RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8251
(434 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 32.7 bits (75), Expect = 0.016
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 104 NLLQHQPVHTGQRKYNCTVCGKAFSR 129
NL +H HTG++ Y C VCGK+FS
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 28.1 bits (63), Expect = 0.69
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 76 SLGIHERIHTGQRPYICDWCGVGFRS 101
+L H R HTG++PY C CG F S
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 26.6 bits (59), Expect = 2.4
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 306 HHCDRPYDCDVCGAKFTQ 323
H ++PY C VCG F+
Sbjct: 9 HTGEKPYKCPVCGKSFSS 26
>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 = 31.2 bits (71), Expect = 0.051
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 120 CTVCGKAFSRKSFVTTHMRVH 140
C CGK+FSRKS + H+R H
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 25.8 bits (57), Expect = 4.5
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 31 CHICKETFYKHSELVRHLER 50
C C ++F + S L RHL
Sbjct: 2 CPDCGKSFSRKSNLKRHLRT 21
Score = 25.0 bits (55), Expect = 6.8
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 314 CDVCGAKFTQVGDMRRHRKKH 334
C CG F++ +++RH + H
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 31.2 bits (70), Expect = 0.097
Identities = 12/48 (25%), Positives = 25/48 (52%)
Query: 118 YNCTVCGKAFSRKSFVTTHMRVHTGKLTGKFGQKMSALSGTAFAVEYE 165
Y C +CG+ + ++ + TH+R H L +++S +G ++ E
Sbjct: 6 YECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEYIEIKAE 53
Score = 25.8 bits (56), Expect = 7.7
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 312 YDCDVCGAKFTQVGDMRRHRKKHDEN 337
Y+C +CG + + M H +KH+ N
Sbjct: 6 YECPICGEIYIKRKSMITHLRKHNTN 31
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 30.1 bits (68), Expect = 0.10
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 118 YNCTVCGKAFSRKSFVTTHMRVH 140
Y C CGK F KS + HMR H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 28.6 bits (64), Expect = 0.36
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 312 YDCDVCGAKFTQVGDMRRHRKKH 334
Y C CG F +R H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 27.0 bits (60), Expect = 1.5
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 90 YICDWCGVGFRSKANLLQHQPVH 112
Y C CG F+SK+ L +H H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>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 = 33.5 bits (77), Expect = 0.19
Identities = 12/32 (37%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 31 CHICKETFYKHSELVRHLEREHN---IPRSES 59
C C + F E HLE+EH P SE
Sbjct: 60 CRTCSKKFSSSEECKNHLEQEHAAKFKPSSEM 91
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 31.4 bits (71), Expect = 0.35
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 89 PYICDWCGVGFRSKANLLQHQPVHTGQRKYNCTVCGKAFSRKSFVTTHM 137
PY+C C + F S +L QH + + C VCGK F H+
Sbjct: 73 PYVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDHV 119
>gnl|CDD|227673 COG5383, COG5383, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 295
Score = 31.4 bits (71), Expect = 0.79
Identities = 31/143 (21%), Positives = 47/143 (32%), Gaps = 31/143 (21%)
Query: 110 PVHTGQRKYNCTVCGKAFSRKSFVTTHMRVHTGKLTGKFG---QKMSALSGTAFAVEYEI 166
PVH+ AF SF H G T +FG Q+ AL+ + ++
Sbjct: 101 PVHS-----------TAFEPVSFADEDGERHPGVHTARFGEIEQRGVALTPKGRVLYDDL 149
Query: 167 IQECLFAKNGGKAFSRKSFVTTHMRVHTGKLTGKFGQKISALSGIRTQHLQIESHQTTQP 226
+Q N ++ F Q ++S +R Q L +
Sbjct: 150 LQAASTGFNA--------------MAYSATAREIFEQFPDSMSEMREQGLAQFRYLLE-- 193
Query: 227 QRWAAYRQIGYYGREPIQGFHSN 249
AA+RQ G +P QG
Sbjct: 194 LVAAAHRQSLEEGDDP-QGLIER 215
>gnl|CDD|147147 pfam04838, Baculo_LEF5, Baculoviridae late expression factor 5.
Length = 159
Score = 29.9 bits (68), Expect = 1.3
Identities = 16/44 (36%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 381 NSPSELIL-LTCSEPTIFTNFNVKTQILNLTSTFHLFHPLTKYN 423
ELI L + P NVK + N +T HLFH L Y
Sbjct: 15 KDYKELIDYLITNYPK-----NVKNKTFNFANTGHLFHSLYAYI 53
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 30.4 bits (68), Expect = 1.7
Identities = 29/139 (20%), Positives = 41/139 (29%), Gaps = 12/139 (8%)
Query: 21 EHGGNLSFDNCHICKETFYKHSELVRHLEREHNIPRSESSPWCCRF--CNKRMMTKLSLG 78
G C +F + S L RHL R N P+ C + C K +L
Sbjct: 282 SEKGFSLPIKSKQCNISFSRSSPLTRHL-RSVNHSGESLKPFSCPYSLCGKLFSRNDALK 340
Query: 79 IHERIHTGQRPYICDW--CGVGFRSKANLLQHQPVH-----TGQRKYNCTV--CGKAFSR 129
H +HT P F N Q + +K C + F R
Sbjct: 341 RHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKR 400
Query: 130 KSFVTTHMRVHTGKLTGKF 148
S ++ H+ H
Sbjct: 401 DSNLSLHIITHLSFRPYNC 419
>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 = 2.9
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 312 YDCDVCGAKFTQVGDMRRHRKKH 334
+ C +CG F+ ++RH +KH
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 25.7 bits (56), Expect = 4.4
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 118 YNCTVCGKAFSRKSFVTTHMRVH 140
+ C +CGK+FS K + H+R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|222045 pfam13323, HPIH, N-terminal domain with HPIH motif. This family is
found in fungi on proteins carrying the PAS, pfam00989,
domain. There is a well-conserved characteristic HPIH
motif, but the function is not known.
Length = 152
Score = 28.4 bits (64), Expect = 4.7
Identities = 8/60 (13%), Positives = 17/60 (28%), Gaps = 3/60 (5%)
Query: 364 TEHKLVIQHFSLVQMNFNSPSELILLTCSEPTIFTNFNVKTQILNLTSTFHLFHPLTKYN 423
H +LV + F + + + L ST + F ++ +
Sbjct: 85 EAPADNADHLALVTLVFPDSNSASSAPALDNVPLPSNLSAYL---LPSTSNSFSSYSQDS 141
>gnl|CDD|205978 pfam13805, Pil1, Eisosome component PIL1. In the budding yeast, S.
cerevisiae, Pil1 and another cytoplasmic protein, Lsp1,
together form large immobile assemblies at the plasma
membrane that mark sites for endocytosis, called
eisosomes. Endocytosis functions to recycle plasma
membrane components, to regulate cell-surface expression
of signalling receptors and to internalise nutrients in
all eukaryotic cells.
Length = 271
Score = 28.7 bits (64), Expect = 5.1
Identities = 12/65 (18%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 177 GKAFSRKSFVTTHMRVHTGKLTGKFGQKISALSGIRTQHLQIESHQTTQPQRWAAYRQIG 236
G+ F + + + G +K+S L ++ + + S + T +R A +Q+
Sbjct: 31 GRFFGKGPLSHSFRKNAAGAFGPDLSRKLSQL--VKMEKNVMRSMEVTARERRDAAKQLS 88
Query: 237 YYGRE 241
+G +
Sbjct: 89 LWGED 93
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 28.9 bits (65), Expect = 5.7
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 200 KFGQKISALSGIRTQHLQIES-HQTT 224
K + I+ALSGI HL+ T
Sbjct: 251 KLKKVINALSGIDLSHLETPKIQPKT 276
>gnl|CDD|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein
Lost in Neoplasm (Eplin) like proteins. The Lim domain
of Epithelial Protein Lost in Neoplasm (Eplin) like
proteins: This family contains Epithelial Protein Lost
in Neoplasm in Neoplasm (Eplin), xin actin-binding
repeat-containing protein 2 (XIRP2) and a group of
protein with unknown function. The members of this
family all contain a single LIM domain. Epithelial
Protein Lost in Neoplasm is a cytoskeleton-associated
tumor suppressor whose expression inversely correlates
with cell growth, motility, invasion and cancer
mortality. Eplin interacts and stabilizes F-actin
filaments and stress fibers, which correlates with its
ability to suppress anchorage independent growth. In
epithelial cells, Eplin is required for formation of
the F-actin adhesion belt by binding to the
E-cadherin-catenin complex through alpha-catenin. Eplin
is expressed in two isoforms, a longer Eplin-beta and a
shorter Eplin-alpha. Eplin-alpha mRNA is detected in
various tissues and cell lines, but is absent or down
regulated in cancer cells. Xirp2 contains a LIM domain
and Xin re peats for binding to and stabilising
F-actin. Xirp2 is expressed in muscles and is
significantly induced in the heart in response to
systemic administration of angiotensin II. Xirp2 is an
important effector of the Ang II signaling pathway in
the heart. The expression of Xirp2 is activated by
myocyte enhancer factor (MEF)2A, whose transcriptional
activity is stimulated by angiotersin II. Thus, Xirp2
plays important pathological roles in the angiotensin
II induced hypertension. 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 = 53
Score = 25.9 bits (57), Expect = 6.8
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 10/54 (18%)
Query: 31 CHICKETFYKHSELVRHLEREHNIPRSESSPWCCRFCNKRMMTKLSLGIHERIH 84
C +C++ Y L+ + H S + C CN +KLSLG + +H
Sbjct: 1 CTVCQKRVYPMERLIADKQNFHK------SCFRCEHCN----SKLSLGNYASLH 44
>gnl|CDD|180247 PRK05767, rpl44e, 50S ribosomal protein L44e; Validated.
Length = 92
Score = 26.8 bits (60), Expect = 7.2
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 117 KYNCTVCGKAFSRKSF 132
+Y CT CGKA +R+ F
Sbjct: 67 RYRCTECGKAHTREGF 82
>gnl|CDD|233315 TIGR01213, pseudo_Pus10arc, tRNA pseudouridine(54/55) synthase.
Members of this family show twilight-zone similarity to
several predicted RNA pseudouridine synthases. All
trusted members of this family are archaeal. Several
eukaryotic homologs lack N-terminal homology including
two CXXC motifs [Hypothetical proteins, Conserved].
Length = 388
Score = 28.6 bits (64), Expect = 7.3
Identities = 20/72 (27%), Positives = 24/72 (33%), Gaps = 12/72 (16%)
Query: 58 ESSPWCCRFCNKRMMTKLSLGIHERIHTGQRPYICDWCGVGFRSKANLLQHQPVHTGQRK 117
P C R C R+ KL G R +R G + L +PV
Sbjct: 6 AKYPLCDR-CLGRLFAKLGHGTSNR----ER-------GEALQLALALELGRPVKEFVES 53
Query: 118 YNCTVCGKAFSR 129
C VCG F R
Sbjct: 54 EPCDVCGGIFDR 65
>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 = 8.0
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 309 DRPYDCDVCGAKFTQVGDMRRHRK 332
D+PY C+VC ++ + ++ HRK
Sbjct: 396 DKPYRCEVCDKRYKNLNGLKYHRK 419
>gnl|CDD|144512 pfam00935, Ribosomal_L44, Ribosomal protein L44.
Length = 77
Score = 26.0 bits (58), Expect = 9.6
Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 5/54 (9%)
Query: 86 GQRPYICDWCGVGFRSKANLLQHQPVHTGQR---KYNCTVCGKAFSRKSFVTTH 136
G+R Y D G+ + + + ++ + CT C KA R
Sbjct: 21 GKRRY--DRKQKGYGGQTKPVPGKKAKPTKKIVLRLRCTECKKAHQRPGKRCKK 72
>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 = 26.5 bits (59), Expect = 9.9
Identities = 22/80 (27%), Positives = 30/80 (37%), Gaps = 14/80 (17%)
Query: 31 CHICKETFYKHSELVRHLEREH--NIPRSESSPWCCRFCNKRMMTKLSLGIHERIHTGQR 88
C C T E + H+ + H IP E + L + E+IH G
Sbjct: 2 CLFCNHTSDTVEENLEHMFKSHGFFIPEREY------LVDL---EGLLNYLREKIHEG-- 50
Query: 89 PYICDWCGVGFRSKANLLQH 108
C +CG F+S L QH
Sbjct: 51 -NECLYCGKQFKSLEALRQH 69
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
0.322 0.136 0.428
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: 21,171,924
Number of extensions: 1933824
Number of successful extensions: 1574
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1569
Number of HSP's successfully gapped: 45
Length of query: 434
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 334
Effective length of database: 6,502,202
Effective search space: 2171735468
Effective search space used: 2171735468
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 (21.9 bits)
S2: 60 (27.0 bits)