RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5891
(259 letters)
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 137 bits (345), Expect = 1e-36
Identities = 50/131 (38%), Positives = 79/131 (60%), Gaps = 7/131 (5%)
Query: 64 AEVTKKLKLTGVPMKIYKKTAFIKDMFNSTLEVAKFEGAKIRTVSGIRGQIKKALNKPQG 123
A++ KKLKL G P +I + T F++DMF S LEV KFEGA ++ VSG+RGQ+K K G
Sbjct: 843 AKLVKKLKLVGYPKQIVQNTVFVRDMFTSDLEVLKFEGASLKAVSGLRGQVKGPHGK-NG 901
Query: 124 AFRATFEDKIMLSDIVFCRTWYKVDIPKLYNPVTSLLLPPEQKDSWTGMKTTGQLKRERG 183
+RA FE K+++SDI+ R + V++ +++ PV +LL W G++ +++ G
Sbjct: 902 EYRAVFEGKMLMSDIITLRCFVPVEVHRIFIPVDNLLG------KWRGLRRLHEIRESLG 955
Query: 184 LHNDPQFDSMY 194
L + +
Sbjct: 956 LTHSYAPQNDS 966
>gnl|CDD|218343 pfam04950, DUF663, Protein of unknown function (DUF663). This
family contains several uncharacterized eukaryotic
proteins.
Length = 293
Score = 117 bits (295), Expect = 1e-31
Identities = 38/83 (45%), Positives = 54/83 (65%), Gaps = 1/83 (1%)
Query: 65 EVTKKLKLTGVPMKIYKKTAFIKDMFNSTLEVAKFEGAKIRTVSGIRGQIKKALNKPQGA 124
+ KKLKLTG P KI+KKTAF++ MF + +V F+ + T SG RG IK+AL G
Sbjct: 212 IIAKKLKLTGHPYKIFKKTAFVRYMFFNPEDVEWFKPVPLFTKSGRRGHIKEALG-THGY 270
Query: 125 FRATFEDKIMLSDIVFCRTWYKV 147
F+ATF+ K+ + DIV + + +V
Sbjct: 271 FKATFDGKLNMQDIVIMKLYKRV 293
>gnl|CDD|227504 COG5177, COG5177, Uncharacterized conserved protein [Function
unknown].
Length = 769
Score = 52.0 bits (124), Expect = 1e-07
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 66 VTKKLKLTGVPMKIYKKTAFIKDMFNSTLEVAKFEGAKIRTVSGIRGQIKKALNKPQGAF 125
+ K+ LTG P K +K+ ++ MF S +V F+ ++ T G G IK+ L G F
Sbjct: 678 IAKRAVLTGHPFKNHKRYVTVRYMFFSPEDVMWFKNIQLFTKRGRTGFIKEPLGT-HGYF 736
Query: 126 RATFEDKIMLSDIV 139
+ATF KI D V
Sbjct: 737 KATFSGKIKSQDKV 750
>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 = 33.9 bits (78), Expect = 0.054
Identities = 23/67 (34%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 27 NSKEEEEEEQEDSAFSDESADDNSSDEDETVEPKVFYAEVTKK-----LKLTGVPMKIYK 81
+EEEEEE+ DS F D D+ SD++E E ++ E KK K P K K
Sbjct: 44 EIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLKKKKRVKTKAYKEPTKKKK 103
Query: 82 KTAFIKD 88
K
Sbjct: 104 KKDPTAA 110
>gnl|CDD|201520 pfam00945, Rhabdo_ncap, Rhabdovirus nucleocapsid protein. The
Nucleocapsid (N) Protein is said to have a "tight"
structure. The carboxyl end of the N-terminal domain
possesses an RNA binding domain. Sequence alignments
show 2 regions of reasonable conservation, approx.
64-103 and 201-329. A whole functional protein is
required for encapsidation to take place.
Length = 406
Score = 31.6 bits (72), Expect = 0.39
Identities = 14/67 (20%), Positives = 24/67 (35%), Gaps = 5/67 (7%)
Query: 2 SKIKAEDLFVPTARRHKITSALA-GLNSKEEEEEEQEDSAFSDESADDNSSDED----ET 56
++ L + A K T + K+ E +D +D D+ DE +
Sbjct: 317 HELTVAALLLSYAFGSKATLEQRFFRDEKKYTEYRDDDGDNTDAPLADDGDDEAPKSRDV 376
Query: 57 VEPKVFY 63
VE +Y
Sbjct: 377 VEWLAWY 383
>gnl|CDD|221333 pfam11942, Spt5_N, Spt5 transcription elongation factor, acidic
N-terminal. This is the very acidic N-terminal region
of the early transcription elongation factor Spt5. The
Spt5-Spt4 complex regulates early transcription
elongation by RNA polymerase II and has an imputed role
in pre-mRNA processing via its physical association
with mRNA capping enzymes. The actual function of this
N-terminal domain is not known although it is
dispensable for binding to Spt4.
Length = 92
Score = 28.6 bits (64), Expect = 1.0
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 30 EEEEEEQEDSAFSDESADDNSSDEDETVEPKVF 62
EEEEEE+E+ D S +D DE E + +
Sbjct: 11 EEEEEEEEEDDLEDLSDEDEFIDEAEAEDDRRH 43
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.4 bits (68), Expect = 1.2
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 7 EDLFVPTARRHKITSALAGLNSKEEEEEEQEDSAFSDESADDNSSDEDETVEPK 60
EDL + K+ + E E++ E SA ++ES + D+++ +E K
Sbjct: 3897 EDL--SNSLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKALEDK 3948
>gnl|CDD|221620 pfam12527, DUF3727, Protein of unknown function (DUF3727). This
domain family is found in bacteria and eukaryotes, and
is approximately 100 amino acids in length.
Length = 100
Score = 28.3 bits (64), Expect = 1.4
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 31 EEEEEQEDSAFSDESADDNSSDEDETVEPKV-FYAE 65
E E +ED E DD+ DE+E E FY E
Sbjct: 17 ELPEPEEDEILELEEEDDDDEDEEEEYELLASFYHE 52
>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 = 1.5
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 28 SKEEEEEEQEDSAFSDESADDNSSDEDET 56
+EEEEEE ED S E +DD +ED+
Sbjct: 395 DEEEEEEEDEDEGPSKEHSDDEEFEEDDV 423
>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 = 28.2 bits (62), Expect = 1.9
Identities = 14/43 (32%), Positives = 20/43 (46%)
Query: 23 LAGLNSKEEEEEEQEDSAFSDESADDNSSDEDETVEPKVFYAE 65
L G + + +E+ED DE DD DED+ P + E
Sbjct: 6 LEGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDEVPVPSFGE 48
>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 = 29.2 bits (66), Expect = 2.3
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 30 EEEEEEQEDSAFSDESADDNSSDEDETVEPKVFYAEVTKK 69
EEEEE D + +E +D SD+++ E + E KK
Sbjct: 342 LEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKK 381
Score = 29.2 bits (66), Expect = 2.6
Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 28 SKEEEEEEQEDSAFSDESADDNSSDEDETVEPKVFYAEVTKK 69
EEEEE+ + S ++ D++S DED+ E + + KK
Sbjct: 341 DLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKK 382
Score = 27.3 bits (61), Expect = 9.2
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 30 EEEEEEQEDSAFSDESADDNSSDEDETVEPKVFYAEVTKKLKLTGVPM 77
+EEE E+ SD+ DD +E+E + K AE T+ P
Sbjct: 351 LSDEEEDEEDEDSDDE-DDEEEEEEEKEKKKKKSAESTRSELPFTFPC 397
>gnl|CDD|235865 PRK06814, PRK06814, acylglycerophosphoethanolamine acyltransferase;
Provisional.
Length = 1140
Score = 29.2 bits (66), Expect = 2.5
Identities = 11/50 (22%), Positives = 24/50 (48%)
Query: 69 KLKLTGVPMKIYKKTAFIKDMFNSTLEVAKFEGAKIRTVSGIRGQIKKAL 118
++ +TG MKIY I D + + + +G + S ++ Q+++
Sbjct: 533 RITVTGSLMKIYDGPGMIADKAGAMVVPVRIDGLQFTHFSRLKNQVRRKW 582
>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 = 28.8 bits (65), Expect = 2.9
Identities = 9/41 (21%), Positives = 20/41 (48%)
Query: 15 RRHKITSALAGLNSKEEEEEEQEDSAFSDESADDNSSDEDE 55
R L + +EE +E+++ + E +D+ D+D+
Sbjct: 115 RYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDD 155
Score = 28.4 bits (64), Expect = 3.9
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 27 NSKEEEEEEQEDSAFSDESADDNSSDEDE 55
+ + +EE+E+ + DE DD+ D+D
Sbjct: 130 DEESDEEDEESSKSEDDEDDDDDDDDDDI 158
Score = 28.4 bits (64), Expect = 4.0
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 30 EEEEEEQEDSAFSDESADDNSSDEDETVEPK 60
E +EE++E S D+ DD+ D+D+ +
Sbjct: 132 ESDEEDEESSKSEDDEDDDDDDDDDDIATRE 162
>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 = 26.8 bits (60), Expect = 3.6
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 31 EEEEEQEDSAFSDESADDNSSDEDE 55
EEEEE ED E +D D+D+
Sbjct: 49 EEEEEGED--LESEDEEDEEEDDDD 71
>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain
fusion protein; Provisional.
Length = 131
Score = 27.6 bits (61), Expect = 3.6
Identities = 7/35 (20%), Positives = 18/35 (51%)
Query: 24 AGLNSKEEEEEEQEDSAFSDESADDNSSDEDETVE 58
A ++ + +E ++ +DE+ D+ + + D E
Sbjct: 85 ADEAAEADAADEADEEEETDEAVDETADEADAEAE 119
>gnl|CDD|203546 pfam06917, Pectate_lyase_2, Periplasmic pectate lyase. This family
consists of several Enterobacterial periplasmic pectate
lyase proteins (EC:4.2.2.2). A major virulence
determinant of the plant-pathogenic enterobacterium
Erwinia chrysanthemi is the production of pectate lyase
enzymes that degrade plant cell walls.
Length = 533
Score = 28.6 bits (64), Expect = 3.6
Identities = 22/68 (32%), Positives = 28/68 (41%), Gaps = 5/68 (7%)
Query: 100 EGAKIR--TVSGIRGQIKKALNKPQGAFRATFEDKIMLSDIVFCRTWY---KVDIPKLYN 154
GA++ TV G++ K A N P FR + LSD V R Y K + K Y
Sbjct: 311 PGAELLTWTVDGLKAFAKYAYNVPDNTFRPMLANGTDLSDYVLKRDGYYGKKGTVLKPYP 370
Query: 155 PVTSLLLP 162
LL
Sbjct: 371 AGNEFLLS 378
>gnl|CDD|165442 PHA03171, PHA03171, UL37 tegument protein; Provisional.
Length = 499
Score = 28.1 bits (62), Expect = 4.9
Identities = 14/49 (28%), Positives = 26/49 (53%)
Query: 13 TARRHKITSALAGLNSKEEEEEEQEDSAFSDESADDNSSDEDETVEPKV 61
T R +T+AL +E EEE+ + E+ +++ +E E +P+V
Sbjct: 68 TERPRDLTAALFAEAGEEAEEEDNDRECPDTEAEEEDEEEEIEAPDPEV 116
>gnl|CDD|151773 pfam11332, DUF3134, Protein of unknown function (DUF3134). This
family of proteins with unknown function appears to be
restricted to Cyanobacteria.
Length = 72
Score = 26.2 bits (58), Expect = 5.0
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 28 SKEEEEEEQEDSAFSDESADDNSSDEDETVE 58
+ EEE+E S + DD+ D+D+ +
Sbjct: 43 PEVSTEEEEEISELIGD--DDDYYDDDDDED 71
>gnl|CDD|182033 PRK09697, PRK09697, protein secretion protein GspB; Provisional.
Length = 139
Score = 27.4 bits (60), Expect = 5.1
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 31 EEEEEQEDSAFSDESADDNSSDEDETVEPKVFYAEVTKKLK 71
E EE+++ + E+A +S DE+ TVE A + +++K
Sbjct: 91 ESVEEEDEPGVAVENAPSSSEDEENTVEESDEKAGLRERVK 131
>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 = 27.3 bits (61), Expect = 5.2
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 16 RHKITSALAGLNSKEEEEEEQEDSAFSDESADDNSSDEDETVEPKV 61
+H + S + EE+EEE++D +E D++ S+E+E+ KV
Sbjct: 104 QHLVASEEDESDDDEEDEEEEDD----EEDDDEDESEEEESPVKKV 145
>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II). Bone
sialoprotein (BSP) is a major structural protein of the
bone matrix that is specifically expressed by
fully-differentiated osteoblasts. The expression of
bone sialoprotein (BSP) is normally restricted to
mineralised connective tissues of bones and teeth where
it has been associated with mineral crystal formation.
However, it has been found that ectopic expression of
BSP occurs in various lesions, including oral and
extraoral carcinomas, in which it has been associated
with the formation of microcrystalline deposits and the
metastasis of cancer cells to bone.
Length = 291
Score = 27.7 bits (61), Expect = 5.3
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 27 NSKEEEEEEQEDSAFSDESADDNSSDEDETVE 58
+ EEE +E+++ +E+ +D+ +EDE E
Sbjct: 56 DGDSSEEEGEEETSNEEENNEDSDGNEDEEAE 87
>gnl|CDD|217829 pfam03985, Paf1, Paf1. Members of this family are components of
the RNA polymerase II associated Paf1 complex. The Paf1
complex functions during the elongation phase of
transcription in conjunction with Spt4-Spt5 and
Spt16-Pob3i.
Length = 431
Score = 28.2 bits (63), Expect = 5.3
Identities = 10/30 (33%), Positives = 12/30 (40%)
Query: 27 NSKEEEEEEQEDSAFSDESADDNSSDEDET 56
EEE Q S ES+ D SD +
Sbjct: 390 GEDSEEEGSQSREDGSSESSSDVGSDSESK 419
>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 = 27.3 bits (61), Expect = 5.6
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 30 EEEEEEQEDSAFSDESADDNSSDEDETVEPK 60
+E +E+E D+ D+ S E+E +
Sbjct: 23 DESSDEEEVDL-PDDEQDEESDSEEEQIFVT 52
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This
is a family of uncharacterized proteins.
Length = 449
Score = 28.0 bits (62), Expect = 6.2
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 29 KEEEEEEQEDSAFSDESADDNSSDEDE 55
+E EEE +D D+ D++ D+D+
Sbjct: 47 EEAMEEEDDDEEDDDDDDDEDEDDDDD 73
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 28.0 bits (62), Expect = 6.3
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 30 EEEEEEQEDSAFSDESADDNSSDEDETVEP 59
EEEEEE+E+ +E ++ +E+E EP
Sbjct: 864 EEEEEEEEEEEEEEEEEEEEEEEEEENEEP 893
>gnl|CDD|148314 pfam06632, XRCC4, DNA double-strand break repair and V(D)J
recombination protein XRCC4. This family consists of
several eukaryotic DNA double-strand break repair and
V(D)J recombination protein XRCC4 sequences. In the
non-homologous end joining pathway of DNA double-strand
break repair, the ligation step is catalyzed by a
complex of XRCC4 and DNA ligase IV. It is thought that
XRCC4 and ligase IV are essential for alignment-based
gap filling, as well as for final ligation of the
breaks.
Length = 331
Score = 27.5 bits (61), Expect = 6.8
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 9/55 (16%)
Query: 15 RRHKITSALAGLNSKEEEE----EEQEDSAFSDESAD-----DNSSDEDETVEPK 60
++ KI S L+ +E E +++E SA SD++ D D S+DE++ PK
Sbjct: 187 KKAKIRSLHKLLSEAQELEKSIKQKKETSACSDKTPDEDSKYDGSTDEEQEAPPK 241
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 27.7 bits (61), Expect = 7.6
Identities = 11/48 (22%), Positives = 24/48 (50%)
Query: 21 SALAGLNSKEEEEEEQEDSAFSDESADDNSSDEDETVEPKVFYAEVTK 68
++ K+E E E S +++ D +E+ V+P+++Y +K
Sbjct: 44 QCFVTMSEKKEHVMEGEKKVRSVQASKDKKKEEEAEVDPRLYYENRSK 91
>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 = 27.6 bits (61), Expect = 8.4
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 28 SKEEEEEEQEDSAFSDESADDNSSDEDETVEPKV 61
EEEEE+E+ +E + EDE E +V
Sbjct: 443 ESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEV 476
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localised exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 27.5 bits (61), Expect = 8.6
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 23 LAGLNSKEEEEEEQEDSAFSDESADDNSSDEDETVEPKVFYAEVTKKLKL 72
A +S+ E E + ED DE DD ++E K + K L L
Sbjct: 666 EAIEDSESESESDGEDGE-EDEQEDDAEANEGVVPIDKAVRRALPKVLNL 714
>gnl|CDD|240226 PTZ00007, PTZ00007, (NAP-L) nucleosome assembly protein -L;
Provisional.
Length = 337
Score = 27.1 bits (60), Expect = 9.1
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 30 EEEEEEQEDSAFSDESADDNSSDEDETVE 58
+ +E +D S +S+D SSD + V+
Sbjct: 285 DYSSDEDDDDYDSYDSSDSASSDSNSDVD 313
>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 = 27.0 bits (60), Expect = 9.7
Identities = 12/55 (21%), Positives = 26/55 (47%)
Query: 1 MSKIKAEDLFVPTARRHKITSALAGLNSKEEEEEEQEDSAFSDESADDNSSDEDE 55
+ + ED+ + K L + EE+E+++E+ +E +D D+D+
Sbjct: 141 LFTEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDD 195
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 27.1 bits (60), Expect = 9.9
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 28 SKEEEEEEQEDSAFSDESADDNSSDEDETVE 58
+EEE E ED + S+ESA+D+S DE+E
Sbjct: 169 KDDEEESESEDESKSEESAEDDSDDEEEEDS 199
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
0.315 0.130 0.368
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,890,070
Number of extensions: 1192819
Number of successful extensions: 2051
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1876
Number of HSP's successfully gapped: 102
Length of query: 259
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 164
Effective length of database: 6,723,972
Effective search space: 1102731408
Effective search space used: 1102731408
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 (26.2 bits)