RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8286
(858 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 39.7 bits (93), Expect = 1e-04
Identities = 16/26 (61%), Positives = 18/26 (69%)
Query: 546 SLTLHMRTHLKIKPYKCDVCDKSFVT 571
+L HMRTH KPYKC VC KSF +
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 34.7 bits (80), Expect = 0.006
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 699 LKSHMRIHDNAKPFSCTVCKKSFYT 723
L+ HMR H KP+ C VC KSF +
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 32.7 bits (75), Expect = 0.025
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 812 YLTAHVRVHNGERPFSCHICGKTSTT 837
L H+R H GE+P+ C +CGK+ ++
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 31.6 bits (72), Expect = 0.082
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 787 RHVREHELKKKYSCTICGKTFHR 809
RH+R H +K Y C +CGK+F
Sbjct: 4 RHMRTHTGEKPYKCPVCGKSFSS 26
Score = 31.2 bits (71), Expect = 0.11
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 575 LSDHKNTHTGNAPFPCNMCDRHFKR 599
L H THTG P+ C +C + F
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 30.8 bits (70), Expect = 0.12
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 756 EYQAHLRSHRNIRPFTCNYCGRKFIR 781
+ H+R+H +P+ C CG+ F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 36.4 bits (84), Expect = 0.015
Identities = 21/54 (38%), Positives = 23/54 (42%), Gaps = 6/54 (11%)
Query: 527 KNVHPLPCPVCSKTFPSKPSLTLHMR--THLKIKPYKCDVCDKSFVTAQKLSDH 578
K V P CP+C F S SL H+R H K C VC K F DH
Sbjct: 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSK----VCPVCGKEFRNTDSTLDH 118
Score = 33.7 bits (77), Expect = 0.12
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 3/70 (4%)
Query: 753 SSSEYQAHLRSHRNIRPFTCNYCGRKFIRKFNCIRHVREHELKKKYSCTICGKTFHRSYY 812
S Y L + + + P+ C C F + +H+R E K C +CGK F +
Sbjct: 57 DESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKV--CPVCGKEFRNTDS 114
Query: 813 LTAHV-RVHN 821
HV + HN
Sbjct: 115 TLDHVCKKHN 124
Score = 30.2 bits (68), Expect = 2.1
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 509 CDTCSEVFDKLKDYQEHIK-NVHPLPCPVCSKTFPSKPSLTLHM 551
C C F ++HI+ H CPVC K F + S H+
Sbjct: 76 CPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHV 119
Score = 28.3 bits (63), Expect = 8.3
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 2/60 (3%)
Query: 612 LKKKKIKDFYCH-CGEIFQSRGKLLWHQETHATVPKQCTYCTEKFTHTSSLTRHIRKNHD 670
L K + + C C F S L H + K C C ++F +T S H+ K H+
Sbjct: 66 LTSKAVSPYVCPLCLMPFSSSVSLKQHIR-YTEHSKVCPVCGKEFRNTDSTLDHVCKKHN 124
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 33.2 bits (76), Expect = 0.022
Identities = 13/21 (61%), Positives = 14/21 (66%)
Query: 534 CPVCSKTFPSKPSLTLHMRTH 554
CP C K F SK +L HMRTH
Sbjct: 3 CPECGKVFKSKSALREHMRTH 23
Score = 32.4 bits (74), Expect = 0.039
Identities = 10/23 (43%), Positives = 11/23 (47%)
Query: 798 YSCTICGKTFHRSYYLTAHVRVH 820
Y C CGK F L H+R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 30.9 bits (70), Expect = 0.12
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 826 FSCHICGKTSTTKSNHNKHVKTH 848
+ C CGK +KS +H++TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 30.5 bits (69), Expect = 0.17
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 560 YKCDVCDKSFVTAQKLSDHKNTH 582
Y+C C K F + L +H TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 29.4 bits (66), Expect = 0.49
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 770 FTCNYCGRKFIRKFNCIRHVREH 792
+ C CG+ F K H+R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 28.6 bits (64), Expect = 0.91
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 742 FKCKSCNRGFYSSSEYQAHLRSH 764
++C C + F S S + H+R+H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.7 bits (59), Expect = 3.6
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 588 FPCNMCDRHFKRYSNLAQHKKV 609
+ C C + FK S L +H +
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
Score = 26.7 bits (59), Expect = 3.9
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 647 QCTYCTEKFTHTSSLTRHIRK 667
+C C + F S+L H+R
Sbjct: 2 RCPECGKVFKSKSALREHMRT 22
>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 = 32.3 bits (74), Expect = 0.042
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 799 SCTICGKTFHRSYYLTAHVRVH 820
C CGK+F R L H+R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 31.5 bits (72), Expect = 0.083
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 534 CPVCSKTFPSKPSLTLHMRTH 554
CP C K+F K +L H+RTH
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 29.2 bits (66), Expect = 0.51
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 647 QCTYCTEKFTHTSSLTRHIRK 667
+C C + F+ S+L RH+R
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRT 21
Score = 28.5 bits (64), Expect = 0.81
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 743 KCKSCNRGFYSSSEYQAHLRSH 764
KC C + F S + HLR+H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 28.5 bits (64), Expect = 0.85
Identities = 10/22 (45%), Positives = 10/22 (45%)
Query: 561 KCDVCDKSFVTAQKLSDHKNTH 582
KC C KSF L H TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 27.3 bits (61), Expect = 2.6
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 590 CNMCDRHFKRYSNLAQHKKV 609
C C + F R SNL +H +
Sbjct: 2 CPDCGKSFSRKSNLKRHLRT 21
Score = 26.9 bits (60), Expect = 3.4
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 827 SCHICGKTSTTKSNHNKHVKTH 848
C CGK+ + KSN +H++TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.4 bits (56), Expect = 9.7
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 771 TCNYCGRKFIRKFNCIRHVREH 792
C CG+ F RK N RH+R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>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 = 31.3 bits (72), Expect = 0.092
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 742 FKCKSCNRGFYSSSEYQAHLRSHR 765
F C+ CN F S S+ ++HLR +
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGKK 24
>gnl|CDD|203088 pfam04780, DUF629, Protein of unknown function (DUF629). This
family represents a region of several plant proteins of
unknown function. A C2H2 zinc finger is predicted in
this region in some family members, but the spacing
between the cysteine residues is not conserved
throughout the family.
Length = 463
Score = 35.1 bits (81), Expect = 0.15
Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 484 SNSFGTQIQEFLPPSLTSIKNKQR----RCDTCSEVFDKLKDYQEHIKNVH 530
+G + +E L L+ + ++ C TCS+ F ++ + H++ H
Sbjct: 31 ERVYGREGREALEQVLSFARENRKWRFWMCRTCSKKFSSSEECKNHLEQEH 81
>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 = 30.3 bits (68), Expect = 0.18
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 826 FSCHICGKTSTTKSNHNKHVKTHH 849
F C +CGK+ ++K +H++ HH
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 30.3 bits (68), Expect = 0.24
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 533 PCPVCSKTFPSKPSLTLHMRTH 554
CP+C K+F SK +L H+R H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKH 23
Score = 28.8 bits (64), Expect = 0.69
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 560 YKCDVCDKSFVTAQKLSDHKNTH 582
+KC +C KSF + L H H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 28.8 bits (64), Expect = 0.81
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 798 YSCTICGKTFHRSYYLTAHVRVH 820
+ C +CGK+F L H+R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 28.0 bits (62), Expect = 1.6
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 742 FKCKSCNRGFYSSSEYQAHLRSH 764
FKC C + F S + HLR H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 27.6 bits (61), Expect = 2.2
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 770 FTCNYCGRKFIRKFNCIRHVREH 792
F C CG+ F K RH+R+H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 27.2 bits (60), Expect = 2.3
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 588 FPCNMCDRHFKRYSNLAQHKKVIH 611
F C +C + F L +H + H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 26.1 bits (57), Expect = 7.5
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 647 QCTYCTEKFTHTSSLTRHIRKNH 669
+C C + F+ +L RH+RK+H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKHH 24
Score = 26.1 bits (57), Expect = 7.6
Identities = 5/23 (21%), Positives = 10/23 (43%)
Query: 508 RCDTCSEVFDKLKDYQEHIKNVH 530
+C C + F + H++ H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 34.3 bits (78), Expect = 0.25
Identities = 71/474 (14%), Positives = 126/474 (26%), Gaps = 45/474 (9%)
Query: 372 SNSNSFRTKIEKIEPINSLPDNIKMEESVSILPIISSLDIAKKKKHACIY--CKKTFTGW 429
S S + +S P+ S +K C Y C K+F+
Sbjct: 18 STPKSTLKSLSNAPRPDSCPNC-TDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRP 76
Query: 430 KLRKYHMKAEHPELFNEPETIKLLSKTQASTSTVISEPSTSFVSQAVCPIKFENSNSFGT 489
H++ H + LS ++AS+S++ S S S + + S+
Sbjct: 77 LELSRHLRTHHNNPSDLNSKSLPLSNSKASSSSLSSSSSNSNDNNLLSSHSLPPSSRDPQ 136
Query: 490 QIQEFLPPSLTSIKNKQRRCDTCSEVFDKLKDYQEHIKNVHPLPCPVCSKTFPSKPSLTL 549
+ R + + + PLP SK S SL +
Sbjct: 137 LP--------DLLSISNLRNNPLPGNNSSSVNTPQSNSLHPPLPANSLSKDPSSNLSLLI 188
Query: 550 HMRTHLKIKPYKCDVCDKSFVTAQKLSDHKNTHTGNAPFPCN----MCDRHFKRYSNLAQ 605
I + S + S +N ++ P + + S +
Sbjct: 189 SSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSL 248
Query: 606 HKKVIHLKKKKIKDFYCHCGEIFQSRGKLLWHQETHA--TVPKQCTYCTEKFTHTSSLTR 663
QS + ++P + C F+ +S LTR
Sbjct: 249 SSS-DSSSSASESPRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPLTR 307
Query: 664 HIRKNHD--PRYLPVDRKKTDENVNCDICKIVVLKSTLKSHMRIHDNAKPFSCTVCKKSF 721
H+R + P + LK H+ +H + P + +
Sbjct: 308 HLRSVNHSGESLKPFSCPYSLCGKLFS------RNDALKRHILLHTSISPAKEKLL--NS 359
Query: 722 YTKWNLGLHQWTHVSRMHMPFKCKSCNRGFYSSSEYQAHLRSHRNIRPFTCNYCGRKFIR 781
+K++ L+ S + R
Sbjct: 360 SSKFSPLLNNEPPQSLQQY-----------KDLKNDKKSETLS----NSCIRNFKRDSNL 404
Query: 782 KFNCIRHVREHELKKKYSCTICGKTFHRSYYLTAHVRVHNGERPFSCHICGKTS 835
+ I H+ C K+F+R Y L H ++H P C I
Sbjct: 405 SLHIITHLSFRP--YNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKSFR 456
>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 = 29.1 bits (66), Expect = 0.50
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 741 PFKCKSCNRGFYSSSEYQAHLRS 763
F C +C++ F S + + HL+S
Sbjct: 1 QFYCVACDKYFKSENALENHLKS 23
Score = 27.2 bits (61), Expect = 3.1
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 559 PYKCDVCDKSFVTAQKLSDHKNT 581
+ C CDK F + L +H +
Sbjct: 1 QFYCVACDKYFKSENALENHLKS 23
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 29.1 bits (66), Expect = 0.50
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 560 YKCDVCDKSFVTAQKLSDHKNTH 582
+ C VC K+F + Q L HK +H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
Score = 26.4 bits (59), Expect = 5.7
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 534 CPVCSKTFPSKPSLTLHMRTH 554
C VC KTF S +L H ++H
Sbjct: 4 CGVCGKTFSSLQALGGHKKSH 24
Score = 26.0 bits (58), Expect = 8.1
Identities = 7/24 (29%), Positives = 9/24 (37%)
Query: 742 FKCKSCNRGFYSSSEYQAHLRSHR 765
C C + F S H +SH
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSHC 25
>gnl|CDD|188230 TIGR02510, NrdE-prime, ribonucleoside-diphosphate reductase, alpha
chain. This model represents a small clade of
ribonucleoside-diphosphate reductase, alpha chains which
are sufficiently divergent from the usual Class I RNR
alpha chains (NrdE or NrdA, TIGR02506) as to warrant
their own model. The genes from Thermus thermophilus,
Dichelobacter and Salinibacter are adjacent to the usual
RNR beta chain [Purines, pyrimidines, nucleosides, and
nucleotides, 2'-Deoxyribonucleotide metabolism].
Length = 548
Score = 33.0 bits (75), Expect = 0.70
Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 7/91 (7%)
Query: 406 ISSLDIAKKKKHACIYCKKTFTGWKLRKYHMKAEHPELFNEPETIKLLSKTQASTSTVIS 465
+ S I + A I + + K R E E + EPE + + A+ +
Sbjct: 330 LQSNRIPFESGEAHILNAEIYKTIKERAEEASRELAERYGEPEVCEGTGRRNATLIAIAP 389
Query: 466 EPSTSF----VSQAVCPIKFENSNSFGTQIQ 492
S++F VS ++ P+ SN F
Sbjct: 390 TKSSAFILGQVSPSIEPLV---SNYFIQDSN 417
>gnl|CDD|234777 PRK00481, PRK00481, NAD-dependent deacetylase; Provisional.
Length = 242
Score = 32.5 bits (75), Expect = 0.78
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 11/48 (22%)
Query: 787 RHVRE-H-ELKKKYSCTICGKTFHRSYYLTAHVRVHNGERPFSCHICG 832
++V E H L + CT CG+T+ YL P C CG
Sbjct: 111 KNVIELHGSLLRAR-CTKCGQTYDLDEYL--------KPEPPRCPKCG 149
>gnl|CDD|226782 COG4332, COG4332, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 203
Score = 31.7 bits (72), Expect = 0.95
Identities = 20/65 (30%), Positives = 24/65 (36%), Gaps = 15/65 (23%)
Query: 761 LRSHRNIRPFT-------CNYCGRKFIRKFNCIRHVREHELKKK------YSCTICGKTF 807
LR I P CN CG K R F C R + K Y CT C T+
Sbjct: 2 LRVIWTITPVGAPQPAKRCNSCGVK--RAFTCSGKFRVNAQGKVLDVWLIYKCTHCDYTW 59
Query: 808 HRSYY 812
+ S +
Sbjct: 60 NISIF 64
>gnl|CDD|216581 pfam01577, Peptidase_S30, Potyvirus P1 protease. The potyviridae
family positive stand RNA viruses with genome encoding a
polyprotein. members include zucchini yellow mosaic
virus, and turnip mosaic viruses which cause
considerable losses of crops worldwide. This family
consists of a C terminus region from various plant
potyvirus P1 proteins (found at the N terminus of the
polyprotein). The C terminus of P1 is a serine-type
protease responsible for autocatalytic cleavage between
P1 and the helper component protease pfam00851. The
entire P1 protein may be involved in virus-host
interactions.
Length = 245
Score = 31.5 bits (72), Expect = 1.4
Identities = 13/63 (20%), Positives = 18/63 (28%), Gaps = 11/63 (17%)
Query: 795 KKKYSCTICGKTFHRSYYLTAHVRVHNGERP---FSC--------HICGKTSTTKSNHNK 843
KKK + K S L + G+R S C KT+T +
Sbjct: 132 KKKKRTRVTFKRKGGSRLLKVSLAHERGKRRRRDLSLDNFTQKLALHCAKTTTRHLRVDD 191
Query: 844 HVK 846
Sbjct: 192 IKL 194
>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 = 29.5 bits (67), Expect = 1.8
Identities = 12/26 (46%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 534 CPVCSKTFPSKPSLTLHMRT--HLKI 557
C C K F S +L HMR H KI
Sbjct: 53 CLYCGKQFKSLEALRQHMRDKGHCKI 78
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 31.9 bits (73), Expect = 1.9
Identities = 21/120 (17%), Positives = 36/120 (30%), Gaps = 19/120 (15%)
Query: 148 NTSSSSQQAQSSVIQHPVKTEPPPPYDTKHGILYCQPGSSKTSATNPEPPKNSAGNFLGI 207
+ S S + P K+ PPP + + + P P
Sbjct: 511 ESQSGSASNTAKTPPPPQKSPPPPA--PTPPLPQPTATAPPPTPPPPPPTAT-------- 560
Query: 208 DLPSVSNLPQLDRPPTVDITPSKYLPTNLNSPSLESPIQDYNFLVANTKLDRLSNLHNGE 267
+ SN P + P SP+ +S ++ + K L++ NGE
Sbjct: 561 --QASSNAPAQIPADSSPPPPIP--EEPTPSPTKDSSPEEID---KAAK--NLADFFNGE 611
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 31.5 bits (71), Expect = 2.0
Identities = 28/123 (22%), Positives = 42/123 (34%), Gaps = 25/123 (20%)
Query: 510 DTCSEVFDKLKDYQEHIKNVH-PLPCPVC---SKTFP------SKPSLTLHMRTHLKIKP 559
C LK+ ++H K H + C C K F +L H L+ +
Sbjct: 157 SKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEG 216
Query: 560 YK----CDVCDKSFVTAQKLSDHKNTHTGNAPFPCNMCD-------RHFKRYSNLAQHKK 608
+K C C F D H C++CD ++FK Y +L H +
Sbjct: 217 FKGHPLCIFCKIYFYD----DDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFR 272
Query: 609 VIH 611
H
Sbjct: 273 NAH 275
>gnl|CDD|219584 pfam07800, DUF1644, Protein of unknown function (DUF1644). This
family consists of sequences found in a number of
hypothetical plant proteins of unknown function. The
region of interest contains nine highly conserved
cysteine residues and is approximately 160 amino acids
in length, and is probably a zinc-binding domain.
Length = 148
Score = 30.4 bits (69), Expect = 2.0
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 1/73 (1%)
Query: 651 CTEKFTHTSSLTRHIRKNHDPRYLPVDRKKTDE-NVNCDICKIVVLKSTLKSHMRIHDNA 709
C H++ L + + R D +K D + C +C+ V T+ R N+
Sbjct: 32 CDTSHRHSNCLDQFKKAYSKKRNSGKDSEKEDSTELTCPLCRGEVKGWTVVEPARRFLNS 91
Query: 710 KPFSCTVCKKSFY 722
K SC SF
Sbjct: 92 KKRSCMQEGCSFS 104
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 28.5 bits (63), Expect = 2.1
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 798 YSCTICGKTFHRSYYLTAHVRVHN 821
Y C ICG+ + + + H+R HN
Sbjct: 6 YECPICGEIYIKRKSMITHLRKHN 29
Score = 27.3 bits (60), Expect = 4.3
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 534 CPVCSKTFPSKPSLTLHMRTH 554
CP+C + + + S+ H+R H
Sbjct: 8 CPICGEIYIKRKSMITHLRKH 28
>gnl|CDD|177300 PHA00732, PHA00732, hypothetical protein.
Length = 79
Score = 29.0 bits (65), Expect = 2.4
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 770 FTCNYCGRKFIRKFNCIRHVR-EHELKKKYSCTICGKTFHR 809
F C CG + F +H R H L K C +C K++ R
Sbjct: 2 FKCPICGFTTVTLFALKQHARRNHTLTK---CPVCNKSYRR 39
>gnl|CDD|221737 pfam12726, SEN1_N, SEN1 N terminal. This domain is found at the N
terminal of the helicase SEN1. SEN1 is a Pol II
termination factor for noncoding RNA genes. The N
terminal of SEN1, unlike the C terminal, is not required
for growth.
Length = 724
Score = 31.1 bits (71), Expect = 3.1
Identities = 12/60 (20%), Positives = 28/60 (46%), Gaps = 5/60 (8%)
Query: 360 WDEMD----HEVMDNISNSNSFRTKIEKIEPINSLPDNIKMEESVS-ILPIISSLDIAKK 414
W M +++ I N+ +F + + + L + + + +S I P +SSL +++
Sbjct: 250 WSAMAPISPSTILEEIFNNPAFSKLLLESQEEPPLESSDDLSDLLSWIPPFLSSLSGSQR 309
>gnl|CDD|173905 cd00808, GluRS_core, catalytic core domain of discriminating
glutamyl-tRNA synthetase. Discriminating Glutamyl-tRNA
synthetase (GluRS) catalytic core domain . The
discriminating form of GluRS is only found in bacteria
and cellular organelles. GluRS is a monomer that
attaches Glu to the appropriate tRNA. Like other class
I tRNA synthetases, GluRS aminoacylates the 2'-OH of the
nucleotide at the 3' end of the tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding.
Length = 239
Score = 29.9 bits (68), Expect = 4.4
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 39 HIPTIKNETSEECSKMQSSTNIYDYK 64
H+P I N ++ SK + T+I DY+
Sbjct: 151 HLPLILNPDGKKLSKRKGDTSISDYR 176
>gnl|CDD|234912 PRK01170, PRK01170, phosphopantetheine adenylyltransferase/unknown
domain fusion protein; Provisional.
Length = 322
Score = 30.2 bits (68), Expect = 4.9
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 80 LSEIKTEPGVVSKPITVNKVPKV--EDTIPTSTSNFLDYNAAQRGKQRKTVKI 130
++EI+ + G+ P+ + +VP V ED P S++ ++ GK+ K +KI
Sbjct: 102 INEIRIKNGL--PPLKIVRVPYVLAEDLFPISSTRIINGEIDGNGKRLKPLKI 152
>gnl|CDD|222704 pfam14353, CpXC, CpXC protein. This presumed domain is
functionally uncharacterized. This domain is found in
bacteria and archaea, and is typically between 122 and
134 amino acids in length. It contains four conserved
cysteines forming two CpXC motifs.
Length = 128
Score = 28.9 bits (65), Expect = 5.5
Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 9/50 (18%)
Query: 771 TCNYCGRKFIRKFNCIRHVREH-ELKKK--------YSCTICGKTFHRSY 811
TC CG +F + + E EL++ ++C CG F Y
Sbjct: 3 TCPSCGHEFEAEVWTSVNADEDPELREAILDGTLFTFTCPSCGHEFRLDY 52
>gnl|CDD|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like
proteins. The first LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated
ERK activation. Ajuba also recruits the TNF
receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the formation
or stabilization of adheren junctions by linking
adhesive receptors to the actin cytoskeleton. Although
Ajuba is a cytoplasmic protein, it can shuttle into the
nucleus. In nucleus, Ajuba functions as a corepressor
for the zinc finger-protein Snail. It binds to the SNAG
repression domain of Snail through its LIM region.
Arginine methyltransferase-5 (Prmt5), a protein in the
complex, is recruited to Snai l through an interaction
with Ajuba. This ternary complex functions to repress
E-cadherin, a Snail target gene. In addition, Ajuba
contains functional nuclear-receptor interacting motifs
and selectively interacts with retinoic acid receptors
(RARs) and rexinoid receptor (RXRs) to negatively
regulate retinoic acid signaling. Wtip, the
Wt1-interacting protein, was originally identified as an
interaction partner of the Wilms tumour protein 1 (WT1).
Wtip is involved in kidney and neural crest development.
Wtip interacts with the receptor tyrosine kinase Ror2
and inhibits canonical Wnt signaling. LIMD1 was reported
to inhibit cell growth and metastases. The inhibition
may be mediated through an interaction with the protein
barrier-to-autointegration (BAF), a component of SWI/SNF
chromatin-remodeling protein; or through the interaction
with retinoblastoma protein (pRB), resulting in
inhibition of E2F-mediated transcription, and expression
of the majority of genes with E2F1- responsive elements.
Recently, Limd1 was shown to interact with the
p62/sequestosome protein and influence IL-1 and RANKL
signaling by facilitating the assembly of a
p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62
interaction affects both NF-kappaB and AP-1 activity in
epithelial cells and osteoclasts. Moreover, LIMD1
functions as tumor repressor to block lung tumor cell
line in vitro and in vivo. Recent studies revealed that
LIM proteins Wtip, LIMD1 and Ajuba interact with
components of RNA induced silencing complexes (RISC) as
well as eIF4E and the mRNA m7GTP cap-protein complex and
are required for microRNA-mediated gene silencing. As
in other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 27.0 bits (60), Expect = 6.2
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 744 CKSCNRGFYSSSEYQAHLRSHRNIRPFTCNYCGRK 778
C C +G Y +S+ + + + FTC CGR
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRT 35
>gnl|CDD|115907 pfam07282, OrfB_Zn_ribbon, Putative transposase DNA-binding domain.
This putative domain is found at the C-terminus of a
large number of transposase proteins. This domain
contains four conserved cysteines suggestive of a zinc
binding domain. Given the need for transposases to bind
DNA as well as the large number of DNA-binding zinc
fingers we hypothesise this domain is DNA-binding.
Length = 69
Score = 27.2 bits (61), Expect = 6.7
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 10/39 (25%)
Query: 771 TCNYCGRKFIRKFNCIRHVREHELKKKYSCTICGKTFHR 809
TC+ CG K +E + + C CG R
Sbjct: 30 TCSVCGHK----------NKESLSGRTFKCPNCGFVADR 58
>gnl|CDD|184135 PRK13551, PRK13551, agmatine deiminase; Provisional.
Length = 362
Score = 29.5 bits (67), Expect = 8.0
Identities = 11/20 (55%), Positives = 11/20 (55%)
Query: 32 KLSVHKLHIPTIKNETSEEC 51
KL VHKL IP T EE
Sbjct: 259 KLKVHKLPIPGPLYATEEES 278
>gnl|CDD|235068 PRK02769, PRK02769, histidine decarboxylase; Provisional.
Length = 380
Score = 29.6 bits (67), Expect = 8.3
Identities = 8/41 (19%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 125 RKTVKILKIKNAKTREQPDGAQMNTSSSSQQAQSSVIQHPV 165
K ++L+IK+ P+G +++ + + + Q P+
Sbjct: 124 SKIARLLRIKSRVITSLPNG-EIDYDDLISKIKENKNQPPI 163
>gnl|CDD|224399 COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and
metabolism].
Length = 312
Score = 29.2 bits (66), Expect = 9.7
Identities = 15/63 (23%), Positives = 21/63 (33%), Gaps = 10/63 (15%)
Query: 54 MQSSTN---IYDYKTPMPSTSSTPDVGVLLSEIKTEPGVVSKPITVNKVPKVEDTIPTST 110
MQ+S N +YD D+G L + V T + E T P
Sbjct: 187 MQNSDNTYRVYDTDRYD-------DIGELRELHLFKAKDVITLPTQPRKQGAELTYPVPN 239
Query: 111 SNF 113
+F
Sbjct: 240 EDF 242
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 0.130 0.399
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: 41,098,301
Number of extensions: 3782210
Number of successful extensions: 3692
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3658
Number of HSP's successfully gapped: 121
Length of query: 858
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 753
Effective length of database: 6,280,432
Effective search space: 4729165296
Effective search space used: 4729165296
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: 63 (28.1 bits)