RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7353
(139 letters)
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 38.7 bits (90), Expect = 1e-04
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 55 FPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDKMKNHMKTVHD 107
+ CP+C FS +K H++ KV CPVCGKEF D +H+ H+
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIRYTEHSKV--CPVCGKEFRNTDSTLDHVCKKHN 124
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 35.5 bits (81), Expect = 0.004
Identities = 21/76 (27%), Positives = 30/76 (39%), Gaps = 21/76 (27%)
Query: 53 KVFPCPV--CGKEFSRPDKMKNHMKTGCQR-------------------KVFPCPVCGKE 91
K + CPV C K++ + +K HM G Q K + C VC K
Sbjct: 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKR 407
Query: 92 FSRPDKMKNHMKTVHD 107
+ + +K H K HD
Sbjct: 408 YKNLNGLKYHRKHSHD 423
>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 = 30.7 bits (69), Expect = 0.020
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 83 FPCPVCGKEFSRPDKMKNHMKTVH 106
F CP+CGK FS D +K H++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 27.6 bits (61), Expect = 0.27
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 55 FPCPVCGKEFSRPDKMKNHMKT 76
F CP+CGK FS D +K H++
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRK 22
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 32.8 bits (75), Expect = 0.042
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 85 CPVCGKEFSRPDKMKNHMKTVH 106
C VC EFS D++ H +T H
Sbjct: 76 CNVCMAEFSSMDQLAEHQRTTH 97
Score = 29.7 bits (67), Expect = 0.49
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 57 CPVCGKEFSRPDKMKNHMKT 76
C VC EFS D++ H +T
Sbjct: 76 CNVCMAEFSSMDQLAEHQRT 95
>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 = 31.1 bits (71), Expect = 0.068
Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 23/86 (26%)
Query: 57 CPVCGKEFSRPDKMKNHMKTG--------------------CQRKVFP---CPVCGKEFS 93
C C ++ HM + K+ C CGK+F
Sbjct: 2 CLFCNHTSDTVEENLEHMFKSHGFFIPEREYLVDLEGLLNYLREKIHEGNECLYCGKQFK 61
Query: 94 RPDKMKNHMKTVHDCFMPATTPQGQR 119
+ ++ HM+ C +P T + +
Sbjct: 62 SLEALRQHMRDKGHCKIPYETEEEKD 87
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 31.6 bits (71), Expect = 0.12
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 51 QRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKE--FSRPDKMKNHMKTVH 106
+ CP C FSR + + H+++ K C G + FSRP ++ H++T H
Sbjct: 30 APRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHH 87
Score = 31.2 bits (70), Expect = 0.14
Identities = 20/76 (26%), Positives = 25/76 (32%), Gaps = 5/76 (6%)
Query: 31 KTFKNKYSFQRHAFLY-HEGCQRKVFPCPV--CGKEFSRPDKMKNHMKTGCQRKVFPCP- 86
+F RH H G K F CP CGK FSR D +K H+
Sbjct: 297 ISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356
Query: 87 -VCGKEFSRPDKMKNH 101
+FS +
Sbjct: 357 LNSSSKFSPLLNNEPP 372
Score = 30.0 bits (67), Expect = 0.40
Identities = 17/72 (23%), Positives = 24/72 (33%), Gaps = 2/72 (2%)
Query: 30 IKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCG 89
I+ FK + H + H + P C K F+R + H K
Sbjct: 395 IRNFKRDSNLSLH-IITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIH-TNHAPLLCSIL 452
Query: 90 KEFSRPDKMKNH 101
K F R + NH
Sbjct: 453 KSFRRDLDLSNH 464
Score = 27.0 bits (59), Expect = 3.9
Identities = 20/74 (27%), Positives = 27/74 (36%), Gaps = 7/74 (9%)
Query: 37 YSFQRHAFLYHEGCQRKVFPCPVCGKEFSRP----DKMKNHMKTGCQRKVFPCPV--CGK 90
S +G C FSR +++ +G K F CP CGK
Sbjct: 273 SSPNESDSSSEKGFS-LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGK 331
Query: 91 EFSRPDKMKNHMKT 104
FSR D +K H+
Sbjct: 332 LFSRNDALKRHILL 345
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 28.6 bits (64), Expect = 0.14
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 55 FPCPVCGKEFSRPDKMKNHMKT 76
+ CP CGK F ++ HM+T
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
Score = 28.6 bits (64), Expect = 0.14
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 83 FPCPVCGKEFSRPDKMKNHMKT 104
+ CP CGK F ++ HM+T
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|234899 PRK01103, PRK01103, formamidopyrimidine/5-formyluracil/
5-hydroxymethyluracil DNA glycosylase; Validated.
Length = 274
Score = 30.8 bits (71), Expect = 0.17
Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 18/64 (28%)
Query: 30 IKTFKNKY----SFQRHAFLY-HEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFP 84
++ + N FQ+ +Y EG PC CG + +K G R F
Sbjct: 221 LRDYVNADGKPGYFQQSLQVYGREG-----EPCRRCGTPIEK-------IKQG-GRSTFF 267
Query: 85 CPVC 88
CP C
Sbjct: 268 CPRC 271
>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 = 28.1 bits (63), Expect = 0.18
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 57 CPVCGKEFSRPDKMKNHMKT 76
CP CGK FSR +K H++T
Sbjct: 2 CPDCGKSFSRKSNLKRHLRT 21
Score = 28.1 bits (63), Expect = 0.18
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 85 CPVCGKEFSRPDKMKNHMKT 104
CP CGK FSR +K H++T
Sbjct: 2 CPDCGKSFSRKSNLKRHLRT 21
>gnl|CDD|222968 PHA03065, PHA03065, Hypothetical protein; Provisional.
Length = 438
Score = 30.3 bits (69), Expect = 0.25
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 6/38 (15%)
Query: 27 VDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEF 64
VD I F N+Y+ E R+V PC +EF
Sbjct: 290 VDNIIDFINRYA------SLDESVYREVPPCACTVQEF 321
>gnl|CDD|224272 COG1353, COG1353, Predicted CRISPR-associated polymerase [Defense
mechanisms].
Length = 799
Score = 30.1 bits (68), Expect = 0.37
Identities = 13/79 (16%), Positives = 24/79 (30%), Gaps = 6/79 (7%)
Query: 22 MECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRK 81
+ +++ K + F +E C VCG + ++ D K R
Sbjct: 363 EKVSELPSRKKLRRFEVELGILFPRYELDGPGERTCSVCGNKRAKGDSEK------EMRA 416
Query: 82 VFPCPVCGKEFSRPDKMKN 100
C VC + +
Sbjct: 417 ETLCDVCRVLYELGSILIE 435
>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 = 27.6 bits (62), Expect = 0.63
Identities = 11/38 (28%), Positives = 13/38 (34%), Gaps = 10/38 (26%)
Query: 57 CPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSR 94
C VCG + K + F CP CG R
Sbjct: 31 CSVCGHK----------NKESLSGRTFKCPNCGFVADR 58
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 26.6 bits (59), Expect = 0.74
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 70 MKNHMKTGCQRKVFPCPVCGKEFSR 94
++ HM+T K + CPVCGK FS
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|233031 TIGR00577, fpg, formamidopyrimidine-DNA glycosylase (fpg). All
proteins in the FPG family with known functions are
FAPY-DNA glycosylases that function in base excision
repair. Homologous to endonuclease VIII (nei). 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 = 272
Score = 28.8 bits (65), Expect = 0.76
Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 16/63 (25%)
Query: 30 IKTFKNKY----SFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPC 85
I+ + N FQ+ +Y RK PC CG + +K G R C
Sbjct: 221 IRDYSNSDGHNGYFQQELQVY----GRKGEPCRRCGTPIEK-------IKVG-GRGTHFC 268
Query: 86 PVC 88
P C
Sbjct: 269 PQC 271
>gnl|CDD|218790 pfam05876, Terminase_GpA, Phage terminase large subunit (GpA).
This family consists of several phage terminase large
subunit proteins as well as related sequences from
several bacterial species. The DNA packaging enzyme of
bacteriophage lambda, terminase, is a heteromultimer
composed of a small subunit, gpNu1, and a large subunit,
gpA, products of the Nu1 and A genes, respectively.
Terminase is involved in the site-specific binding and
cutting of the DNA in the initial stages of packaging.
It is now known that gpA is actively involved in late
stages of packaging, including DNA translocation, and
that this enzyme contains separate functional domains
for its early and late packaging activities.
Length = 552
Score = 29.1 bits (66), Expect = 0.82
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 6/61 (9%)
Query: 45 LYHEGCQRKVF-PCPVCGKEFS-RPDKMKNHMKTGCQRKV-FPCPVCGKEFSRPDKMKNH 101
LY E QR+ + PCP CG+E R +++K K + CP CG + K
Sbjct: 190 LYEESDQRRYYVPCPHCGEEQELRWERLKWD-KGEAPETARYVCPHCGCVIE--EHHKRA 246
Query: 102 M 102
M
Sbjct: 247 M 247
>gnl|CDD|238698 cd01407, SIR2-fam, SIR2 family of proteins includes silent
information regulator 2 (Sir2) enzymes which catalyze
NAD+-dependent protein/histone deacetylation, where the
acetyl group from the lysine epsilon-amino group is
transferred to the ADP-ribose moiety of NAD+, producing
nicotinamide and the novel metabolite
O-acetyl-ADP-ribose. Sir2 proteins, also known as
sirtuins, are found in all eukaryotes and many archaea
and prokaryotes and have been shown to regulate gene
silencing, DNA repair, metabolic enzymes, and life span.
The most-studied function, gene silencing, involves the
inactivation of chromosome domains containing key
regulatory genes by packaging them into a specialized
chromatin structure that is inaccessible to DNA-binding
proteins. The oligomerization state of Sir2 appears to
be organism-dependent, sometimes occurring as a monomer
and sometimes as a multimer.
Length = 218
Score = 28.7 bits (65), Expect = 0.88
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 57 CPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPD 96
C CGKE+ R + + + +V CP CG RPD
Sbjct: 112 CTKCGKEYPRDELQADIDR----EEVPRCPKCGGLL-RPD 146
>gnl|CDD|218188 pfam04641, Rtf2, Replication termination factor 2. It is vital for
effective cell-replication that replication is not
stalled at any point by, for instance, damaged bases.
Rtf2 stabilizes the replication fork stalled at the
site-specific replication barrier RTS1 by preventing
replication restart until completion of DNA synthesis by
a converging replication fork initiated at a flanking
origin. The RTS1 element terminates replication forks
that are moving in the cen2-distal direction while
allowing forks moving in the cen2-proximal direction to
pass through the region. Rtf2 contains a C2HC2 motif
related to the C3HC4 RING-finger motif, and would appear
to fold up, creating a RING finger-like structure but
forming only one functional Zn2+ ion-binding site.
Length = 254
Score = 28.5 bits (64), Expect = 1.1
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 8/61 (13%)
Query: 47 HEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGC--------QRKVFPCPVCGKEFSRPDKM 98
+ + F CPV G E + K GC + K CPVCGK +S D +
Sbjct: 101 KDDNKEAPFICPVTGLEMNGKYKFVALWPCGCVFSEKALKEVKSKVCPVCGKPYSEEDVV 160
Query: 99 K 99
Sbjct: 161 P 161
>gnl|CDD|223915 COG0846, SIR2, NAD-dependent protein deacetylases, SIR2 family
[Transcription].
Length = 250
Score = 28.4 bits (64), Expect = 1.3
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 57 CPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPD 96
C CG ++ D +K + CP CG RPD
Sbjct: 125 CSKCGNQYYDEDVIKFIED----GLIPRCPKCGGPVLRPD 160
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 28.4 bits (63), Expect = 1.4
Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 11/97 (11%)
Query: 19 YKCMECAKVDVIKTFK--NKYSFQRHAFLYHEGC--QRKVFPCPVCGKEFSRPDKMKNHM 74
+KC + + K K+ +H F+ C +K F + R +++H
Sbjct: 152 FKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEI---RLFRSSTLRDHK 208
Query: 75 KTGCQRKVFP----CPVCGKEFSRPDKMKNHMKTVHD 107
G + + F C C F D+++ H + H+
Sbjct: 209 NGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRHE 245
>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 = 28.1 bits (63), Expect = 1.5
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 85 CPVCGKEFSRPDKMKNHMKTVHDC-FMPATTP 115
C C K+FS ++ KNH++ H F P++
Sbjct: 60 CRTCSKKFSSSEECKNHLEQEHAAKFKPSSEM 91
>gnl|CDD|218654 pfam05605, Di19, Drought induced 19 protein (Di19). This family
consists of several drought induced 19 (Di19) like
proteins. Di19 has been found to be strongly expressed
in both the roots and leaves of Arabidopsis thaliana
during progressive drought. The precise function of Di19
is unknown.
Length = 209
Score = 27.8 bits (62), Expect = 1.9
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 11/79 (13%)
Query: 36 KYSFQRHAFLYH------EGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQ--RKVFPCPV 87
+ + + LY E R+ FPCP C ++F + H+ K CPV
Sbjct: 9 QRALPSRSDLYLFEDIEGEDEVREEFPCPFCYEDFDIVS-LCCHIDEEHPFEAKNGVCPV 67
Query: 88 CGKEFSRPDKMKNHMKTVH 106
C + M H+ H
Sbjct: 68 CADRVGK--DMVAHITVQH 84
>gnl|CDD|223344 COG0266, Nei, Formamidopyrimidine-DNA glycosylase [DNA replication,
recombination, and repair].
Length = 273
Score = 27.6 bits (62), Expect = 2.0
Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 12/50 (24%)
Query: 39 FQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVC 88
FQ+ +Y R PC CG + +K G R F CPVC
Sbjct: 234 FQQELKVYG----RAGEPCRRCGTPIEK-------IKLG-GRSTFYCPVC 271
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 27.9 bits (63), Expect = 2.0
Identities = 18/83 (21%), Positives = 27/83 (32%), Gaps = 27/83 (32%)
Query: 17 GIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKT 76
G KC C K TF + CP CG + + + +
Sbjct: 625 GRRKCPSCGKE----TFYRR--------------------CPFCG---THTEPVYRCPRC 657
Query: 77 GCQRKVFPCPVCGKEFSRPDKMK 99
G + + C CG+E + K K
Sbjct: 658 GIEVEEDECEKCGREPTPYSKRK 680
>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 = 25.2 bits (56), Expect = 2.4
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 55 FPCPVCGKEFSRPDKMKNHMKT 76
F C C K F + ++NH+K+
Sbjct: 2 FYCVACDKYFKSENALENHLKS 23
Score = 25.2 bits (56), Expect = 2.4
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 83 FPCPVCGKEFSRPDKMKNHMKT 104
F C C K F + ++NH+K+
Sbjct: 2 FYCVACDKYFKSENALENHLKS 23
>gnl|CDD|216219 pfam00965, TIMP, Tissue inhibitor of metalloproteinase. Members of
this family are common in extracellular regions of
vertebrate species.
Length = 174
Score = 27.0 bits (60), Expect = 3.0
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 8/54 (14%)
Query: 40 QRHAF--LYHEGCQRKVFPCPVCGKEFSRPDK------MKNHMKTGCQRKVFPC 85
Q+ Y +GC K+ PC S PD+ + +GCQ K + C
Sbjct: 111 QKKGLKGRYQQGCGCKITPCFSIPCSLSAPDECLWTDWVLEESYSGCQAKHYAC 164
>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 = 26.2 bits (58), Expect = 3.0
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 57 CPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKE 91
C C ++FS + +K+ + CP CG +
Sbjct: 3 CKNCNEKFSYKELLKSLFS---LYRPIKCPNCGTK 34
>gnl|CDD|236318 PRK08639, PRK08639, threonine dehydratase; Validated.
Length = 420
Score = 27.1 bits (61), Expect = 3.1
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 109 FMPATTPQGQRGQ 121
FMP TTPQ + Q
Sbjct: 102 FMPVTTPQQKIDQ 114
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 27.4 bits (61), Expect = 3.1
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 7/36 (19%)
Query: 55 FP-CPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCG 89
FP CP C KE+ P + H + CP CG
Sbjct: 118 FPLCPDCAKEYKDPLDRRFHAQPIA------CPRCG 147
>gnl|CDD|177300 PHA00732, PHA00732, hypothetical protein.
Length = 79
Score = 25.9 bits (57), Expect = 3.5
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 54 VFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSR 94
+F CP+CG +K H + + CPVC K + R
Sbjct: 1 MFKCPICGFTTVTLFALKQHARR--NHTLTKCPVCNKSYRR 39
>gnl|CDD|214746 smart00614, ZnF_BED, BED zinc finger. DNA-binding domain in
chromatin-boundary-element-binding proteins and
transposases.
Length = 50
Score = 25.1 bits (55), Expect = 3.7
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 5/27 (18%)
Query: 85 CPVCGKEFSRPDK-----MKNHMKTVH 106
C CGK+ SR K ++ H++ H
Sbjct: 21 CKYCGKKLSRSSKGGTSNLRRHLRRKH 47
>gnl|CDD|227515 COG5188, PRP9, Splicing factor 3a, subunit 3 [RNA processing and
modification].
Length = 470
Score = 26.9 bits (59), Expect = 4.6
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 71 KNHMKTGCQRKVFPCPVCGKEFSRPDKMKNHMK 103
KN M+ C CG+EFSR + H++
Sbjct: 227 KNGMEGAEWFPKVYCVKCGREFSRSKVFEYHLE 259
Score = 26.1 bits (57), Expect = 7.3
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 53 KVFPCPVCGKEFSRPDKMKNHMK 75
C CG+EFSR + H++
Sbjct: 237 PKVYCVKCGREFSRSKVFEYHLE 259
>gnl|CDD|221473 pfam12230, PRP21_like_P, Pre-mRNA splicing factor PRP21 like
protein. This domain family is found in eukaryotes, and
is typically between 212 and 238 amino acids in length.
The family is found in association with pfam01805. There
are two completely conserved residues (W and H) that may
be functionally important. PRP21 is required for
assembly of the prespliceosome and it interacts with U2
snRNP and/or pre-mRNA in the prespliceosome. This family
also contains proteins similar to PRP21, such as the
mammalian SF3a. SF3a also interacts with U2 snRNP from
the prespliceosome, converting it to its active form.
Length = 230
Score = 26.6 bits (59), Expect = 4.6
Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 10/51 (19%)
Query: 62 KEFSRPDKMKNHMKTGCQRKVFP-------CPVCGKEFSRP-DKMKNHMKT 104
SR K+++ +G + + CP+ G+ P D+ HM+
Sbjct: 142 AGESRLKIRKDYVPSGNKPRAEKPKKKMIKCPITGELI--PEDEFDEHMRI 190
Score = 25.5 bits (56), Expect = 9.4
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 3/21 (14%)
Query: 57 CPVCGKEFSRP-DKMKNHMKT 76
CP+ G+ P D+ HM+
Sbjct: 172 CPITGELI--PEDEFDEHMRI 190
>gnl|CDD|215520 PLN02964, PLN02964, phosphatidylserine decarboxylase.
Length = 644
Score = 26.7 bits (59), Expect = 4.8
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 85 CPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRG 120
CPVCG+ DK+ N M + CF T Q G
Sbjct: 254 CPVCGEALGVSDKL-NAMIHMTLCFDEGTGNQVMTG 288
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 26.7 bits (60), Expect = 5.0
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 5/31 (16%)
Query: 34 KNKYSFQRHAFLYHEGCQRKVFPCPVCGKEF 64
+ +Y + F G +RK C CG F
Sbjct: 4 EEEYRLE---FFEENGFERKQ--CKKCGSYF 29
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 23.7 bits (52), Expect = 7.6
Identities = 11/27 (40%), Positives = 13/27 (48%)
Query: 54 VFPCPVCGKEFSRPDKMKNHMKTGCQR 80
V C VCGK FS + H K+ C
Sbjct: 1 VHTCGVCGKTFSSLQALGGHKKSHCSL 27
>gnl|CDD|233712 TIGR02079, THD1, threonine dehydratase. This model represents
threonine dehydratase, the first step in the pathway
converting threonine into isoleucine. At least two other
clades of biosynthetic threonine dehydratases have been
charcterized (TIGR01124 and TIGR01127). Those sequences
described by this model are exclusively found in species
containg the rest of the isoleucine pathway and which
are generally lacking in members of the those other two
clades of threonine dehydratases. Members of this clade
are also often gene clustered with other elements of the
isoleucine pathway [Amino acid biosynthesis, Pyruvate
family].
Length = 409
Score = 25.9 bits (57), Expect = 8.3
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 100 NHMKTVHDCFMPATTPQGQRGQ 121
H+ FMPATTP+ + +
Sbjct: 84 RHLGVHGTVFMPATTPKQKIDR 105
>gnl|CDD|150637 pfam09986, DUF2225, Uncharacterized protein conserved in bacteria
(DUF2225). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 214
Score = 25.7 bits (57), Expect = 8.6
Identities = 14/66 (21%), Positives = 20/66 (30%), Gaps = 30/66 (45%)
Query: 57 CPVCGKEFSRPDKMKNHMKTG-----------CQR--KVFP-------CPVCG-----KE 91
CPVC EF +K+ C + + P CP CG +
Sbjct: 8 CPVCNNEFKTKK-----VKSSGLRLIKRDSDFCIKYKGINPYFYDVWVCPHCGYAAFESD 62
Query: 92 FSRPDK 97
F+
Sbjct: 63 FNNISP 68
>gnl|CDD|218956 pfam06248, Zw10, Centromere/kinetochore Zw10. Zw10 and rough deal
proteins are both required for correct metaphase
check-pointing during mitosis. These proteins bind to
the centromere/kinetochore.
Length = 593
Score = 25.8 bits (57), Expect = 8.8
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 7/60 (11%)
Query: 20 KCMECAKVDVIKTFKNKYSFQRHAFLYH--EGCQRKV-FPCPVCGKEFSRPDKMKNHMKT 76
K + ++++ K+ + +Y+ Q LYH E R V + P +N KT
Sbjct: 142 KSRKGEELEIYKSLRLEYTVQSQNLLYHLGEEWDRLVQWKLP----SSKELGSAQNTKKT 197
>gnl|CDD|203007 pfam04423, Rad50_zn_hook, Rad50 zinc hook motif. The Mre11
complex (Mre11 Rad50 Nbs1) is central to chromosomal
maintenance and functions in homologous recombination,
telomere maintenance and sister chromatid association.
The Rad50 coiled-coil region contains a dimer interface
at the apex of the coiled coils in which pairs of
conserved Cys-X-X-Cys motifs form interlocking hooks
that bind one Zn ion. This alignment includes the zinc
hook motif and a short stretch of coiled-coil on either
side.
Length = 54
Score = 24.2 bits (53), Expect = 8.8
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 57 CPVCGKEFSRPDKMK 71
CPVCG+ K +
Sbjct: 23 CPVCGRPLDEEHKQE 37
Score = 24.2 bits (53), Expect = 8.8
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 85 CPVCGKEFSRPDKMK 99
CPVCG+ K +
Sbjct: 23 CPVCGRPLDEEHKQE 37
>gnl|CDD|224487 COG1571, COG1571, Predicted DNA-binding protein containing a
Zn-ribbon domain [General function prediction only].
Length = 421
Score = 25.8 bits (57), Expect = 9.4
Identities = 11/41 (26%), Positives = 14/41 (34%), Gaps = 11/41 (26%)
Query: 57 CPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDK 97
CP CG +MK+ + G F C CG
Sbjct: 353 CPRCGG------RMKSAGRNG-----FRCKKCGTRARETLI 382
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
0.326 0.138 0.454
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,612,826
Number of extensions: 533512
Number of successful extensions: 1002
Number of sequences better than 10.0: 1
Number of HSP's gapped: 965
Number of HSP's successfully gapped: 119
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (24.6 bits)