RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11049
(237 letters)
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 146 bits (369), Expect = 2e-40
Identities = 64/183 (34%), Positives = 92/183 (50%), Gaps = 15/183 (8%)
Query: 39 MLGGCCVCSDDSGWAENPLVYCDGQGCNVAVHQACYGIVTVPVGSWFCRKCESQEKSTKV 98
C C+ N +V+CDG C + VHQ+CYGI +P G W CRKC E +
Sbjct: 192 FDDICTKCTSTHNENSNAIVFCDG--CEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRC 249
Query: 99 RCELCPSKDGALKRTDNNGWAHVVCALYIPEVRFGNVTSMEPI-LLEEIPPERFNKVCYI 157
C CPS DGA K+T + W HV+CA++ PE+ FG++ S +PI + + R+ C I
Sbjct: 250 -CSFCPSSDGAFKQTSDGRWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLI 308
Query: 158 CEENGHKASRSKFGACMMCNKPGCRQQFHVTCAQTQGL--LCEEAGN-YLDNVKYCGYCS 214
C+E G C+ C+ C + +HVTCA+ G L + N + + C
Sbjct: 309 CKE--------FGGTCIQCSYFNCTRAYHVTCARRAGYFDLNIYSHNGISYCIDHEPLCR 360
Query: 215 HHY 217
HY
Sbjct: 361 KHY 363
>gnl|CDD|206003 pfam13832, zf-HC5HC2H_2, PHD-zinc-finger like domain.
Length = 109
Score = 123 bits (311), Expect = 2e-36
Identities = 48/119 (40%), Positives = 67/119 (56%), Gaps = 10/119 (8%)
Query: 98 VRCELCPSKDGALKRTDNNGWAHVVCALYIPEVRFGNVTSMEPILLEEIPPERFNKVCYI 157
C LCP + GALK+T + W HV+CA+++PEVRFGN +MEPI + IP ER+ C
Sbjct: 1 AECCLCPLRGGALKKTTDGRWVHVLCAIFVPEVRFGNGATMEPIDVSRIPKERWKLKCCF 60
Query: 158 CEENGHKASRSKFGACMMCNKPGCRQQFHVTCAQTQGLLCEEAGNYLDNVKYCGYCSHH 216
C++ GAC+ C+ C+ FHVTCA+ G+ E N++ YC H
Sbjct: 61 CKKRS--------GACIQCSYGRCQTSFHVTCARAAGVYMEIEDW--PNLQVIAYCQKH 109
>gnl|CDD|222368 pfam13771, zf-HC5HC2H, PHD-like zinc-binding domain. The members
of this family are annotated as containing PHD domain,
but the zinc-binding region here is not typical of PHD
domains. The conformation here is a well-conserved
cysteine-histidine rich region spanning 90 residues,
where the Cys and His are arranged as
HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.
Length = 89
Score = 80.1 bits (198), Expect = 1e-19
Identities = 37/100 (37%), Positives = 46/100 (46%), Gaps = 15/100 (15%)
Query: 120 HVVCALYIPEVRFGNVTSMEPILLE---EIPPERFNKVCYICEENGHKASRSKFGACMMC 176
HV CAL+ PEV ME LE + R C +C+ K GAC+ C
Sbjct: 1 HVNCALWSPEVVQRGDDDMEGFPLEDVDKAVKRRRKLKCSLCK---------KKGACIGC 51
Query: 177 NKPGCRQQFHVTCAQTQGLLCEEAGNYLDNVKYCGYCSHH 216
CR+ FHVTCA+ G L + G DN K+ YC H
Sbjct: 52 CVKNCRRAFHVTCAREAGCLFQFDG---DNGKFKSYCPKH 88
>gnl|CDD|222406 pfam13831, PHD_2, PHD-finger. PHD folds into an interleaved type
of Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 33
Score = 42.2 bits (100), Expect = 4e-06
Identities = 17/35 (48%), Positives = 23/35 (65%), Gaps = 2/35 (5%)
Query: 55 NPLVYCDGQGCNVAVHQACYGIVTVPVGSWFCRKC 89
NPL+ C C+VAVH +CYG+ + G W CR+C
Sbjct: 1 NPLLVC--SKCSVAVHASCYGVPELSDGPWLCRRC 33
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type
of Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 51
Score = 35.2 bits (81), Expect = 0.002
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 43 CCVCSDDSGWAENPLVYCDGQGCNVAVHQACYGI----VTVPVGSWFCRKC 89
C VC + L+ CDG C+ H AC G +P G W+C +C
Sbjct: 2 CAVCGKVD--DDGELLLCDG--CDRWFHLACLGPPLEPEEIPEGEWYCPEC 48
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 35.3 bits (81), Expect = 0.019
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 56 PLVYCDGQGCNVA-VHQACYGIVTVPVGSWFCRKCESQ 92
+V CD C H C G+ P G W+C +C+
Sbjct: 233 QMVACDNANCKREWFHLECVGLKEPPKGKWYCPECKKA 270
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet
known if PHD fingers have a common molecular function.
Several reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is
a ubiquitin ligase have been refuted as these domains
were RING fingers misidentified as PHD fingers.
Length = 47
Score = 29.1 bits (65), Expect = 0.22
Identities = 19/50 (38%), Positives = 22/50 (44%), Gaps = 7/50 (14%)
Query: 43 CCVCSDDSGWAENPLVYCDGQGCNVAVHQACYGI---VTVPVGSWFCRKC 89
C VC E L+ CDG C+ HQ C G P G W+C KC
Sbjct: 2 CSVCGKPDDGGE--LLQCDG--CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
>gnl|CDD|191251 pfam05283, MGC-24, Multi-glycosylated core protein 24 (MGC-24).
This family consists of several MGC-24 (or Cd164
antigen) proteins from eukaryotic organisms.
MGC-24/CD164 is a sialomucin expressed in many normal
and cancerous tissues. In humans, soluble and
transmembrane forms of MGC-24 are produced by
alternative splicing.
Length = 187
Score = 29.2 bits (65), Expect = 1.4
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 1/55 (1%)
Query: 38 LMLGGCCVCSDDSGWAENPLVYCDGQGCNV-AVHQACYGIVTVPVGSWFCRKCES 91
L LG C+ + S WA+ P V + ++ + T P G C S
Sbjct: 10 LCLGALCLLAAGSNWAQLPNVTKGARIFGRTSLLVLNVWLTTYPEGCEHLNSCVS 64
>gnl|CDD|240236 PTZ00037, PTZ00037, DnaJ_C chaperone protein; Provisional.
Length = 421
Score = 29.4 bits (66), Expect = 1.9
Identities = 23/80 (28%), Positives = 27/80 (33%), Gaps = 17/80 (21%)
Query: 154 VCYICEENGHKASRSKFGACMMCNKPGCR----------QQFHVTCAQTQGLLCEEAGNY 203
+C CE GH + F C +CN G R Q TC C G
Sbjct: 152 ICANCE--GHGGPKDAFVDCKLCNGQGIRVQIRQMGSMIHQTQSTCNS-----CNGQGKI 204
Query: 204 LDNVKYCGYCSHHYSKLVRK 223
+ K C CS K RK
Sbjct: 205 IPESKKCKNCSGKGVKKTRK 224
>gnl|CDD|215224 PLN02400, PLN02400, cellulose synthase.
Length = 1085
Score = 29.2 bits (65), Expect = 2.0
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 153 KVCYICEEN-GHKASRSKFGACMMCNKPGCR 182
++C IC ++ G + F AC C P CR
Sbjct: 37 QICQICGDDVGVTETGDVFVACNECAFPVCR 67
Score = 27.2 bits (60), Expect = 9.3
Identities = 21/85 (24%), Positives = 31/85 (36%), Gaps = 14/85 (16%)
Query: 13 DDSGWAENPLVYCDGQGCNVAVHQELMLGGCCVCSDDSGWAENPLVYCDGQGCNVAVHQA 72
DS PL +GQ C + C DD G E V+ C V +
Sbjct: 22 HDSDSGPKPLKNLNGQICQI-------------CGDDVGVTETGDVFVACNECAFPVCRP 68
Query: 73 CYGIVTVPVGSWFCRKCESQEKSTK 97
CY G+ C +C+++ + K
Sbjct: 69 CYEY-ERKDGTQCCPQCKTRYRRHK 92
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein,
contains RING Zn-finger [Posttranslational modification,
protein turnover, chaperones / Intracellular trafficking
and secretion].
Length = 190
Score = 28.3 bits (63), Expect = 2.5
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 152 NKVCYICEENGHKASRSKFGACMMCNKPGCRQQ 184
N VC+ C +NGH C C+ G R
Sbjct: 60 NPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSN 92
>gnl|CDD|215343 PLN02638, PLN02638, cellulose synthase A (UDP-forming), catalytic
subunit.
Length = 1079
Score = 28.4 bits (63), Expect = 4.1
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 153 KVCYICEEN-GHKASRSKFGACMMCNKPGCR 182
+VC IC +N G F AC +C P CR
Sbjct: 18 QVCQICGDNVGKTVDGEPFVACDVCAFPVCR 48
>gnl|CDD|215124 PLN02195, PLN02195, cellulose synthase A.
Length = 977
Score = 27.6 bits (61), Expect = 6.6
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 154 VCYIC-EENGHKASRSKFGACMMCNKPGCR 182
+C C EE G ++ F AC C+ P C+
Sbjct: 8 ICATCGEEVGVDSNGEAFVACHECSYPLCK 37
>gnl|CDD|188825 cd09441, LIM2_SF3, The second Lim domain of pollen specific protein
SF3. The second Lim domain of pollen specific protein
SF3: SF3 is a Lim protein that is found exclusively in
mature plant pollen grains. It contains two LIM domains.
The exact function of SF3 is unknown. It may be a
transcription factor required for the expression of late
pollen genes. It is possible that SF3 protein is
involved in controlling pollen-specific processes such
as male gamete maturation, pollen tube formation, or
even fertilization. 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 = 61
Score = 25.1 bits (55), Expect = 9.1
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 212 YCSHHYSKLVRKKG 225
YC HH+S+L ++KG
Sbjct: 48 YCKHHHSQLFKEKG 61
>gnl|CDD|238779 cd01521, RHOD_PspE2, Member of the Rhodanese Homology Domain
superfamily. This CD includes the putative
rhodanese-like protein, Psp2, of Yersinia pestis biovar
Medievalis and other similar uncharacterized proteins.
Length = 110
Score = 26.2 bits (58), Expect = 9.3
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 58 VYCDGQGCNVAVHQA 72
VYCDG GCN A A
Sbjct: 69 VYCDGPGCNGATKAA 83
Score = 25.8 bits (57), Expect = 9.8
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 23 VYCDGQGCNVA 33
VYCDG GCN A
Sbjct: 69 VYCDGPGCNGA 79
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 0.138 0.481
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: 11,370,629
Number of extensions: 967891
Number of successful extensions: 814
Number of sequences better than 10.0: 1
Number of HSP's gapped: 800
Number of HSP's successfully gapped: 38
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
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: 57 (25.9 bits)