RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5202
(343 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 37.8 bits (88), Expect = 2e-04
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 200 NLTVHRRSHTGEKPYKCELCSYACAQ 225
NL H R+HTGEKPYKC +C + +
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 37.8 bits (88), Expect = 2e-04
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 107 LQAHRRNHTGEKPFKCTVCDHACSQ 131
L+ H R HTGEKP+KC VC + S
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 27.7 bits (62), Expect = 0.80
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 229 LTRHMKTHGRLGKDVYRCRFCEMPFS 254
L RHM+TH G+ Y+C C FS
Sbjct: 2 LRRHMRTH--TGEKPYKCPVCGKSFS 25
>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 = 31.9 bits (73), Expect = 0.019
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 187 TCEFCGKVFKNCSNLTVHRRSH 208
C CGK F SNL H R+H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 28.5 bits (64), Expect = 0.36
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 93 ECEFCGKKFKYENTLQAHRRNH 114
+C CGK F ++ L+ H R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 28.5 bits (64), Expect = 0.41
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 215 KCELCSYACAQSSKLTRHMKTH 236
KC C + ++ S L RH++TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 28.1 bits (63), Expect = 0.44
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 121 KCTVCDHACSQSAKLKKHMKIH 142
KC C + S+ + LK+H++ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 27.3 bits (61), Expect = 1.0
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 245 RCRFCEMPFSVPSTLEKHMRKC 266
+C C FS S L++H+R
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 31.7 bits (72), Expect = 0.027
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 214 YKCELCSYACAQSSKLTRHMKTH 236
Y+C C S L HM+TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 30.5 bits (69), Expect = 0.065
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 120 FKCTVCDHACSQSAKLKKHMKIH 142
++C C + L++HM+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 29.7 bits (67), Expect = 0.12
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 187 TCEFCGKVFKNCSNLTVHRRSH 208
C CGKVFK+ S L H R+H
Sbjct: 2 RCPECGKVFKSKSALREHMRTH 23
Score = 28.6 bits (64), Expect = 0.32
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 93 ECEFCGKKFKYENTLQAHRRNH 114
C CGK FK ++ L+ H R H
Sbjct: 2 RCPECGKVFKSKSALREHMRTH 23
Score = 25.9 bits (57), Expect = 2.7
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 244 YRCRFCEMPFSVPSTLEKHMRK 265
YRC C F S L +HMR
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|178748 PLN03209, PLN03209, translocon at the inner envelope of chloroplast
subunit 62; Provisional.
Length = 576
Score = 34.5 bits (79), Expect = 0.071
Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 4/85 (4%)
Query: 2 SPPYTSPNSGTPLGLITSPQTMNNNNNNSSMSNNNNICFESPSGTLEKELQRPKSPTNKI 61
+PP +SP S + + P + + S SN E +E + RP SP +
Sbjct: 389 TPPSSSPASSKSVDAVAKPAEPDVVPSPGSASN----VPEVEPAQVEAKKTRPLSPYARY 444
Query: 62 ADLSSSTSPSKQEDFQLSYAMSTTS 86
DL TSPS +S ++S+TS
Sbjct: 445 EDLKPPTSPSPTAPTGVSPSVSSTS 469
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 32.3 bits (74), Expect = 0.44
Identities = 9/36 (25%), Positives = 11/36 (30%), Gaps = 3/36 (8%)
Query: 93 ECEFCGKKF---KYENTLQAHRRNHTGEKPFKCTVC 125
EC C K L+ H + P C C
Sbjct: 446 ECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPEC 481
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 28.3 bits (64), Expect = 0.44
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 187 TCEFCGKVFKNCSNLTVHRRSH 208
TC CGK F + L H++SH
Sbjct: 3 TCGVCGKTFSSLQALGGHKKSH 24
Score = 28.0 bits (63), Expect = 0.53
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 93 ECEFCGKKFKYENTLQAHRRNH 114
C CGK F L H+++H
Sbjct: 3 TCGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|218738 pfam05766, NinG, Bacteriophage Lambda NinG protein. NinG or Rap is
involved in recombination. Rap (recombination adept with
plasmid) increases lambda-by-plasmid recombination
catalyzed by Escherichia coli's RecBCD pathway.
Length = 188
Score = 31.2 bits (71), Expect = 0.50
Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 14/64 (21%)
Query: 90 KNKECEFCGKKFKYENTLQAHRRNHTGEKPFKCTVCDHACSQSAKLKKHMKIHDEDGDKE 149
K K+C+ CG F + Q VC C+ + K +K + + +
Sbjct: 5 KPKKCKVCGVYFVPARSGQ--------------KVCSPECALALKREKAQEKKRKAEAQA 50
Query: 150 DREE 153
+R E
Sbjct: 51 ERRE 54
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 29.9 bits (68), Expect = 0.60
Identities = 16/83 (19%), Positives = 25/83 (30%), Gaps = 15/83 (18%)
Query: 187 TCEFCGKVFKNCSNLTVH-RRSHT---GEKPYKCELCSYACAQSSKLTRHMKTHGRLGKD 242
C FC H +SH E+ Y L ++ ++ +
Sbjct: 1 DCLFCNHTSDTVEENLEHMFKSHGFFIPEREY--------LVDLEGLLNYL--REKIHEG 50
Query: 243 VYRCRFCEMPFSVPSTLEKHMRK 265
C +C F L +HMR
Sbjct: 51 -NECLYCGKQFKSLEALRQHMRD 72
>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 = 27.6 bits (61), Expect = 0.74
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 93 ECEFCGKKFKYENTLQAHRRNH 114
+C CGK F ++ L+ H R H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKH 23
Score = 27.6 bits (61), Expect = 0.84
Identities = 9/21 (42%), Positives = 10/21 (47%)
Query: 188 CEFCGKVFKNCSNLTVHRRSH 208
C CGK F + L H R H
Sbjct: 3 CPLCGKSFSSKDALKRHLRKH 23
Score = 26.8 bits (59), Expect = 1.4
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 214 YKCELCSYACAQSSKLTRHMKTH 236
+KC LC + + L RH++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 26.4 bits (58), Expect = 2.0
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 244 YRCRFCEMPFSVPSTLEKHMRKC 266
++C C FS L++H+RK
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 26.4 bits (58), Expect = 2.4
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 120 FKCTVCDHACSQSAKLKKHMKIH 142
FKC +C + S LK+H++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 31.2 bits (70), Expect = 0.75
Identities = 40/223 (17%), Positives = 70/223 (31%), Gaps = 14/223 (6%)
Query: 12 TPLGLITSPQTMNNNNNNSSMSNNNNICFESPSGT--------LEKELQRPKSPTNKIAD 63
+ L + ++ ++S S++ + S T E + K + I
Sbjct: 233 SQLSPKSLLSQSPSSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGFSLPIKS 292
Query: 64 LSSSTSPSKQEDFQ-LSYAMSTTSQEEKNKEC--EFCGKKFKYENTLQAHRRNHTGEKPF 120
+ S S+ +++ + + K C CGK F + L+ H HT P
Sbjct: 293 KQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPA 352
Query: 121 KC--TVCDHACSQSAKLKKHMKIHDEDGDKEDREEGPSASSLAAAAAAAALNLCLPNSHM 178
K S + + K D++ ++S + NL L
Sbjct: 353 KEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDS-NLSLHIITH 411
Query: 179 KKESRRNDTCEFCGKVFKNCSNLTVHRRSHTGEKPYKCELCSY 221
N C K F NL H++ HT P C +
Sbjct: 412 LSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKS 454
>gnl|CDD|234471 TIGR04104, cxxc_20_cxxc, cxxc_20_cxxc protein. This small,
uncommon, poorly conserved protein is found primarily in
the Firmicutes. It features are pair of CxxC motifs
separated by about 20 amino acids, followed by a highly
hydrophobic region of about 45 amino acids. It has no
conserved gene neighborhood, and its function is
unknown.
Length = 94
Score = 28.5 bits (64), Expect = 1.6
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 92 KECEFCGKKFKYENTLQAHRRNHTGEKPFKCTVC 125
C+ C +KF Y+ L + + +P KC C
Sbjct: 1 PICKNCNEKFSYKELL---KSLFSLYRPIKCPNC 31
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 26.8 bits (60), Expect = 1.6
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 214 YKCELCSYACAQSSKLTRHMKTH 236
YKC C Y+ KL RH+K H
Sbjct: 1 YKCSHCPYSS-TPKKLERHLKLH 22
>gnl|CDD|227536 COG5211, SSU72, RNA polymerase II-interacting protein involved in
transcription start site selection [Transcription].
Length = 197
Score = 29.4 bits (66), Expect = 2.2
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 254 SVPSTLEKHMRKCVVNQNMKMESHNIMQN 282
P K C NQN ME+H+++
Sbjct: 1 MAPMPNLKLAVTCASNQNRSMETHDVLAK 29
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 29.7 bits (67), Expect = 2.2
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 94 CEFCGKKFKYENTLQAHRR 112
CEFC K K + LQ H +
Sbjct: 201 CEFCLKFMKRKEQLQRHMK 219
>gnl|CDD|222739 pfam14411, LHH, A nuclease of the HNH/ENDO VII superfamily with
conserved LHH. LHH is a predicted nuclease of the
HNH/ENDO VII superfamily of the treble clef fold. The
name is derived from the conserved motif, LHH. It is
found in bacterial polymorphic toxin systems and
functions as a toxin module. Like WHH and AHH, LHH
nuclease contain 4 conserved histidines of which, the
first one is predicted to bind metal-ion and other three
ones are involved in activation of water molecule for
hydrolysis.
Length = 81
Score = 27.7 bits (62), Expect = 2.7
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 7/39 (17%)
Query: 288 HNIIQNMKLDGHMME-----NMKLDNHNVIHNLKMDGHS 321
H+I Q DG + E + N+ ++H L S
Sbjct: 23 HHIGQKN--DGPLAELTRSEHKGNGNNKILHPLGKGSES 59
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 29.3 bits (65), Expect = 2.8
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 82 MSTTSQEEKNKECEFCGKKFKYENTLQAHRRNHT 115
M+ S ++K CE C K++K N L+ HR++
Sbjct: 389 MNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKHSH 422
Score = 28.9 bits (64), Expect = 4.7
Identities = 25/96 (26%), Positives = 33/96 (34%), Gaps = 21/96 (21%)
Query: 116 GEKPFKCTV--CDHACSQSAKLKKHMKIHDEDGDKEDREEGPSASSLAAAAAAAALNLCL 173
KP+KC V C+ LK HM + E PS + +A
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHML---HGHQNQKLHENPSPEKMNIFSAK------- 395
Query: 174 PNSHMKKESRRNDTCEFCGKVFKNCSNLTVHRRSHT 209
K R CE C K +KN + L HR+
Sbjct: 396 -----DKPYR----CEVCDKRYKNLNGLKYHRKHSH 422
>gnl|CDD|223002 PHA03150, PHA03150, hypothetical protein; Provisional.
Length = 456
Score = 29.0 bits (65), Expect = 3.6
Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 12/62 (19%)
Query: 193 KVFKNCS--NLTVHRRSHTGEKPYKCELCSYACAQSSKLTRHMKTHGRLG-KDVYRCRFC 249
+ N + ++ V+ KC Y C+ S++ G LG +D+++
Sbjct: 157 YMLSNSTVEDIEVY---------IKCTEGLYYCSSSAEPPLKKTQDGALGIEDIFKIEDH 207
Query: 250 EM 251
Sbjct: 208 SF 209
>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 = 24.8 bits (55), Expect = 6.3
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 94 CEFCGKKFKYENTLQAHRR 112
C C K FK EN L+ H +
Sbjct: 4 CVACDKYFKSENALENHLK 22
>gnl|CDD|173544 PTZ00351, PTZ00351, adenylosuccinate synthetase; Provisional.
Length = 710
Score = 28.5 bits (63), Expect = 7.2
Identities = 21/100 (21%), Positives = 35/100 (35%), Gaps = 12/100 (12%)
Query: 3 PPYTSPNSGTPLGLI---TSPQTMNNNNNNSSMSNNNNICFESPSGTLEKE--------- 50
P SP G+ PQ + + + F PS +E E
Sbjct: 30 PLSPSPAEGSKPASTHHDPVPQEAYYVKDEADACHQQQAPFREPSVEVEVEIIDDEPPRG 89
Query: 51 LQRPKSPTNKIADLSSSTSPSKQEDFQLSYAMSTTSQEEK 90
Q+P S A+ ++S+ SK S T++++K
Sbjct: 90 SQKPLSVAPHTANANNSSGSSKCNAITASDYTFYTNEDQK 129
>gnl|CDD|205417 pfam13237, Fer4_10, 4Fe-4S dicluster domain. This family includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. The structure of
the domain is an alpha-antiparallel beta sandwich.
Length = 51
Score = 25.4 bits (55), Expect = 7.2
Identities = 9/37 (24%), Positives = 10/37 (27%)
Query: 215 KCELCSYACAQSSKLTRHMKTHGRLGKDVYRCRFCEM 251
C C AC G + D RC C
Sbjct: 9 GCGRCVAACPARVGAGAIRDEGGAVEIDPDRCIGCGA 45
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 0.124 0.365
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,537,729
Number of extensions: 1334551
Number of successful extensions: 1436
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1419
Number of HSP's successfully gapped: 71
Length of query: 343
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 245
Effective length of database: 6,590,910
Effective search space: 1614772950
Effective search space used: 1614772950
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 (21.9 bits)
S2: 59 (26.7 bits)