RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15118
(132 letters)
>gnl|CDD|185400 PTZ00018, PTZ00018, histone H3; Provisional.
Length = 136
Score = 215 bits (550), Expect = 8e-74
Identities = 112/118 (94%), Positives = 117/118 (99%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE 60
MARTKQTARKSTGGKAPRKQLA+KAARKSAP TGG+KKPHRYRPGTVALREIRRYQKSTE
Sbjct: 1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTE 60
Query: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRM 118
LLIRKLPFQRLVREIAQDFKTDLRFQSSAV+ALQEA+EAYLVGLFEDTNLCAIHAKR+
Sbjct: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRV 118
>gnl|CDD|177733 PLN00121, PLN00121, histone H3; Provisional.
Length = 136
Score = 194 bits (493), Expect = 3e-65
Identities = 114/118 (96%), Positives = 118/118 (100%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE 60
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIR+YQKSTE
Sbjct: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTE 60
Query: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRM 118
LLIRKLPFQRLVREIAQDFKTDLRFQSSAV+ALQEA+EAYLVGLFEDTNLCAIHAKR+
Sbjct: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRV 118
>gnl|CDD|128705 smart00428, H3, Histone H3.
Length = 105
Score = 143 bits (362), Expect = 1e-45
Identities = 71/86 (82%), Positives = 75/86 (87%), Gaps = 2/86 (2%)
Query: 34 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVM 91
GG K RYRPG VALREIR+YQKST+LLIRK PFQRLVREIAQ F T DLRFQSSA+M
Sbjct: 1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIM 60
Query: 92 ALQEASEAYLVGLFEDTNLCAIHAKR 117
ALQEA+EAYLVGLFEDTNL AIHAKR
Sbjct: 61 ALQEAAEAYLVGLFEDTNLLAIHAKR 86
>gnl|CDD|215082 PLN00161, PLN00161, histone H3; Provisional.
Length = 135
Score = 116 bits (292), Expect = 1e-34
Identities = 68/119 (57%), Positives = 86/119 (72%), Gaps = 8/119 (6%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE 60
MAR Q ++ GK P+K+ + ++ KKPHRYRPGTVALREIR+YQKSTE
Sbjct: 1 MARRLQ-GKRFRKGKKPQKEASGVTRQELD------KKPHRYRPGTVALREIRKYQKSTE 53
Query: 61 LLIRKLPFQRLVREIAQDFKTD-LRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRM 118
LLIRKLPF RLVREI+ + + R+ + A++ALQEA+E +LV LFED NLCAIHAKR+
Sbjct: 54 LLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRV 112
>gnl|CDD|165727 PLN00160, PLN00160, histone H3; Provisional.
Length = 97
Score = 96.3 bits (239), Expect = 4e-27
Identities = 51/77 (66%), Positives = 64/77 (83%), Gaps = 1/77 (1%)
Query: 43 RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYL 101
RPG AL+EI+ YQKST+LLIR+LPF RLVREI + + R+Q SA++ALQEA+EA+L
Sbjct: 2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHL 61
Query: 102 VGLFEDTNLCAIHAKRM 118
VGLFED+NLCAIH KR+
Sbjct: 62 VGLFEDSNLCAIHGKRV 78
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 82.0 bits (203), Expect = 1e-21
Identities = 36/74 (48%), Positives = 47/74 (63%), Gaps = 5/74 (6%)
Query: 44 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVG 103
PG V L+EIRRYQ+ST+LL+ K P +R++R+ + R SSA+ LQEA E YL
Sbjct: 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-----RVSSSAIEELQEALEEYLEE 55
Query: 104 LFEDTNLCAIHAKR 117
+ ED A HAKR
Sbjct: 56 IAEDAVELAEHAKR 69
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 78.8 bits (195), Expect = 1e-20
Identities = 32/60 (53%), Positives = 39/60 (65%)
Query: 58 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 117
S+ LLI KLPF R+VRE+ + F +LR S A +ALQEA E L + ED L A HAKR
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 30.3 bits (69), Expect = 0.27
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEA 99
E LI K+ F R+ ++A+ K R+Q AV+AL A
Sbjct: 368 EPLIGKVRFSRIGIKLAETHKKGYRWQHEAVIALASPDNA 407
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 30.3 bits (68), Expect = 0.30
Identities = 14/37 (37%), Positives = 17/37 (45%)
Query: 5 KQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHR 41
K A+K KAP K++A K A K A K R
Sbjct: 1014 KAAAKKKVAKKAPAKKVARKPAAKKAAKKPARKAAGR 1050
Score = 28.4 bits (63), Expect = 1.2
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 2 ARTKQTARKSTGGKAP------RKQLATKAARKSAPATGGVKKPHR 41
A K+ A+K+ KA +K A K K APA +KP
Sbjct: 991 AMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAA 1036
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 28.5 bits (64), Expect = 0.35
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 59 TELLIRKLPFQRLVREIAQDFKT 81
+++L+R +PF+ V+E+ + F T
Sbjct: 1 SKILVRNIPFEATVKELRELFST 23
>gnl|CDD|215271 PLN02491, PLN02491, carotenoid 9,10(9',10')-cleavage dioxygenase.
Length = 545
Score = 28.3 bits (63), Expect = 1.2
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 81 TDLRFQSSAVMALQEASEAYLVGLFEDTNL 110
T L + ++AL EA + Y+V + ED +L
Sbjct: 178 TALIYHHGKLLALSEADKPYVVKVLEDGDL 207
>gnl|CDD|212542 cd11600, HDAC_Clr3, Class II Histone deacetylase Clr3 and similar
proteins. Clr3 is a class II Histone deacetylase
Zn-dependent enzyme that catalyzes hydrolysis of an
N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Clr3 is the homolog
of the class-II HDAC HdaI in S. cerevisiae, and is
essential for silencing in heterochromatin regions, such
as centromeric regions, ribosomal DNA, the mating-type
region and telomeric loci. Clr3 has also been implicated
in the regulation of stress-related genes; the histone
acetyltransferase, Gcn5, in S. cerevisiae,
preferentially acetylates global histone H3K14 while
Clr3 preferentially deacetylates H3K14ac, and therefore,
interplay between Gcn5 and Clr3 is crucial for the
regulation of many stress-response genes.
Length = 313
Score = 27.7 bits (62), Expect = 1.6
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 10/67 (14%)
Query: 68 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL----- 122
FQR+V IA +F DL S+ +A++ +G T H M+ SL
Sbjct: 225 FQRIVMPIAYEFDPDLVIISAGF----DAADGDELGQCHVTPAGYAHMTHMLMSLAGGKL 280
Query: 123 -VSLVGG 128
V+L GG
Sbjct: 281 VVALEGG 287
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 27.8 bits (62), Expect = 2.1
Identities = 10/30 (33%), Positives = 11/30 (36%), Gaps = 2/30 (6%)
Query: 11 STGGKAPRKQLATKAARKSAPATGGVKKPH 40
KAPR+QL K R KK
Sbjct: 467 FGNVKAPRQQLNIK--RPEESEESEGKKQS 494
>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 27.2 bits (60), Expect = 2.9
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 2 ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVK 37
K A+K A K A +K+AP G+K
Sbjct: 882 PAKKAAAKKVAAKTAAAKTPRKAAKKKAAPPAAGLK 917
>gnl|CDD|225055 COG2144, COG2144, Selenophosphate synthetase-related proteins
[General function prediction only].
Length = 324
Score = 26.6 bits (59), Expect = 4.4
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 49 LREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD 82
L ++ + E ++RK P + VRE +F
Sbjct: 3 LEDLISELRLFEGILRKNPIKDAVREFLDEFYGA 36
>gnl|CDD|185507 PTZ00191, PTZ00191, 60S ribosomal protein L23a; Provisional.
Length = 145
Score = 26.2 bits (58), Expect = 4.9
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 15 KAPRKQLATKAARKSAPATGGVKK--------PHRYRPGTVALREIRRYQKSTELLIRKL 66
KAP K+ KA + + A GVK +RP T+ L + +Y + + +KL
Sbjct: 1 KAPAKKAKKKAKKAAKAAKKGVKVKKRKVRTSVRFFRPKTLRLPKKPKYPRRVKPASKKL 60
Query: 67 PFQRLVR 73
+++
Sbjct: 61 DKYSIIK 67
>gnl|CDD|237549 PRK13897, PRK13897, type IV secretion system component VirD4;
Provisional.
Length = 606
Score = 26.7 bits (59), Expect = 5.1
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 55 YQKSTELLIRKLP 67
YQ++TE L RKLP
Sbjct: 388 YQQATEFLCRKLP 400
>gnl|CDD|180917 PRK07279, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1034
Score = 26.5 bits (59), Expect = 5.1
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 71 LVREIAQDFKTDL---RF--QSSAVMALQEASEAYLV 102
LV I+ DF TDL RF AV L+E +E L
Sbjct: 215 LVSGISYDFDTDLKLPRFNRDRPAVEELRELAELGLK 251
>gnl|CDD|165564 PHA03309, PHA03309, transcriptional regulator ICP4; Provisional.
Length = 2033
Score = 26.4 bits (57), Expect = 6.3
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 8 ARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKL 66
A + +G K PR+ +AR+S + PH P VALR + R Q+ L+ +L
Sbjct: 1689 APRRSGAKDPRQGQYCPSARRS-------EAPHSPSPRDVALRLLERQQELNRQLLLEL 1740
>gnl|CDD|162338 TIGR01398, FlhA, flagellar biosynthesis protein FlhA. This model
describes flagellar biosynthesis protein FlhA, one of a
large number of genes associated with the biosynthesis
of functional bacterial flagella. Homologs of many such
proteins, including FlhA, function in type III protein
secretion systems. A separate model describes InvA
(Salmonella enterica), LcrD (Yersinia enterocolitica),
HrcV (Xanthomonas), etc., all of which score below the
noise cutoff for this model [Cellular processes,
Chemotaxis and motility].
Length = 678
Score = 26.1 bits (58), Expect = 6.6
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 48 ALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD------LRFQSSAVMALQEA 96
L + K +LL+ + QRL R+I Q + + + AL EA
Sbjct: 544 TLADYAPITKDPDLLVEHVR-QRLGRQITQQYLDEDGVLPVITLDPDLEAALAEA 597
>gnl|CDD|202084 pfam01997, Translin, Translin family. Members of this family
include Translin that interacts with DNA and forms a
ring around the DNA. This family also includes human
translin-associated protein X, which was found to
interact with translin with yeast two-hybrid screen.
Length = 187
Score = 25.6 bits (57), Expect = 7.9
Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 12/64 (18%)
Query: 50 REIRRYQKSTELLIRKLPF----------QRLVREIAQDFKT--DLRFQSSAVMALQEAS 97
R+I R K + + + L+ ++ + K R+ + ALQE
Sbjct: 12 RDITRLSKKAIFALHRGDAEEAEELLKEAKELLAKLKELLKGHPYYRYSGAWSNALQEYV 71
Query: 98 EAYL 101
EA
Sbjct: 72 EALT 75
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 25.7 bits (56), Expect = 8.6
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 58 STELLIRKLPFQRLVR 73
STE +++ LPFQRL R
Sbjct: 437 STEKVLKSLPFQRLKR 452
>gnl|CDD|224668 COG1754, COG1754, Uncharacterized C-terminal domain of
topoisomerase IA [General function prediction only].
Length = 298
Score = 25.8 bits (57), Expect = 8.7
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 4 TKQTARKSTGGKAPRKQLATKAARKSAPAT 33
K+ A+K+T KA +K A KAA K A T
Sbjct: 262 GKKPAKKATAAKA-KKTTAKKAAAKKAAKT 290
>gnl|CDD|234474 TIGR04113, cas_csx17, CRISPR-associated protein Csx17, subtype
Dpsyc. Members of this protein family are found
exclusively in CRISPR-associated (cas) type I system
gene clusters of the Dpsyc subtype. Markers for that
type include a variant form of cas3 (model TIGR02621)
and the GSU0054-like protein family (model TIGR02165).
This family occurs in less than half of known Dpsyc
clusters.
Length = 704
Score = 25.8 bits (57), Expect = 8.8
Identities = 15/73 (20%), Positives = 24/73 (32%), Gaps = 10/73 (13%)
Query: 54 RYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAI 113
R Q +L+ + R +D K F S+ ++EA A
Sbjct: 371 RRQPRADLINELDGWLNRFRSFPRDGKAPASFLSAR-RRIEEAIFAAAT---------HP 420
Query: 114 HAKRMIASLVSLV 126
H R L++L
Sbjct: 421 HPSRFQELLIALG 433
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 25.8 bits (57), Expect = 9.0
Identities = 17/68 (25%), Positives = 24/68 (35%)
Query: 31 PATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAV 90
G V+ Y G +L ++R ELL +RLV I + D+ A
Sbjct: 681 RGVGRVRARKLYNAGYKSLEDLRLIADPAELLPLTGIGERLVEAILESLGRDVLLSGRAY 740
Query: 91 MALQEASE 98
E E
Sbjct: 741 FFSIEVRE 748
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
0.319 0.130 0.352
Gapped
Lambda K H
0.267 0.0663 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,456,404
Number of extensions: 565754
Number of successful extensions: 549
Number of sequences better than 10.0: 1
Number of HSP's gapped: 541
Number of HSP's successfully gapped: 57
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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: 53 (24.3 bits)