
Identities = 44/162 (27%), Positives = 69/162 (42%), Gaps = 16/162 (9%)
Query: 118 VDGTMVLIDAPN---EHEDQFVNRNGDHALNVMAICGPNYKFYAVNANWPGSVHDARVMR 174
+DGT + I+ P E + + L V+ + P+ + V+ WPGSV D R++
Sbjct: 1 IDGTEIPIERPKSLEEQAQTYSGYKKHNTLKVLIVVDPDGRIIFVSVGWPGSVSDKRILE 60
Query: 175 NSMVYRKFDEEGWRPFPDAVILGDSAYPLKEWLIPPRTRNPDAA----ADQRFLRCHKRT 230
NS + K + +L D +PL + L+ P + P A + F R
Sbjct: 61 NSGLLEKLPPGDY-------VLADRGFPLSDSLLAPPAKKPGGAQLTEEEVEFNRRIASA 113
Query: 231 RRLIENSFGILKEKFPCLN-YMRLS-PQFAGMVVLASTTLHN 270
R +E G LK +F L +R+S +VL LHN
Sbjct: 114 RIHVERVIGRLKGRFRILRGRLRISKLTTLDKIVLVCCALHN 155
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 34.5 bits (79), Expect = 0.091
Identities = 12/48 (25%), Positives = 25/48 (52%)
Query: 275 IDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRNNPGTQ 322
+ + E + E ++E ED+ EEE V+ + +EE + + + G +
Sbjct: 451 EEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEE 498
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 33.4 bits (77), Expect = 0.16
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 274 TIDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEE 310
D + E V+ D+E +DD EE +D D DEEE
Sbjct: 320 EEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEE 356
Score = 30.4 bits (69), Expect = 1.5
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 275 IDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQP 312
D D E + ++ + E+D E+E DD D+ +EEE+
Sbjct: 338 DDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEE 375
>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor
[Transcription].
Length = 392
Score = 32.8 bits (74), Expect = 0.23
Identities = 18/41 (43%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 291 AEDDGEEEAVDDPDEIDE--EEQPRQDRNNPGTQRLARLLN 329
AE EE D PDEI E EE + N T+ LA LN
Sbjct: 304 AEAHKEEVQSDRPDEIGEEKEEDDENEENERHTELLADELN 344
>gnl|CDD|176557 cd08620, PI-PLCXDc_like_1, Catalytic domain of uncharacterized
hypothetical proteins similar to eukaryotic
phosphatidylinositol-specific phospholipase C, X domain
containing proteins. This subfamily corresponds to the
catalytic domain present in a group of uncharacterized
hypothetical proteins found in bacteria and fungi, which
are similar to eukaryotic phosphatidylinositol-specific
phospholipase C, X domain containing proteins
(PI-PLCXD). The typical eukaryotic
phosphoinositide-specific phospholipase C (PI-PLC, EC
3.1.4.11) has a multidomain organization that consists
of a PLC catalytic core domain, and various regulatory
domains. The catalytic core domain is assembled from two
highly conserved X- and Y-regions split by a divergent
linker sequence. In contrast, eukaryotic PI-PLCXDs
contain a single TIM-barrel type catalytic domain, X
domain, and are more closely related to bacterial
PI-PLCs, which participate in Ca2+-independent PI
metabolism, hydrolyzing the membrane lipid
phosphatidylinositol (PI) to produce phosphorylated
myo-inositol and diacylglycerol (DAG). Although the
biological function of eukaryotic PI-PLCXDs still
remains unclear, it may distinct from that of typical
eukaryotic PI-PLCs.
Length = 281
Score = 32.0 bits (73), Expect = 0.38
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 75 IHEVVPVIV-DTFFQRMVKWPEENLNDIPMTFLRKGGFPN 113
H ++P DTF Q +V + + N +I + + GF N
Sbjct: 70 QHNMIPGQGFDTFLQDVVTFLKANPTEIVVVHITWDGFDN 109
>gnl|CDD|219904 pfam08561, Ribosomal_L37, Mitochondrial ribosomal protein L37.
This family includes yeast MRPL37 a mitochondrial
ribosomal protein.
Length = 80
Score = 29.2 bits (66), Expect = 0.55
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 12/54 (22%)
Query: 191 PDAVILGDSAYPLKEWL--------IPPRTRNPDAAADQRFLRCHKRTRRLIEN 236
PD V L DS YP EWL + + +++ R ++ I+
Sbjct: 24 PDPVALPDSEYP--EWLWTLLDPAPKALELADANLKDRRKYWR--LLRKQNIKE 73
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 30.4 bits (69), Expect = 0.67
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 7/46 (15%)
Query: 268 LHNIALTIDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPR 313
H +A D ++ D+E E++ ++E DD DE +EEE P
Sbjct: 104 QHLVASEEDESDD-------DEEDEEEEDDEEDDDEDESEEEESPV 142
Score = 30.0 bits (68), Expect = 0.85
Identities = 11/32 (34%), Positives = 22/32 (68%)
Query: 284 VEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQD 315
V +DE++DD E+E +D +E D+E++ ++
Sbjct: 107 VASEEDESDDDEEDEEEEDDEEDDDEDESEEE 138
>gnl|CDD|234000 TIGR02760, TraI_TIGR, conjugative transfer relaxase protein TraI.
This protein is a component of the relaxosome complex. In
the process of conjugative plasmid transfer the
realaxosome binds to the plasmid at the oriT (origin of
transfer) site. The relaxase protein TraI mediates the
single-strand nicking and ATP-dependent unwinding
(relaxation, helicase activity) of the plasmid molecule.
These two activities reside in separate domains of the
protein.
Length = 1960
Score = 31.8 bits (72), Expect = 0.68
Identities = 22/133 (16%), Positives = 45/133 (33%), Gaps = 18/133 (13%)
Query: 214 NPDAAADQRFLRCHKRTRRLIENSFGILKEKFPCLNYMRLSPQF----------AGMVVL 263
+ D A + + +KR + I F ++ + + ++ V+
Sbjct: 1743 DKDDANKDKDMDNNKRVKGSISGQFVVINKGMQ-GDRSYIAEGIETGLSIALANPKATVV 1801
Query: 264 ASTTLHNIALTIDRDNENQNVEI-HDDEAEDDGEEEAVDD------PDEIDEEEQPRQDR 316
+ N I +NV I D++ E+ + A++ D I D
Sbjct: 1802 IAVGGKNNLSPIIPKFIPKNVVIVLDNDGEEAKSQRAIEKIINKFKQDNISARIVFPDDW 1861
Query: 317 NNPGTQRLARLLN 329
N+ G + L + L
Sbjct: 1862 NDIGEEELQKQLM 1874
>gnl|CDD|219922 pfam08595, RXT2_N, RXT2-like, N-terminal. The family represents
the N-terminal region of RXT2-like proteins. In S.
cerevisiae, RXT2 has been demonstrated to be involved in
conjugation with cellular fusion (mating) and invasive
growth. A high throughput localisation study has
localised RXT2 to the nucleus.
Length = 141
Score = 30.1 bits (68), Expect = 0.84
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 274 TIDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQP 312
I +N + E D +DD ++E ++ D D++E P
Sbjct: 38 RIKFNNPPRIDEDGGDIDDDDEDDEDDEEADAEDDDENP 76
Score = 28.9 bits (65), Expect = 2.2
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 269 HNIALTIDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRNNP 319
++ L+ R N I +D + D + D+ DE DEE D NP
Sbjct: 31 RDV-LSRKRIKFNNPPRIDEDGGDIDDD----DEDDEDDEEADAEDDDENP 76
>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family.
Prothymosin alpha and parathymosin are two ubiquitous
small acidic nuclear proteins that are thought to be
involved in cell cycle progression, proliferation, and
cell differentiation.
Length = 106
Score = 29.2 bits (65), Expect = 1.1
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 276 DRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDE 308
D E + V+ D+E E +GEEE ++ +E +
Sbjct: 49 DEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEG 81
Score = 29.2 bits (65), Expect = 1.3
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 278 DNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQP 312
D + E+ +D+ E++GE E + +E + E
Sbjct: 49 DEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGAT 83
Score = 28.4 bits (63), Expect = 2.0
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 278 DNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQ 311
+ +E ++ EDD EEE + +E +EEE+
Sbjct: 45 QEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEE 78
>gnl|CDD|150797 pfam10171, DUF2366, Uncharacterized conserved protein (DUF2366).
This is a family of proteins conserved from nematodes to
humans. The function is not known.
Length = 173
Score = 30.0 bits (68), Expect = 1.2
Identities = 13/37 (35%), Positives = 16/37 (43%), Gaps = 6/37 (16%)
Query: 207 LIPPRTRNPDAAAD-QRFLRCH--KRTRRLIENSFGI 240
L+PP RNP + Q R R R L S G+
Sbjct: 82 LVPPTIRNPTSDKHLQTLERLRNQGRLRHL---SLGL 115
>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2. Transcripts
harbouring premature signals for translation termination
are recognised and rapidly degraded by eukaryotic cells
through a pathway known as nonsense-mediated mRNA decay.
In Saccharomyces cerevisiae, three trans-acting factors
(Upf1 to Upf3) are required for nonsense-mediated mRNA
decay.
Length = 171
Score = 29.7 bits (67), Expect = 1.3
Identities = 12/39 (30%), Positives = 20/39 (51%)
Query: 272 ALTIDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEE 310
+ + D E +DE ++ +EE VD PD+ +EE
Sbjct: 3 SESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEE 41
>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 = 28.4 bits (64), Expect = 1.5
Identities = 24/86 (27%), Positives = 33/86 (38%), Gaps = 15/86 (17%)
Query: 195 ILGDSAYP---LKEWL--------IPPRTRNPDAAADQRFLRCHKRTRRLIENSFGILKE 243
+ D Y +EWL IPP R ++ R R +IE SFG LK
Sbjct: 1 VHADKGYRSRRNREWLKERGIRASIPPLGRP---KKPKKQDRADYPRRWVIERSFGWLKR 57
Query: 244 KFP-CLNYMRLSPQFAGMVVLASTTL 268
Y +L+ F G + LA +
Sbjct: 58 FRRLATRYEKLAETFEGFIALAFAVM 83
>gnl|CDD|217827 pfam03979, Sigma70_r1_1, Sigma-70 factor, region 1.1. Region 1.1
modulates DNA binding by region 2 and 4 when sigma is
unbound by the core RNA polymerase. Region 1.1 is also
involved in promoter binding.
Length = 79
Score = 28.0 bits (63), Expect = 1.8
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 280 ENQNVEIHDDEAEDDGEEEAVDDPDEIDEEE 310
E+ +E+ ++ ++ +EE D D +E E
Sbjct: 49 EDMGIEVVEEADSEELDEETSSDEDAEEEAE 79
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation
factor RRN3. This family consists of several eukaryotic
proteins which are homologous to the yeast RRN3 protein.
RRN3 is one of the RRN genes specifically required for
the transcription of rDNA by RNA polymerase I (Pol I) in
Saccharomyces cerevisiae.
Length = 554
Score = 30.0 bits (68), Expect = 1.9
Identities = 28/140 (20%), Positives = 52/140 (37%), Gaps = 27/140 (19%)
Query: 215 PDAAADQRFLRCH---KRTRRLIENSFG----ILKEKFP--------CLNYMR------- 252
P + R H + RL+ +S G IL + FP + Y+R
Sbjct: 135 PPVEQREVLSRVHDALRYILRLVPSSPGFLLPILAKNFPHKTKSKKVLVGYVRNLLRLTE 194
Query: 253 ----LSPQFAGMVVLASTTLHNIALTIDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDE 308
L +++ L ++ + + D+ + E EDD +E+ + D D+ DE
Sbjct: 195 YCPELGFDILELIIERLLKL-DVEIQNELDDIDDEEEERVLADEDDDDEDDMFDMDDDDE 253
Query: 309 EEQPRQDRNNPGTQRLARLL 328
EE + + ++ L
Sbjct: 254 EESDPEVERTSTIKEVSEKL 273
>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region. The domain
is found in the primary vegetative sigma factor. The
function of this domain is unclear and can be removed
without loss of function.
Length = 211
Score = 29.5 bits (67), Expect = 1.9
Identities = 12/44 (27%), Positives = 20/44 (45%)
Query: 275 IDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRNN 318
ID + E+E D E+ DD D+ DE+E ++ +
Sbjct: 30 IDPNAAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADL 73
Score = 28.7 bits (65), Expect = 3.6
Identities = 15/60 (25%), Positives = 29/60 (48%)
Query: 251 MRLSPQFAGMVVLASTTLHNIALTIDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEE 310
RLS +G + + A I+ + + +++E DD+ ED+ E++ + D EE
Sbjct: 20 GRLSDLISGFIDPNAAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLGPDPEE 79
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 30.1 bits (68), Expect = 1.9
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 271 IALTIDRDNENQNVEIH------DDEAEDDGEEEAVDDPDEIDEEEQPRQDRNNPGTQRL 324
AL I+ N ++ E ++E ED+G + D +E +E++ + ++ G L
Sbjct: 377 SALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDSDGNSSL 436
Query: 325 A 325
A
Sbjct: 437 A 437
Score = 27.8 bits (62), Expect = 9.8
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 274 TIDRDNENQNVEIHDDEAEDDGEEEAVDDPD-------EIDEEEQPRQDRNN 318
+ E+ N E D+E ED+ EEE D+ + + +E E+ +
Sbjct: 376 FSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKY 427
>gnl|CDD|223052 PHA03346, PHA03346, US22 family homolog; Provisional.
Length = 520
Score = 29.7 bits (67), Expect = 2.6
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 278 DNENQNVEIHDDEAEDDG---EEEAVDDPDEIDEEEQPRQDRNNPGTQRLARLLNYFR 332
D++++ + DD+ ED G +E+ V D ++DE R+ + RLL+ +
Sbjct: 427 DDDDEGDDEDDDDWEDLGFDLDEDDVYDLKDVDEWRLERRIATAERWELGQRLLDAYM 484
>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 = 27.7 bits (62), Expect = 2.6
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEV 78
LS ++++L L ++ Y I A+ G S+S+ R IH+V
Sbjct: 13 LSLEDQLLLTLVYLREYRTYEHIAASFGISESTANRIIHKV 53
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 29.2 bits (66), Expect = 2.7
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 278 DNENQNVEIHDDEAED-DGEEEAVDDPDEIDEEE 310
D+E + E+ +DE D +GE V+ EI+ +
Sbjct: 98 DDEEEEWEVEEDEDSDDEGEWIDVESDKEIESSD 131
>gnl|CDD|217746 pfam03815, LCCL, LCCL domain.
Length = 95
Score = 27.7 bits (62), Expect = 2.8
Identities = 8/23 (34%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 55 SPYHIIGATHGPSKSSICRS-IH 76
S + G SSIC++ IH
Sbjct: 31 SKASVYGTDIYSDDSSICKAAIH 53
>gnl|CDD|227697 COG5410, COG5410, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 305
Score = 29.2 bits (65), Expect = 3.1
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 20/71 (28%)
Query: 82 IVDTFFQR----------MVKWPEENLNDIPMTFLRKGGFPNVAGCVDGTMVLIDAPNEH 131
+V T R +++ + D P F++ GGFP G I+ P
Sbjct: 187 LVSTVKSRKASPDTPIIVIMQRLAQ---DDPTGFIQSGGFP-------GAWECIEIPALI 236
Query: 132 EDQFVNRNGDH 142
+D +V+R +H
Sbjct: 237 DDAYVSRLPEH 247
>gnl|CDD|220172 pfam09309, FCP1_C, FCP1, C-terminal. The C-terminal domain of
FCP-1 is required for interaction with the carboxy
terminal domain of RAP74. Interaction relies extensively
on van der Waals contacts between hydrophobic residues
situated within alpha-helices in both domains.
Length = 263
Score = 29.2 bits (65), Expect = 3.2
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 278 DNENQNVEIHD--DEAEDDGEEEAVDDPDEIDEEEQPRQDR--NNPGTQR 323
D E+ + E+ D E DD + E P +E+EQ Q R PG +R
Sbjct: 144 DLESMDKEVDDILGEGSDDSDSEKKKPPGNEEEQEQAPQPRKQQPPGPRR 193
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 29.2 bits (66), Expect = 3.3
Identities = 8/34 (23%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 278 DNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQ 311
+ E + + + E ED+ +E+ ++ D+ DE ++
Sbjct: 287 EEEEEEDDYSESEDEDEEDEDEEEEEDD-DEGDK 319
Score = 27.7 bits (62), Expect = 8.7
Identities = 11/40 (27%), Positives = 24/40 (60%)
Query: 276 DRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQD 315
D ++ + +E ++E E+D E+ D+ +E ++EE+ D
Sbjct: 275 DEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDD 314
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 29.2 bits (66), Expect = 3.5
Identities = 10/50 (20%), Positives = 26/50 (52%)
Query: 271 IALTIDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRNNPG 320
D D ++ +++ DD+ +DD +++ D DE +E+++ ++
Sbjct: 134 DDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSD 183
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to be
DNA-binding and may be a transcription factor.
Length = 238
Score = 28.9 bits (65), Expect = 3.5
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 278 DNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRN 317
E + E D + +D ++E D +E E+E R++R
Sbjct: 45 IEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERL 84
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel, four-helix
bundle structure with a large hydrophobic patch in which
23 residues of one monomer form van der Waals contacts
with the other monomer. This CENP-B dimer configuration
may be suitable for capturing two distant CENP-B boxes
during centromeric heterochromatin formation.
Length = 101
Score = 27.4 bits (60), Expect = 3.6
Identities = 15/48 (31%), Positives = 22/48 (45%)
Query: 284 VEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRNNPGTQRLARLLNYF 331
+E +D D EEE DD DE D++E +D + + YF
Sbjct: 6 LEGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDEVPVPSFGEAMAYF 53
Score = 27.0 bits (59), Expect = 5.6
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 267 TLHNIALTIDRDNENQNVEIHDDEAEDDGEEEAVDDPDEI 306
TLH + D D+++ E DDE E+D +E+ +D DE+
Sbjct: 2 TLHFLEGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDEV 41
>gnl|CDD|183731 PRK12766, PRK12766, 50S ribosomal protein L32e; Provisional.
Length = 232
Score = 28.7 bits (64), Expect = 3.9
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 288 DDEAEDDGEEEAVDDPDEIDEEEQPR 313
+ E ED+G EE ++ +++ E +PR
Sbjct: 66 EAEVEDEGGEEEEEEDADVETELRPR 91
>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region. The precise
function of this eukaryotic protein family is unknown.
The yeast orthologues have been implicated in cell cycle
progression and biogenesis of 60S ribosomal subunits.
The Schistosoma mansoni Mak16 has been shown to target
protein transport to the nucleolus.
Length = 97
Score = 27.1 bits (60), Expect = 4.3
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 270 NIALTIDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQD 315
AL + EN E ++E ED+GE E V D +E++EE + +D
Sbjct: 52 KKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLED 97
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 28.8 bits (64), Expect = 4.6
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 288 DDEAEDDGEEEAVDDPDEIDEEEQPRQDRNNP 319
D E E++ EEE ++ +E +EEE+ ++ P
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEEEEEENEEP 893
>gnl|CDD|233654 TIGR01953, NusA, transcription termination factor NusA. This model
describes NusA, or N utilization substance protein A, a
bacterial transcription termination factor. It binds to
RNA polymerase alpha subunit and promotes termination at
certain RNA hairpin structures. It is named for the
interaction in E. coli of phage lambda antitermination
protein N with the N-utilization substance, consisting
of NusA, NusB, NusE (ribosomal protein S10), and nusG.
This model represents a region of NusA shared in all
bacterial forms, and including an S1 (pfam00575) and a
KH (pfam00013) RNA binding domains. Proteobacterial
forms have an additional C-terminal region, not included
in this model, with two repeats of 50-residue domain
rich in acidic amino acids [Transcription, Transcription
factors].
Length = 341
Score = 28.4 bits (64), Expect = 5.4
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 269 HNIALTIDRDNENQNVEIH---DDEAEDDGEEEAVDDPDEIDEEEQ 311
N+ + IDR + NV +E ED E +++D EID + Q
Sbjct: 40 ENVEVNIDRKTGDINVYRRKEVVEEVEDPSLEISLEDAREIDPDVQ 85
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 28.8 bits (64), Expect = 5.6
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 275 IDRDNENQNVEIHDDEAEDDGEEEA--VDDPDEIDEEEQPRQDRNNPGTQRL 324
+ ++++N+ +E D + ++D EE + V DEI + Q + P + L
Sbjct: 3936 VSKEDDNKALEDKDRQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDL 3987
>gnl|CDD|220785 pfam10498, IFT57, Intra-flagellar transport protein 57. Eukaryotic
cilia and flagella are specialised organelles found at
the periphery of cells of diverse organisms.
Intra-flagellar transport (IFT) is required for the
assembly and maintenance of eukaryotic cilia and
flagella, and consists of the bidirectional movement of
large protein particles between the base and the distal
tip of the organelle. IFT particles contain multiple
copies of two distinct protein complexes, A and B, which
contain at least 6 and 11 protein subunits. IFT57 is
part of complex B but is not, however, required for the
core subunits to stay associated. This protein is known
as Huntington-interacting protein-1 in humans.
Length = 355
Score = 28.5 bits (64), Expect = 5.7
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 279 NENQNVEIH-DDEAEDDGEEEAVDDPDEIDEEEQPRQDRNNPGT 321
NE E +D+AE EE + E ++++ Q+
Sbjct: 128 NEEDEEENVDEDDAEIILEEVEEEVEIEEVDDDEGTQETKYKRG 171
Score = 27.7 bits (62), Expect = 8.5
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 276 DRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRN 317
+++ EI +E E++ E E VDD + E + R D +
Sbjct: 136 VDEDDA---EIILEEVEEEVEIEEVDDDEGTQETKYKRGDTS 174
>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 = 28.0 bits (62), Expect = 6.3
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 3/59 (5%)
Query: 188 RPFPDAVILGDSAYPLKEW-LIPPRTRNPDAAADQRFLRCHKRTRRLIENSFGILKEKF 245
R + L D YP EW R P + F + + R+ +E +FG+L+ +F
Sbjct: 112 RQYNMGYYLADGIYP--EWATFVKSIRLPQLEKHKLFAQQQEACRKDVERAFGVLQARF 168
>gnl|CDD|181631 PRK09059, PRK09059, dihydroorotase; Validated.
Length = 429
Score = 28.5 bits (64), Expect = 6.3
Identities = 9/19 (47%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 166 SVHDARVMRNSMVY-RKFD 183
SV + +VMR ++ Y R FD
Sbjct: 161 SVANTQVMRRALTYARDFD 179
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 28.4 bits (64), Expect = 6.3
Identities = 10/49 (20%), Positives = 21/49 (42%)
Query: 278 DNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRNNPGTQRLAR 326
D+++ +DE E++ DD D+ D++ R+ +R
Sbjct: 126 DDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIATRERSLERRRRRREW 174
Score = 28.0 bits (63), Expect = 8.3
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 276 DRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRNNPGTQR 323
D E DD+ E D E+E E DE++ D ++ T+
Sbjct: 116 YDDAYRDLEEDDDDDEESDEEDEESSK-SEDDEDDDDDDDDDDIATRE 162
>gnl|CDD|223073 PHA03394, lef-8, DNA-directed RNA polymerase subunit beta-like
protein; Provisional.
Length = 865
Score = 28.3 bits (64), Expect = 6.8
Identities = 11/44 (25%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 75 IHEVVPVIVDTFFQRMVKWPEENLNDIPMTFLRKGG---FPNVA 115
+H+ V V+ T+ + + +E+ + TF+ G FPN+
Sbjct: 59 LHKCVVVVFGTWLDKRFRDIDEDEQNFGGTFMIDGRHLSFPNIM 102
>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A. The CAF-1
or chromatin assembly factor-1 consists of three
subunits, and this is the first, or A. The A domain is
uniquely required for the progression of S phase in
mouse cells, independent of its ability to promote
histone deposition but dependent on its ability to
interact with HP1 - heterochromatin protein 1-rich
heterochromatin domains next to centromeres that are
crucial for chromosome segregation during mitosis. This
HP1-CAF-1 interaction module functions as a built-in
replication control for heterochromatin, which, like a
control barrier, has an impact on S-phase progression in
addition to DNA-based checkpoints.
Length = 76
Score = 26.0 bits (58), Expect = 7.3
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 288 DDEAEDDGEEEAVDDPDEIDEEE 310
D E E++ E E ++ DE DEEE
Sbjct: 45 DAEWEEEEEGEDLESEDEEDEEE 67
>gnl|CDD|227931 COG5644, COG5644, Uncharacterized conserved protein [Function
unknown].
Length = 869
Score = 28.1 bits (62), Expect = 7.5
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 276 DRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRNNPGTQRLARLLNY 330
D + +N+ D + +D E E D EI+ + D N+ +L L NY
Sbjct: 145 DHATDKENLLESDASSSNDSESEESDSESEIESSDSDHDDENS--DSKLDNLRNY 197
>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein. This family includes proteins
related to Mpp10 (M phase phosphoprotein 10). The U3
small nucleolar ribonucleoprotein (snoRNP) is required
for three cleavage events that generate the mature 18S
rRNA from the pre-rRNA. In Saccharomyces cerevisiae,
depletion of Mpp10, a U3 snoRNP-specific protein, halts
18S rRNA production and impairs cleavage at the three U3
snoRNP-dependent sites.
Length = 613
Score = 28.0 bits (62), Expect = 7.6
Identities = 10/41 (24%), Positives = 20/41 (48%)
Query: 280 ENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRNNPG 320
E+ ++ DDE EDD E++ ++ ++E + R
Sbjct: 145 ESSLEDLSDDETEDDEEKKMEEEEAGEEKESVEQATREKKF 185
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 27.8 bits (62), Expect = 7.7
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 6/40 (15%)
Query: 272 ALTIDRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQ 311
A +D ++E D+E E++ EEE D D+ D+++
Sbjct: 165 AEDVDEEDEK------DEEEEEEEEEEDEDFDDDDDDDDD 198
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 28.1 bits (63), Expect = 7.9
Identities = 8/42 (19%), Positives = 18/42 (42%)
Query: 276 DRDNENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQPRQDRN 317
+R N Q + + E E + ++++ PR++R
Sbjct: 639 NRRNRRQAQQQTAETRESQQAEVTEKARTQDEQQQAPRRERQ 680
>gnl|CDD|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta;
Reviewed.
Length = 129
Score = 26.9 bits (60), Expect = 8.0
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 277 RDNENQNVEIHDDEAEDDG--EEEAVDDPDEIDEEE 310
+ + + I DD DD EE+ ++ DE +E+E
Sbjct: 93 KFMDGDDDIIDDDILPDDDFDEEDLDEEDDEDEEDE 128
>gnl|CDD|185059 PRK15104, PRK15104, oligopeptide ABC transporter substrate-binding
protein OppA; Provisional.
Length = 543
Score = 28.2 bits (63), Expect = 8.1
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 167 VHDARVMRNSMVYRKFDEEGWRPFPDAVILGDSAYPLKEWLIPPRT---RNP 215
VH + KF E+ +P A I+ + AY LK+W++ R RNP
Sbjct: 186 VHPSMSPVPKAAVEKFGEKWTQP---ANIVTNGAYKLKDWVVNERIVLERNP 234
>gnl|CDD|224946 COG2035, COG2035, Predicted membrane protein [Function unknown].
Length = 276
Score = 27.6 bits (62), Expect = 8.2
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 232 RLIENSFGILKEKFPCLNYMRLSPQFAGMVV 262
RLIE GI K N + L P GM++
Sbjct: 37 RLIEAIAGIFKLDEFKRNVLFLIPLGIGMLL 67
>gnl|CDD|215257 PLN02464, PLN02464, glycerol-3-phosphate dehydrogenase.
Length = 627
Score = 27.8 bits (62), Expect = 8.5
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 16 QVEFILEEIAPALTTPTERNVALSA 40
+++FIL+ I+ L R+ LSA
Sbjct: 373 EIQFILDAISDYLNVKVRRSDVLSA 397
>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional.
Length = 191
Score = 27.3 bits (61), Expect = 9.3
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 279 NENQNVEIHDDEAEDDGEEEAVDDPDEIDEEEQ 311
E + E +DE E++ EE + +E+ +
Sbjct: 13 EETEVEEAVEDEVEEETVEEESEAELLDEEQAK 45
>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional.
Length = 211
Score = 27.4 bits (61), Expect = 9.6
Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 270 NIALTIDRDNENQNVEIHDD---EAEDDGEEEAVDDPDEIDE-EEQPRQDRNN 318
N+ ++NEN+ + + E E+ +EE ++D +E +E + + +D NN
Sbjct: 12 NMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENN 64
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
0.320 0.137 0.422
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: 17,791,275
Number of extensions: 1749818
Number of successful extensions: 2614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2368
Number of HSP's successfully gapped: 95
Length of query: 332
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 235
Effective length of database: 6,635,264
Effective search space: 1559287040
Effective search space used: 1559287040
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 (21.8 bits)
S2: 59 (26.5 bits)