RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16257
(346 letters)
>gnl|CDD|217519 pfam03371, PRP38, PRP38 family. Members of this family are related
to the pre mRNA splicing factor PRP38 from yeast.
Therefore all the members of this family could be
involved in splicing. This conserved region could be
involved in RNA binding. The putative domain is about
180 amino acids in length. PRP38 is a unique component
of the U4/U6.U5 tri-small nuclear ribonucleoprotein
(snRNP) particle and is necessary for an essential step
late in spliceosome maturation.
Length = 173
Score = 207 bits (530), Expect = 7e-67
Identities = 57/182 (31%), Positives = 85/182 (46%), Gaps = 22/182 (12%)
Query: 27 LPLWGNERTMNMNPLILTNIQSSHYFKVNLYELKTYHEVLDEVYYKVQHLEPWEKGSRKT 86
L G T+ + +I I S Y+K NL+ L ++DE+ V H+ G+R+
Sbjct: 5 DKLNGTNPTLLIEKIIRDRIYDSPYYKENLFGLNA-ETIVDEIVEIVDHIGGTYGGNRR- 62
Query: 87 SGQTGMCGGVRGVGAGGIVSTAFCLLYKLFTLKMTRKQLNGLINHTDSPYIRGLGFMYIR 146
S CLL KL ++ +++ + L+N+ D YIR LG Y+R
Sbjct: 63 ------------------PSPFLCLLLKLLQIQPSKEIIKELLNNEDFKYIRALGLFYLR 104
Query: 147 YTQPPADLWDWYEPYLEDEEEVDVKAGGGQ--VMTIGNMLRSFLTKLEWHGTLFPRIPVP 204
T PPADL+ W EPYL+D ++ K G G + + + LTK T+ PRIP
Sbjct: 105 LTYPPADLYKWLEPYLQDYRKLRPKLGDGDFKLTHMDEFVDDLLTKDRVCDTILPRIPKR 164
Query: 205 IQ 206
I
Sbjct: 165 II 166
>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated
hydrophilic C-term. This domain is a hydrophilic region
found at the C-terminus of plant and metazoan
pre-mRNA-splicing factor 38 proteins. The function is
not known.
Length = 97
Score = 34.0 bits (78), Expect = 0.017
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 1/71 (1%)
Query: 276 DHKKSDRGDSYKRSYDSKDDRYKSSSRYASPERKKYRDDSRDTYRDRDKYSSSSKYDKYS 335
+K++R R + R +S R S +R++ R RD R RD+ S
Sbjct: 25 IRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRR-RRRDRDRARYRDRDDRDRDRYDRS 83
Query: 336 KDDRYSSSKDD 346
+ S S+D
Sbjct: 84 RSRSRSRSRDR 94
Score = 32.4 bits (74), Expect = 0.077
Identities = 13/72 (18%), Positives = 22/72 (30%), Gaps = 3/72 (4%)
Query: 256 PDNEAHYGEAERHAKTSGYSDHKKSDRGDSYKRSYDSKDDRYKSSSRYASPERKKYRDDS 315
+ + G +T ++ +R D RY+ R + R S
Sbjct: 29 AERDVDRGRRSPRRRTRR-RSRRRKRSRKRRRRRRDRDRARYRD--RDDRDRDRYDRSRS 85
Query: 316 RDTYRDRDKYSS 327
R R RD+
Sbjct: 86 RSRSRSRDRRRR 97
Score = 30.5 bits (69), Expect = 0.35
Identities = 15/79 (18%), Positives = 24/79 (30%), Gaps = 1/79 (1%)
Query: 264 EAERHAKTSGYSDHKKSDRGDSYKRSYDSKDDRYKSSSRYASPERKKYRDDSRDTYRDRD 323
E + + D + R +R+ R +S R + RDRD
Sbjct: 20 EDDEEIRRKAERDVDRGRRSPR-RRTRRRSRRRKRSRKRRRRRRDRDRARYRDRDDRDRD 78
Query: 324 KYSSSSKYDKYSKDDRYSS 342
+Y S + DR
Sbjct: 79 RYDRSRSRSRSRSRDRRRR 97
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 34.9 bits (80), Expect = 0.052
Identities = 14/52 (26%), Positives = 19/52 (36%)
Query: 293 KDDRYKSSSRYASPERKKYRDDSRDTYRDRDKYSSSSKYDKYSKDDRYSSSK 344
DR + R + K R+ SR R RD+ D Y S S+
Sbjct: 2 YRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSR 53
Score = 31.8 bits (72), Expect = 0.50
Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 1/70 (1%)
Query: 278 KKSDRGDSYKRSYDSKDDRYKSSSRYASPERKKYRDDS-RDTYRDRDKYSSSSKYDKYSK 336
+ DR R+ + D+ + SR S R + R RD YR R S S ++Y +
Sbjct: 1 RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYR 60
Query: 337 DDRYSSSKDD 346
S + D
Sbjct: 61 PRGDRSYRRD 70
Score = 30.2 bits (68), Expect = 1.9
Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 7/82 (8%)
Query: 259 EAHYGEAERHAKTSGYSDHKKSDRGDSYKRSYDSK------DDRYKSSSRYASPERKK-Y 311
+ R K S + R S +R R +S +RY P + Y
Sbjct: 8 GRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGDRSY 67
Query: 312 RDDSRDTYRDRDKYSSSSKYDK 333
R D R + R+ + + ++ D
Sbjct: 68 RRDDRRSGRNTKEPLTEAERDD 89
>gnl|CDD|220974 pfam11085, YqhR, Conserved membrane protein YqhR. This family is
conserved in the Bacillaceae family of the Firmicutes.
The function is not known.
Length = 174
Score = 32.7 bits (75), Expect = 0.17
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 5/54 (9%)
Query: 76 LEPWEKGSRKTSGQTGMCGGVRGVGAGGIVSTAFCLLYKLFTLKMTRKQLNGLI 129
L P+ G K G G V + G++S LY LK + G++
Sbjct: 56 LLPFALGEWKK----GWLGNVISIVLIGLISIGAAFLYYAL-LKKVKSMWPGIL 104
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 32.2 bits (73), Expect = 0.43
Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 4/82 (4%)
Query: 266 ERHAKTSGYSDHKKS-DRGDSYKRSYDSKDDRYKSSSRYASPERKKYRDDSRD-TYRDRD 323
+RH ++ S + S R S + RY S R R++ R +R R
Sbjct: 36 DRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRL 95
Query: 324 KYSSSSKYDKYSKDDRYSSSKD 345
+ S S + KDD+ S D
Sbjct: 96 RDRSPSNQWR--KDDKKRSLWD 115
Score = 31.8 bits (72), Expect = 0.51
Identities = 13/59 (22%), Positives = 20/59 (33%), Gaps = 4/59 (6%)
Query: 287 KRSYDSKDDRYKSSSRYASPERKKYRDDSRDTYRDRDKYSSSSKYDKYSKDDRYSSSKD 345
R + R + S ER + R R +RDR + S Y + S+
Sbjct: 6 DREREKSRGRDRDRSS----ERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60
Score = 31.8 bits (72), Expect = 0.58
Identities = 19/82 (23%), Positives = 27/82 (32%), Gaps = 10/82 (12%)
Query: 253 KHIPDNEAHYGEAERHAKTSGYSDHK-KSDRGDSYKRSYDSKDDRYKSSSRYA------- 304
+H E Y E R Y +S R S +RS D R +S
Sbjct: 37 RHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLR 96
Query: 305 --SPERKKYRDDSRDTYRDRDK 324
SP + +DD + + D
Sbjct: 97 DRSPSNQWRKDDKKRSLWDIKP 118
Score = 29.5 bits (66), Expect = 3.3
Identities = 19/76 (25%), Positives = 28/76 (36%), Gaps = 6/76 (7%)
Query: 276 DHKKSDRGDSYKRSYDSKDDRYKSSSRYASPERKKYRDDSR--DTYRDRDKYSSSSKYDK 333
+ DR S +R DR + R+ + YR+DSR D R + S +Y
Sbjct: 11 KSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSS 70
Query: 334 Y----SKDDRYSSSKD 345
+ R S S
Sbjct: 71 VRRSRDRPRRRSRSVR 86
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 30.9 bits (70), Expect = 1.1
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 17/67 (25%)
Query: 152 ADLWDWYEPYLEDEEEVDVKAGGGQVMTIGNMLRSFLTKLEWHGTLFPRIPVPIQQKLEK 211
A L W EPYL + G Q + + + L++ L P +QQ L+
Sbjct: 669 ARLETWLEPYLAGVTSLS----GLQELDLYDALKNLL-------------PWELQQALDA 711
Query: 212 QMSAKFP 218
+ +P
Sbjct: 712 LLPTHWP 718
>gnl|CDD|215581 PLN03109, PLN03109, ETHYLENE-INSENSITIVE3-like3 protein;
Provisional.
Length = 599
Score = 30.6 bits (69), Expect = 1.2
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 315 SRDTYRDRDKYSSSSKYDKYSKDD--RYSSSKDD 346
R++D SS S YD +D SSKDD
Sbjct: 307 GGHEDRNKDAISSDSDYDVDGLEDAPGSVSSKDD 340
>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777). This is
a family of eukaryotic proteins of unknown function.
Some of the proteins in this family are putative nucleic
acid binding proteins.
Length = 158
Score = 28.3 bits (63), Expect = 3.4
Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 299 SSSRYASPERKKYRDDSRD-TYRDRDKYSSSSKYDKYSKDDRYSSSK 344
SR SP R + R SR R+R + S S+ + R S
Sbjct: 2 GRSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPH 48
>gnl|CDD|223044 PHA03325, PHA03325, nuclear-egress-membrane-like protein;
Provisional.
Length = 418
Score = 29.1 bits (65), Expect = 3.8
Identities = 14/91 (15%), Positives = 26/91 (28%), Gaps = 12/91 (13%)
Query: 240 QNRSAPGAMSTNAKHIPDNEAHYGEAERHAKTSGYSD-----------HKKSDRG-DSYK 287
+ GAM A D G + S H ++ +
Sbjct: 275 RRSRRAGAMRAAAGETADLADDDGSEHSDPEPLPASLPPPPVRRPRVKHPEAGKEEPDGA 334
Query: 288 RSYDSKDDRYKSSSRYASPERKKYRDDSRDT 318
R+ ++K+ ++S + DS T
Sbjct: 335 RNAEAKEPAQPATSTSSKGSSSAQNKDSGST 365
>gnl|CDD|235406 PRK05321, PRK05321, nicotinate phosphoribosyltransferase;
Provisional.
Length = 400
Score = 29.0 bits (66), Expect = 4.5
Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 16/60 (26%)
Query: 117 TLKMTRKQLNGLINHTDSPYIRGLGFMYIRYTQPPADLWDWYEPYLEDEEEVDVKAGGGQ 176
TL++T +L+ Y+RGL F D DW + + EV V GQ
Sbjct: 64 TLRLTDDELD---------YLRGLPFF-------KPDFLDWLRLFRLNPYEVTVSIDDGQ 107
>gnl|CDD|220467 pfam09911, DUF2140, Uncharacterized protein conserved in bacteria
(DUF2140). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 187
Score = 27.9 bits (63), Expect = 6.1
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 116 FTLKMTRKQLNGLINH 131
FT+ +KQLN LI
Sbjct: 46 FTITTNKKQLNALIAS 61
>gnl|CDD|221469 pfam12223, DUF3602, Protein of unknown function (DUF3602). This
domain family is found in eukaryotes, and is typically
between 78 and 89 amino acids in length.
Length = 81
Score = 26.3 bits (58), Expect = 8.0
Identities = 11/56 (19%), Positives = 14/56 (25%), Gaps = 3/56 (5%)
Query: 219 PVYSQAGSGNYQQGRGGGGNYQNRSAPGAMSTNAKHIPDNEAHYGEAERHAKTSGY 274
+ GRGG GN RS P + D + T
Sbjct: 21 GITPTIKDSKVSTGRGGAGNM--RSNPERPEL-TRSAQDVDEELPRQAVRESTVAV 73
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
0.312 0.131 0.395
Gapped
Lambda K H
0.267 0.0650 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,395,717
Number of extensions: 1625538
Number of successful extensions: 1126
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1050
Number of HSP's successfully gapped: 42
Length of query: 346
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 248
Effective length of database: 6,590,910
Effective search space: 1634545680
Effective search space used: 1634545680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 59 (26.7 bits)