RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16829
(243 letters)
>gnl|CDD|227515 COG5188, PRP9, Splicing factor 3a, subunit 3 [RNA processing and
modification].
Length = 470
Score = 32.3 bits (73), Expect = 0.20
Identities = 32/146 (21%), Positives = 50/146 (34%), Gaps = 30/146 (20%)
Query: 64 ECNEDFINVNDFVSHLRGHDSTSHVCDICLEAF-----PSSDDRDLHFLSHLTSDGLYQC 118
+ NV HL S LE F PS + R L +LS L
Sbjct: 143 RIFRKYANV-----HLCSDCSYLEFLKK-LERFDLTTEPSKNFRYLEYLSELN------- 189
Query: 119 NECEFVGK--RLTH-LKTHKKIHEKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPFQCE 175
E++G+ ++ + LK +K+ ++ RGF + N + + C
Sbjct: 190 ---EYLGRFIKVKYPLKMFRKVVASAPKIFSRAEARGFGKKNGMEGAEWFP----KVYCV 242
Query: 176 ICHKIFTNKSTMWSHK--KAHKPEDQ 199
C + F+ H K H E Q
Sbjct: 243 KCGREFSRSKVFEYHLEGKRHCKEGQ 268
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 28.6 bits (64), Expect = 0.23
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 202 WECEHCHKVYPNKRSYKRHKQVH 224
+ C C KV+ +K + + H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 28.6 bits (64), Expect = 0.25
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 172 FQCEICHKIFTNKSTMWSHKKAH 194
++C C K+F +KS + H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.9 bits (57), Expect = 2.1
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 116 YQCNECEFVGKRLTHLKTHKKIH 138
Y+C EC V K + L+ H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a zinc-finger
domain with the CxxCx(12)Hx(6)H motif, found in multiple
copies in a wide range of proteins from plants to
metazoans. Some member proteins, particularly those from
plants, are annotated as being RNA-binding.
Length = 25
Score = 28.6 bits (65), Expect = 0.26
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 172 FQCEICHKIFTNKSTMWSHKKAHK 195
F CE+C+ FT++S + SH + K
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGKK 24
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 27.7 bits (62), Expect = 0.44
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 173 QCEICHKIFTNKSTMWSHKKAH 194
+C C K F+ KS + H + H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.9 bits (60), Expect = 0.80
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 203 ECEHCHKVYPNKRSYKRHKQVH 224
+C C K + K + KRH + H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 26.4 bits (58), Expect = 1.3
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 202 WECEHCHKVYPNKRSYKRHKQVH 224
++C C K + +K + KRH + H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 25.7 bits (56), Expect = 2.8
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 172 FQCEICHKIFTNKSTMWSHKKAHK 195
F+C +C K F++K + H + H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|179097 PRK00723, PRK00723, phosphatidylserine decarboxylase; Provisional.
Length = 297
Score = 29.5 bits (67), Expect = 1.4
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 124 VGKRLTHLKTHKKIHEKVYGVYCD 147
+GK L L KKI K+YG YCD
Sbjct: 31 IGKNLLELLIKKKIFSKIYGWYCD 54
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 26.6 bits (59), Expect = 1.5
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 130 HLKTHKKIHEKVYGVYCDVCGRGFHQ 155
+L+ H + H C VCG+ F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 25.0 bits (55), Expect = 5.1
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 162 HKIKEHNAFPFQCEICHKIFTN 183
H P++C +C K F++
Sbjct: 5 HMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|223915 COG0846, SIR2, NAD-dependent protein deacetylases, SIR2 family
[Transcription].
Length = 250
Score = 28.8 bits (65), Expect = 2.5
Identities = 8/43 (18%), Positives = 15/43 (34%), Gaps = 1/43 (2%)
Query: 202 WECEHCHKVYPNKRSYKRHKQVHLGVKHECEGGPI-PALALFE 243
C C Y ++ K + + +C G + P + F
Sbjct: 123 VRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVLRPDVVWFG 165
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 28.5 bits (63), Expect = 3.4
Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 19/70 (27%)
Query: 171 PFQCEI--CHKIFTNKSTMWSHKK-------AHKPEDQI----------PWECEHCHKVY 211
P++C + C+K + N++ + H H+ P+ CE C K Y
Sbjct: 349 PYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRY 408
Query: 212 PNKRSYKRHK 221
N K H+
Sbjct: 409 KNLNGLKYHR 418
>gnl|CDD|150787 pfam10154, DUF2362, Uncharacterized conserved protein (DUF2362).
This is a family of proteins conserved from nematodes to
humans. The function is not known.
Length = 501
Score = 28.6 bits (64), Expect = 3.6
Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 7/58 (12%)
Query: 71 NVNDFVSHLRGHDSTSHVCDICLEAFPSS-------DDRDLHFLSHLTSDGLYQCNEC 121
+V D LRG S + L + +S D L+ + D + CN
Sbjct: 251 DVLDLCKPLRGDYSKLKRLQMALSLYSTSLCGVVLLVDNRLNSYIEIKRDFIKVCNMS 308
>gnl|CDD|237216 PRK12821, PRK12821, aspartyl/glutamyl-tRNA amidotransferase subunit
C-like protein; Provisional.
Length = 477
Score = 28.3 bits (63), Expect = 4.6
Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 9/66 (13%)
Query: 16 KLMIRFKGILGS---------SGLNLLNNESASSQVQYEEDKDYDDGEDKPLLLTCVECN 66
KL + FK I S + + + ++S +DKD K LL C E
Sbjct: 412 KLQVEFKDITSSFKQVEKIDTTNVKPMYAPFSNSPTPLRKDKDVVQKHQKILLKNCKETL 471
Query: 67 EDFINV 72
F+ V
Sbjct: 472 GGFVKV 477
>gnl|CDD|218878 pfam06061, Baculo_ME53, Baculoviridae ME53. ME53 is one of the
major early-transcribed genes. The ME53 protein is
reported to contain a putative zinc finger motif.
Length = 326
Score = 27.7 bits (62), Expect = 5.4
Identities = 14/75 (18%), Positives = 21/75 (28%), Gaps = 12/75 (16%)
Query: 128 LTHLKTHKKIHEKVYGVYCDVCGRGFHQNNEVTL------HKI------KEHNAFPFQCE 175
L K + V CD CG+ F N + I + F F C
Sbjct: 37 LLMGCADLKKVKLVQTTTCDKCGKKFKDNTRKWYLYCVVDNWIDADSESNRPDKFKFVCL 96
Query: 176 ICHKIFTNKSTMWSH 190
C+ + +
Sbjct: 97 DCYNDYKDDPQYDVF 111
>gnl|CDD|234538 TIGR04315, octaheme_Shew, octaheme c-type cytochrome, tetrathionate
reductase family. Members of this protein family bind
heme covalently and contain eight (at least) CXXCH
heme-binding motifs. A characterized member is the
respiratory enzyme octaheme tetrathionate reductase from
Shewanella.
Length = 440
Score = 27.7 bits (62), Expect = 6.7
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 6/51 (11%)
Query: 172 FQCEICHK----IFTNKSTMWSHKKAHKPEDQIPWECEHCHKVYPNKRSYK 218
F C+ CH + S K H ++ CE CH + P+K + K
Sbjct: 188 FTCQDCHTTEGHQISGSRYALSAKDTHDDTNRA--SCESCHGLAPHKSNAK 236
>gnl|CDD|184992 PRK15032, PRK15032, trimethylamine N-oxide reductase cytochrome
c-type subunit; Provisional.
Length = 390
Score = 27.6 bits (61), Expect = 6.9
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 204 CEHCHKVYPNKRSYKR--HKQVHLGVKHECEGGPIP 237
C CH + P YK+ H Q GV+ EC IP
Sbjct: 48 CVSCHSMQPVYEEYKQSVHFQNASGVRAECHDCHIP 83
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 27.8 bits (62), Expect = 7.0
Identities = 26/131 (19%), Positives = 34/131 (25%), Gaps = 35/131 (26%)
Query: 61 TCVECNEDFINVNDFVSHLRGHDSTSH-VCDICLEAFPSSDDRDLHF---LSHLTSDGLY 116
C EC +G C +C SDD D LS T D
Sbjct: 4 KCPEC------------GGKGKIVVGEEECPVC-HGTGFSDDFDPKGVANLSRETVDLFA 50
Query: 117 Q----CNECEFVGKRLTHLKTHKKIHEKVYGVYCDVCGRGFHQNNEVTLHKIKEHNAFPF 172
C +C G +T T + + CD+CG E
Sbjct: 51 SFEIPCPKCRGKGT-VTVYDTCPECGGTGKVLTCDICGDIIVPWEE-------------G 96
Query: 173 QCEICHKIFTN 183
C C +
Sbjct: 97 LCPECRRKPKI 107
>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger. Family of C2H2-type zinc
fingers, present in matrin, U1 small nuclear
ribonucleoprotein C and other RNA-binding proteins.
Length = 35
Score = 24.5 bits (54), Expect = 7.8
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 171 PFQCEICHKIFTNKSTMWSHKKAHK 195
F C++C+ FT++ ++ +H K K
Sbjct: 3 GFYCKLCNVTFTDEISVEAHLKGKK 27
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 25.0 bits (54), Expect = 8.4
Identities = 7/23 (30%), Positives = 15/23 (65%)
Query: 172 FQCEICHKIFTNKSTMWSHKKAH 194
++C IC +I+ + +M +H + H
Sbjct: 6 YECPICGEIYIKRKSMITHLRKH 28
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus,
particularly the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 24.1 bits (53), Expect = 8.7
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 62 CVECNEDFINVNDFVSHLRG 81
CV C++ F + N +HL+
Sbjct: 4 CVACDKYFKSENALENHLKS 23
>gnl|CDD|181958 PRK09564, PRK09564, coenzyme A disulfide reductase; Reviewed.
Length = 444
Score = 27.3 bits (61), Expect = 9.3
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 21 FKGILGSSGLNLLNNESASSQVQYEEDKD 49
FKG LGS+ + +L+ E+A + + EE K
Sbjct: 321 FKGTLGSACIKVLDLEAARTGLTEEEAKK 349
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 0.438
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,707,456
Number of extensions: 1025541
Number of successful extensions: 913
Number of sequences better than 10.0: 1
Number of HSP's gapped: 911
Number of HSP's successfully gapped: 58
Length of query: 243
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 149
Effective length of database: 6,768,326
Effective search space: 1008480574
Effective search space used: 1008480574
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: 58 (26.1 bits)