RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13793
(337 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 36.6 bits (85), Expect = 4e-04
Identities = 14/26 (53%), Positives = 21/26 (80%)
Query: 278 DLKFHLNQHTGERPYKCPFCPRTFAS 303
+L+ H+ HTGE+PYKCP C ++F+S
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 35.4 bits (82), Expect = 0.001
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 251 LRAHMISHSTERPHNCPHCEKTFKR 275
LR HM +H+ E+P+ CP C K+F
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 28.1 bits (63), Expect = 0.57
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 195 NLRRHLQAHKPKGKHTCEICFRIFKT 220
NLRRH++ H + + C +C + F +
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 30.9 bits (70), Expect = 0.050
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 181 YQCPLCNKKINTKSNLRRHLQAH 203
Y+CP C K +KS LR H++ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 28.6 bits (64), Expect = 0.37
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 264 HNCPHCEKTFKRNQDLKFHLNQH 286
+ CP C K FK L+ H+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 28.2 bits (63), Expect = 0.42
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 236 LSCPDCNRVYPTNSTLRAHMISH 258
CP+C +V+ + S LR HM +H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 27.4 bits (61), Expect = 0.79
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 209 HTCEICFRIFKTEINLTRHLECH 231
+ C C ++FK++ L H+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.5 bits (56), Expect = 4.4
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 292 YKCPFCPRTFASSGNCFSHRKR 313
Y+CP C + F S H +
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 34.7 bits (79), Expect = 0.056
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 21/76 (27%)
Query: 261 ERPHNCP--HCEKTFKRNQDLKFHL-----NQHTGE--------------RPYKCPFCPR 299
+P+ CP C K +K LK+H+ NQ E +PY+C C +
Sbjct: 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDK 406
Query: 300 TFASSGNCFSHRKRMH 315
+ + HRK H
Sbjct: 407 RYKNLNGLKYHRKHSH 422
Score = 30.5 bits (68), Expect = 1.2
Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 12/80 (15%)
Query: 211 CEI--CFRIFKTEINLTRH-LECHDTVELSCPDCNRVYPTNSTLRAHMISHSTERPHNCP 267
C + C + +K + L H L H N+ N + I + ++P+ C
Sbjct: 352 CPVEGCNKKYKNQNGLKYHMLHGH---------QNQKLHENPSPEKMNIFSAKDKPYRCE 402
Query: 268 HCEKTFKRNQDLKFHLNQHT 287
C+K +K LK+H
Sbjct: 403 VCDKRYKNLNGLKYHRKHSH 422
>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 = 30.2 bits (69), Expect = 0.096
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 181 YQCPLCNKKINTKSNLRRHLQAHK 204
+ C LCN ++S L+ HL+ K
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGKK 24
>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 = 29.9 bits (67), Expect = 0.12
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 181 YQCPLCNKKINTKSNLRRHLQAHK 204
++CPLC K ++K L+RHL+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 29.1 bits (65), Expect = 0.19
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 264 HNCPHCEKTFKRNQDLKFHLNQH 286
CP C K+F LK HL +H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 27.6 bits (61), Expect = 0.69
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 292 YKCPFCPRTFASSGNCFSHRKRMH 315
+KCP C ++F+S H ++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 26.8 bits (59), Expect = 1.6
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 238 CPDCNRVYPTNSTLRAHMISH 258
CP C + + + L+ H+ H
Sbjct: 3 CPLCGKSFSSKDALKRHLRKH 23
Score = 25.3 bits (55), Expect = 5.5
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 209 HTCEICFRIFKTEINLTRHLECH 231
C +C + F ++ L RHL H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>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 = 29.2 bits (66), Expect = 0.17
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 237 SCPDCNRVYPTNSTLRAHMISH 258
CPDC + + S L+ H+ +H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 28.9 bits (65), Expect = 0.25
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 266 CPHCEKTFKRNQDLKFHLNQH 286
CP C K+F R +LK HL H
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 28.9 bits (65), Expect = 0.26
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 182 QCPLCNKKINTKSNLRRHLQAH 203
+CP C K + KSNL+RHL+ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and recognises
the first three GAG bases of the consensus in a manner
similar to that seen in other classical zinc finger-DNA
complexes. The second basic region forms a helix that
interacts in the major groove recognising the last G of
the consensus, while the first basic region wraps around
the DNA in the minor groove and recognises the A in the
fourth position of the consensus sequence.
Length = 54
Score = 28.0 bits (62), Expect = 0.89
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 9/51 (17%)
Query: 179 TRYQCPLCNKKINTKSNLRRHLQAHKPKGKHTCEICFRIFKTEINLTRHLE 229
R + P +KI +KS Q+ +P TC IC + + NL RHLE
Sbjct: 4 KRAKHPPGTEKIKSKS------QSEQPA---TCPICQAVIRQSRNLRRHLE 45
>gnl|CDD|151508 pfam11062, DUF2863, Protein of unknown function (DUF2863). This
bacterial family of proteins have no known function.
Length = 398
Score = 30.0 bits (68), Expect = 1.7
Identities = 11/25 (44%), Positives = 11/25 (44%)
Query: 179 TRYQCPLCNKKINTKSNLRRHLQAH 203
TRY P LR HLQAH
Sbjct: 108 TRYSIPSGPIPAAVLQALRVHLQAH 132
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 30.0 bits (67), Expect = 1.8
Identities = 25/110 (22%), Positives = 38/110 (34%), Gaps = 11/110 (10%)
Query: 186 CNKKINTKSNLRRHLQAH-----KPKGKHTCE--ICFRIFKTEINLTRHLECH---DTVE 235
+ K + N K K C R FK + NL+ H+ H
Sbjct: 359 SSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYN 418
Query: 236 LSCPDCNRVYPTNSTLRAHMISHSTERPHNCPHCEKTFKRNQDLKFHLNQ 285
P C++ + + L H H+ P C K+F+R+ DL H
Sbjct: 419 CKNPPCSKSFNRHYNLIPHKKIHTNHAPLLC-SILKSFRRDLDLSNHGKD 467
Score = 30.0 bits (67), Expect = 2.0
Identities = 17/54 (31%), Positives = 26/54 (48%)
Query: 262 RPHNCPHCEKTFKRNQDLKFHLNQHTGERPYKCPFCPRTFASSGNCFSHRKRMH 315
RP +CP+C +F R + L H+ HTGE+P +C + + S R
Sbjct: 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRT 85
Score = 29.7 bits (66), Expect = 2.8
Identities = 27/161 (16%), Positives = 54/161 (33%), Gaps = 16/161 (9%)
Query: 152 REKVNWKKTKITASNLLSYNNAMFSSGTRYQCPLCNKKINTKSNLRRHLQAHKPKGKH-- 209
+ ++S S +++ + CN + S L RHL++ G+
Sbjct: 261 PRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPLTRHLRSVNHSGESLK 320
Query: 210 ----TCEICFRIFKTEINLTRHLECHDTVELSCP---DCNRVYPTNST-----LRAHMIS 257
+C ++F L RH+ H ++ + + + +
Sbjct: 321 PFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKD 380
Query: 258 HSTERPHNCPH--CEKTFKRNQDLKFHLNQHTGERPYKCPF 296
++ C + FKR+ +L H+ H RPY C
Sbjct: 381 LKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKN 421
Score = 28.5 bits (63), Expect = 6.1
Identities = 38/172 (22%), Positives = 66/172 (38%), Gaps = 18/172 (10%)
Query: 156 NWKKTKITASNLLSYNNAMFSSG---TRYQCP--LCNKKINTKSNLRRHLQAHKPKGKHT 210
+ +S L + ++ SG + CP LC K + L+RH+ H
Sbjct: 294 QCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353
Query: 211 CEICFRIFK-TEINLTRHLECHDTVELSCPD---------CNRVYPTNSTLRAHMISHST 260
++ K + + + + D C R + +S L H+I+H +
Sbjct: 354 EKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLS 413
Query: 261 ERPHNC--PHCEKTFKRNQDLKFHLNQHTGERPYKCPFCPRTFASSGNCFSH 310
RP+NC P C K+F R+ +L H HT P ++F + +H
Sbjct: 414 FRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPL-LCSILKSFRRDLDLSNH 464
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 505
Score = 30.0 bits (68), Expect = 2.1
Identities = 15/58 (25%), Positives = 19/58 (32%), Gaps = 9/58 (15%)
Query: 228 LECHDT-VELSCPDCNRVYP---TNSTLRAHMISHSTERPHNCPHCEKTFKRNQDLKF 281
L C L CP+C+ LR H + P CP C DL +
Sbjct: 214 LLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE-----DLVY 266
>gnl|CDD|238704 cd01413, SIR2_Af2, SIR2_Af2: Archaeal and prokaryotic group which
includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus
solfataricus ssSir2, and several bacterial homologs; and
are members of the SIR2 family of proteins, silent
information regulator 2 (Sir2) enzymes which catalyze
NAD+-dependent protein/histone deacetylation. Sir2
proteins have been shown to regulate gene silencing, DNA
repair, metabolic enzymes, and life span. The Sir2
homolog from the archaea Sulfolobus solftaricus
deacetylates the non-specific DNA protein Alba to
mediate transcription repression.
Length = 222
Score = 29.3 bits (66), Expect = 2.6
Identities = 10/45 (22%), Positives = 15/45 (33%), Gaps = 9/45 (20%)
Query: 228 LECHDTVE-LSCPDCNRVYPTNSTLRAHMISHSTERPHNCPHCEK 271
+E H T++ C +C Y + H P C K
Sbjct: 105 IELHGTLQTAYCVNCGSKYDLEEVK--------YAKKHEVPRCPK 141
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 29.7 bits (68), Expect = 2.7
Identities = 17/59 (28%), Positives = 19/59 (32%), Gaps = 15/59 (25%)
Query: 230 CHD---TVELSCPDCNRVYPT----NSTLRAHMISHSTERPHNCPHCEKTFKRNQDLKF 281
C D E CP C+ T LR H + P CP C T DL
Sbjct: 384 CRDCGWVAE--CPHCD-ASLTLHRFQRRLRCHHCGYQEPIPKACPECGST-----DLVP 434
>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 = 26.0 bits (58), Expect = 2.8
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 263 PHNCPHCEKTFKRNQDLKFHLN 284
C C+K FK L+ HL
Sbjct: 1 QFYCVACDKYFKSENALENHLK 22
Score = 24.5 bits (54), Expect = 9.9
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 183 CPLCNKKINTKSNLRRHLQ--AHK 204
C C+K +++ L HL+ HK
Sbjct: 4 CVACDKYFKSENALENHLKSKKHK 27
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 29.6 bits (67), Expect = 2.9
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 8/51 (15%)
Query: 228 LECHD---TVELSCPDCN---RVYPTNSTLRAHMISHSTERPHNCPHCEKT 272
L C D E CP+C+ ++ LR H + P +CP C
Sbjct: 436 LLCRDCGYIAE--CPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484
>gnl|CDD|236053 PRK07571, PRK07571, bidirectional hydrogenase complex protein HoxE;
Reviewed.
Length = 169
Score = 28.6 bits (64), Expect = 3.0
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 199 HLQAHKPKGKHTCEIC 214
HL + KP G+HTC +C
Sbjct: 79 HLFSLKPSGEHTCVVC 94
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 27.5 bits (61), Expect = 5.2
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 263 PHNCPHCEKTFKRNQDLKFHLNQHTGERPYKCPFCPRTFASSGNCFSHRKRMH 315
P+ CP C F + LK H+ E CP C + F ++ + H + H
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHI--RYTEHSKVCPVCGKEFRNTDSTLDHVCKKH 123
>gnl|CDD|217819 pfam03966, Trm112p, Trm112p-like protein. The function of this
family is uncertain. The bacterial members are about
60-70 amino acids in length and the eukaryotic examples
are about 120 amino acids in length. The C terminus
contains the strongest conservation. Trm112p is required
for tRNA methylation in S. cerevisiae and is found in
complexes with 2 tRNA methylases (TRM9 and TRM11) also
with putative methyltransferase YDR140W. The zinc-finger
protein Ynr046w is plurifunctional and a component of
the eRF1 methyltransferase in yeast. The crystal
structure of Ynr046w has been determined to 1.7 A
resolution. It comprises a zinc-binding domain built
from both the N- and C-terminal sequences and an
inserted domain, absent from bacterial and archaeal
orthologs of the protein, composed of three
alpha-helices.
Length = 47
Score = 25.3 bits (56), Expect = 7.0
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 235 ELSCPDCNRVYP 246
EL CP+C YP
Sbjct: 32 ELVCPECGLAYP 43
>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 = 24.9 bits (55), Expect = 7.9
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 178 GTRYQCPLCNKKINTKSNLRRHLQAHK 204
+ C LCN + ++ HL+ K
Sbjct: 1 TGGFYCKLCNVTFTDEISVEAHLKGKK 27
>gnl|CDD|99991 cd03821, GT1_Bme6_like, This family is most closely related to the
GT1 family of glycosyltransferases. Bme6 in Brucella
melitensis has been shown to be involved in the
biosynthesis of a polysaccharide.
Length = 375
Score = 28.0 bits (63), Expect = 8.5
Identities = 16/74 (21%), Positives = 24/74 (32%), Gaps = 11/74 (14%)
Query: 70 RKNGPKPYQCAICPRGYYSDIGLQNH--------LWSHRKILKNSNVGIYYTFTEDLRER 121
RK G PY + P G L + R++L+ + + E R
Sbjct: 109 RKYG-IPY--VVSPHGMLDPWALPHKALKKRLAWFLFERRLLQAAAAVHATSEQEAAEIR 165
Query: 122 EDGEKRKHWIDENG 135
G K + NG
Sbjct: 166 RLGLKAPIAVIPNG 179
>gnl|CDD|223158 COG0080, RplK, Ribosomal protein L11 [Translation, ribosomal
structure and biogenesis].
Length = 141
Score = 26.8 bits (60), Expect = 9.6
Identities = 7/34 (20%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 31 KLPSPAKSPAKSKAGSIVVKSLEHLKDLKVTKKK 64
+ + P K+K G + +L ++++ TK
Sbjct: 83 GIEKGSGKPNKNKVGKL---TLAQVREIAKTKMP 113
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
0.316 0.131 0.405
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,148,175
Number of extensions: 1454956
Number of successful extensions: 1612
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1597
Number of HSP's successfully gapped: 76
Length of query: 337
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 240
Effective length of database: 6,635,264
Effective search space: 1592463360
Effective search space used: 1592463360
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: 59 (26.6 bits)