RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16463
(317 letters)
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 98.5 bits (245), Expect = 5e-24
Identities = 71/283 (25%), Positives = 105/283 (37%), Gaps = 41/283 (14%)
Query: 28 PYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIE-----HIASQNGNKIDQFSRK 82
P + D + N+P E T++ E+D +K + + + +
Sbjct: 5 PGLNDITDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMISILKKIIDLDSQTYEEVE 64
Query: 83 RNLLR-VQVALIAAQEIGDEKLSIMQQVQDVIEGKTRQIDGIFY------------NLPS 129
LL+ ++ L+ A I EK + + + ++ + +D N
Sbjct: 65 DGLLKEIRELLLKAIYIQKEKSDLADRAEKLLRRHRKLLDDRIAKRPHEKVAARIENCHD 124
Query: 130 VTSRRE--QEAVETSVKHDEAVSTEKTQQSETPVAPKK---RQRKKNTEVDSEMIECSST 184
SR E + E S +Q S K+ K+ + S E S T
Sbjct: 125 AVSRLERNSYSSAARRSSGEHRSAASSQGSRHTKLKKRKNIHNLKRRSPELSSKREVSFT 184
Query: 185 PLPRSS-ATIAVVKKPSTQSGGKKKKRKTKQQRECEKEATPPPDEDLAIDPNEPTYCLCN 243
S T VK+ +GG K R + E E YC C
Sbjct: 185 LESPSVPDTATRVKE--GNNGGSTKSRGVSSEDNSE---------------GEELYCFCQ 227
Query: 244 QVSFGQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKA 286
QVS+GQMV CDN C +WFH CV + PKGKWYCP C+KA
Sbjct: 228 QVSYGQMVACDNANCKREWFHLECVGLKEPPKGKWYCPECKKA 270
>gnl|CDD|221887 pfam12998, ING, Inhibitor of growth proteins N-terminal
histone-binding. Histones undergo numerous
post-translational modifications, including acetylation
and methylation, at residues which are then probable
docking sites for various chromatin remodelling
complexes. Inhibitor of growth proteins (INGs)
specifically bind to residues that have been thus
modified. INGs carry a well-characterized C-terminal
PHD-type zinc-finger domain, binding with lysine
4-tri-methylated histone H3 (H3K4me3), as well as this
N-terminal domain that binds unmodified H3 tails.
Although these two regions can bind histones
independently, together they increase the apparent
association of the ING for the H3 tail.
Length = 104
Score = 86.0 bits (214), Expect = 3e-21
Identities = 36/98 (36%), Positives = 58/98 (59%), Gaps = 4/98 (4%)
Query: 28 PYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIA----SQNGNKIDQFSRKR 83
Y+E YLD +ENLP E+QR T+IRE+D Q +KE++ +NG+ + +
Sbjct: 1 LYLEDYLDDLENLPLELQRNFTEIREIDAQVQKIIKELDEQIQKFIKENGSNLSNPKEEE 60
Query: 84 NLLRVQVALIAAQEIGDEKLSIMQQVQDVIEGKTRQID 121
L R+Q LI AQE+ DEK+ + Q ++++ R++D
Sbjct: 61 LLKRIQEELIKAQELQDEKVQLANQAYELVDKHIRRLD 98
>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 = 47.1 bits (112), Expect = 1e-07
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 239 YC-LCNQV-SFGQMVMCDNDLCPHQWFHFSCVAVT----NTPKGKWYCPNCR 284
YC +C +V G++++CD C WFH +C+ P+G+WYCP C+
Sbjct: 1 YCAVCGKVDDDGELLLCDG--CDR-WFHLACLGPPLEPEEIPEGEWYCPECK 49
>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 = 45.7 bits (108), Expect = 4e-07
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 239 YC-LCNQV-SFGQMVMCDNDLCPHQWFHFSCVAVT---NTPKGKWYCPNC 283
YC +C + G+++ CD C W+H +C+ P GKWYCP C
Sbjct: 1 YCSVCGKPDDGGELLQCDG--CDR-WYHQTCLGPPLLEEEPDGKWYCPKC 47
>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2
complex component). RNases H are enzymes that
specifically hydrolyse RNA when annealed to a
complementary DNA and are present in all living
organisms. In yeast RNase H2 is composed of a complex of
three proteins (Rnh2Ap, Ydr279p and Ylr154p), this
family represents the homologues of Ydr279p. It is not
known whether non yeast proteins in this family fulfil
the same function.
Length = 287
Score = 31.1 bits (71), Expect = 0.61
Identities = 33/182 (18%), Positives = 65/182 (35%), Gaps = 9/182 (4%)
Query: 35 DIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNKIDQFSRKR--NLLRVQVAL 92
DI+++L + R L L + +K + + + K + S ++ L +V
Sbjct: 102 DILDSLYSHLSRLL-NWENPRNLLEKRLKAVCDVKEEGDEKFYKLSEEKLLEWLLKKVER 160
Query: 93 IAAQEIGDEKLSIMQQVQDVIEGKTR-QIDGIFYNLPSVTSRREQEAVETSVKHDEAVST 151
+ ++ S+++ ++ + + Y + S + + +K
Sbjct: 161 LVKYLPKSKEESLVRSALELDIPDDILNLLRLRYACDLLCSYLPPDLYKELLKSLL--IP 218
Query: 152 EKTQQSETPVAPKKRQRKKNTEVDSEMIECSSTPLPRSSATIAVVKKPSTQSGGKKKKRK 211
E + KK++R+ TE D E E S R S KKP G K K+
Sbjct: 219 EFKPLDKYLKESKKKKRE--TEEDVEAAE-SRAEKKRKSKEEIKKKKPKESKGVKALKKV 275
Query: 212 TK 213
Sbjct: 276 VA 277
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 31.1 bits (70), Expect = 0.82
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 5/35 (14%)
Query: 250 MVMCDN-DLCPHQWFHFSCVAVTNTPKGKWYCPNC 283
+V CD ++C HQ SC + P+G W C C
Sbjct: 210 IVFCDGCEICVHQ----SCYGIQFLPEGFWLCRKC 240
>gnl|CDD|217899 pfam04108, APG17, Autophagy protein Apg17. Apg17 is required for
activating Apg1 protein kinases.
Length = 408
Score = 30.8 bits (70), Expect = 0.86
Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 12/87 (13%)
Query: 30 VETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNKIDQFSRKRNLLRVQ 89
+ T +D +EN ++++L S+M +IE + S +++ + + L
Sbjct: 256 LHTVIDEIENNEKRVKKFL----------SSHMSKIEELHSATKELLEELEKYKERLPRY 305
Query: 90 VALIA--AQEIGDEKLSIMQQVQDVIE 114
+A+ A D K I Q +Q++ E
Sbjct: 306 LAIFADIRALWEDFKEPIQQYIQELSE 332
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 27.7 bits (62), Expect = 1.0
Identities = 14/51 (27%), Positives = 18/51 (35%), Gaps = 16/51 (31%)
Query: 240 CLCNQVSFGQMVMCDNDLCPHQWFHFSCVAVTNTPKGKW-----YCPNCRK 285
CL ++V+ C H FH C+ KW CP CR
Sbjct: 6 CLDEFEPGEEVVVLP---CGH-VFHKECLD-------KWLRSSNTCPLCRA 45
>gnl|CDD|234038 TIGR02865, spore_II_E, stage II sporulation protein E. Stage II
sporulation protein E (SpoIIE) is a multiple membrane
spanning protein with two separable functions. It plays
a role in the switch to polar cell division during
sporulation. By means of it protein phosphatase
activity, located in the C-terminal region, it activates
sigma-F. All proteins that score above the trusted
cutoff to this model are found in endospore-forming
Gram-positive bacteria. Surprisingly, a sequence from
the Cyanobacterium-like (and presumably
non-spore-forming) photosynthesizer Heliobacillus
mobilis is homologous, and scores between the trusted
and noise cutoffs [Cellular processes, Sporulation and
germination].
Length = 764
Score = 30.4 bits (69), Expect = 1.3
Identities = 28/116 (24%), Positives = 45/116 (38%), Gaps = 22/116 (18%)
Query: 40 LPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNKIDQFSRKRNLLRVQVALIAAQEIG 99
LPDE +R K +EL + E I N I++ RKR L L+A Q
Sbjct: 396 LPDEFERKCIKRKEL-------INTTEDIL--NNYIINEMWRKR--LEEGRRLVAEQ--- 441
Query: 100 DEKLSIMQQVQDVIEGKTRQIDG--IFYNLPSVTSRREQEAVETSVKHDEAVSTEK 153
++ V + +E ++I+ +F+ L R + A +TE
Sbjct: 442 ------LKGVAESVEDIAKEINLEIVFHQLLEEKIIRALNKNGIPYEDVLAYNTEG 491
Score = 29.3 bits (66), Expect = 3.3
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 11/67 (16%)
Query: 30 VETYLDIVENLPDEIQRYLTKIREL---------DVLYQSYMKEIEHIASQNGNKIDQFS 80
+E YLD PD + Y+ K+RE+ +V + A + K+
Sbjct: 287 LERYLDGERKQPDLQEDYMRKVREIAAEKLEEFSEVFR--ELSNTFVEALASNEKLTMKR 344
Query: 81 RKRNLLR 87
+ LL
Sbjct: 345 KSSYLLE 351
>gnl|CDD|220545 pfam10058, DUF2296, Predicted integral membrane metal-binding
protein (DUF2296). This domain, found in various
hypothetical bacterial and eukaryotic metal-binding
proteins, has no known function.
Length = 51
Score = 27.2 bits (61), Expect = 1.4
Identities = 5/27 (18%), Positives = 8/27 (29%)
Query: 258 CPHQWFHFSCVAVTNTPKGKWYCPNCR 284
C H + + CP+C
Sbjct: 22 CSKCHSHNGLAPKEEFEEVTYRCPHCG 48
>gnl|CDD|240069 cd04718, BAH_plant_2, BAH, or Bromo Adjacent Homology domain,
plant-specific sub-family with unknown function. BAH
domains are found in a variety of proteins playing roles
in transcriptional silencing and the remodeling of
chromatin. It is assumed that in most or all of these
instances the BAH domain mediates protein-protein
interactions.
Length = 148
Score = 29.1 bits (65), Expect = 1.5
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 263 FHFSCV--AVTNTPKGKWYCPNCRKARS 288
FH C+ + P+G W CP C +S
Sbjct: 2 FHLCCLRPPLKEVPEGDWICPFCEVEKS 29
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 29.4 bits (66), Expect = 2.8
Identities = 24/146 (16%), Positives = 53/146 (36%), Gaps = 26/146 (17%)
Query: 31 ETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNKI-DQFSRKRNLLRVQ 89
E ++E L + K L+ L +KE E + + ++ + R+RN
Sbjct: 511 EEINVLIEKLSALEKELEQKNEHLEKL----LKEQEKLKKELEQEMEELKERERNK---- 562
Query: 90 VALIAAQEIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLPSVTSRREQEAVETSVKHDEAV 149
KL + ++ Q+ ++ ++++ I L + ++ +K E +
Sbjct: 563 ------------KLELEKEAQEALKALKKEVESIIREL-----KEKKIHKAKEIKSIEDL 605
Query: 150 STEKTQQSETPVAPKKRQRKKNTEVD 175
K + + P P Q K +
Sbjct: 606 VKLKETKQKIPQKPTNFQADKIGDKV 631
>gnl|CDD|235665 PRK05996, motB, flagellar motor protein MotB; Validated.
Length = 423
Score = 28.9 bits (65), Expect = 3.7
Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 196 VKKPSTQSGGKKKKRKTKQQRECEKEATPPPD-EDLAIDPNEPT 238
+K P + G++K K+K + + E + +D + T
Sbjct: 83 LKDPVDGAEGEQKPGKSKFEEDQRVEGSSAVTGDDTTRTSGDQT 126
>gnl|CDD|218440 pfam05110, AF-4, AF-4 proto-oncoprotein. This family consists of
AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental
retardation syndrome) nuclear proteins. These proteins
have been linked to human diseases such as acute
lymphoblastic leukaemia and mental retardation. The
family also contains a Drosophila AF4 protein homologue
Lilliputian which contains an AT-hook domain.
Lilliputian represents a novel pair-rule gene that acts
in cytoskeleton regulation, segmentation and
morphogenesis in Drosophila.
Length = 1154
Score = 28.7 bits (64), Expect = 4.4
Identities = 20/95 (21%), Positives = 34/95 (35%), Gaps = 9/95 (9%)
Query: 137 EAVETSVKHDEAVSTEKTQQSETPV---APKKRQRKKNTEVDSEMIECSSTPLPRSSATI 193
+ V +++S K Q S+T + K +++ KN E + + R
Sbjct: 717 KGVPPKPAEKDSLSAPKKQTSKTASEKSSSKGKRKHKNDEEADK----IESKKQRLEEKS 772
Query: 194 AVVKKPSTQSGGKKKKRK--TKQQRECEKEATPPP 226
+ S+ S K K R E+E P P
Sbjct: 773 SSCSPSSSSSHHHSSSNKESRKSSRNKEEEMLPSP 807
>gnl|CDD|115172 pfam06500, DUF1100, Alpha/beta hydrolase of unknown function
(DUF1100). This family consists of several hypothetical
bacterial proteins of unknown function. Members of this
family have an alpha/beta hydrolase fold.
Length = 411
Score = 28.3 bits (63), Expect = 5.8
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 11 QSPNMLNQAVLEAMYSVPYVE 31
+ + L+QAVL A+ VP+V+
Sbjct: 239 EDSSCLHQAVLNALADVPWVD 259
>gnl|CDD|218908 pfam06136, DUF966, Domain of unknown function (DUF966). Family of
plant proteins with unknown function.
Length = 308
Score = 27.8 bits (62), Expect = 7.5
Identities = 15/96 (15%), Positives = 35/96 (36%)
Query: 128 PSVTSRREQEAVETSVKHDEAVSTEKTQQSETPVAPKKRQRKKNTEVDSEMIECSSTPLP 187
+RR ++ +S + V + + +R R + +E+ +P
Sbjct: 112 TPPVNRRANQSWSSSDLAEYKVYKAEEPADASTQTDDRRSRDSSEAESTELSREEISPPS 171
Query: 188 RSSATIAVVKKPSTQSGGKKKKRKTKQQRECEKEAT 223
SS+ + + +S K R + R E++ +
Sbjct: 172 SSSSPSSSSSPETLESLIKADGRLSLSFRSLEEDES 207
>gnl|CDD|212120 cd10809, GH38N_AMII_GMII_SfManIII_like, N-terminal catalytic domain
of Golgi alpha-mannosidase II, Spodoptera frugiperda Sf9
alpha-mannosidase III, and similar proteins; glycoside
hydrolase family 38 (GH38). This subfamily is
represented by Golgi alpha-mannosidase II (GMII, also
known as mannosyl-oligosaccharide 1,3- 1,6-alpha
mannosidase, EC 3.2.1.114, Man2A1), a monomeric,
membrane-anchored class II alpha-mannosidase existing in
the Golgi apparatus of eukaryotes. GMII plays a key role
in the N-glycosylation pathway. It catalyzes the
hydrolysis of the terminal both alpha-1,3-linked and
alpha-1,6-linked mannoses from the high-mannose
oligosaccharide GlcNAc(Man)5(GlcNAc)2 to yield
GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine), which
is the committed step of complex N-glycan synthesis.
GMII is activated by zinc or cobalt ions and is strongly
inhibited by swainsonine. Inhibition of GMII provides a
route to block cancer-induced changes in cell surface
oligosaccharide structures. GMII has a pH optimum of
5.5-6.0, which is intermediate between those of acidic
(lysosomal alpha-mannosidase) and neutral (ER/cytosolic
alpha-mannosidase) enzymes. GMII is a retaining glycosyl
hydrolase of family GH38 that employs a two-step
mechanism involving the formation of a covalent glycosyl
enzyme complex; two carboxylic acids positioned within
the active site act in concert: one as a catalytic
nucleophile and the other as a general acid/base
catalyst. This subfamily also includes human
alpha-mannosidase 2x (MX, also known as
mannosyl-oligosaccharide 1,3- 1,6-alpha mannosidase, EC
3.2.1.114, Man2A2). MX is enzymatically and functionally
very similar to GMII, and is thought to also function in
the N-glycosylation pathway. Also found in this
subfamily is class II alpha-mannosidase encoded by
Spodoptera frugiperda Sf9 cell. This alpha-mannosidase
is an integral membrane glycoprotein localized in the
Golgi apparatus. It shows high sequence homology with
mammalian Golgi alpha-mannosidase II(GMII). It can
hydrolyze p-nitrophenyl alpha-D-mannopyranoside
(pNP-alpha-Man), and it is inhibited by swainsonine.
However, the Sf9 enzyme is stimulated by cobalt and can
hydrolyze (Man)5(GlcNAc)2 to (Man)3(GlcNAc)2, but it
cannot hydrolyze GlcNAc(Man)5(GlcNAc)2, which is
distinct from that of GMII. Thus, this enzyme has been
designated as Sf9 alpha-mannosidase III (SfManIII). It
probably functions in an alternate N-glycan processing
pathway in Sf9 cells.
Length = 340
Score = 28.0 bits (63), Expect = 7.7
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 46 RYLTKIRELDVLYQSYMKEIEHIASQNGNKID-QF 79
RY E D Y +Y K ++I S ++ QF
Sbjct: 264 RY-DSDEEWDAQYDNYQKLFDYINSNPELNVEIQF 297
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 27.9 bits (62), Expect = 8.3
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 162 APKKRQRKKNTE--VDSEMIECSSTPLPRSSATIAVVKKPSTQSGGKKKKRKTKQQRECE 219
APKK KK T+ +SE E + + +A V KP ++G KKK +++E E
Sbjct: 1201 APKKPAPKKTTKKASESETTEETYGSSAMETENVAEVVKPKGRAGAKKKAPAAAKEKEEE 1260
Query: 220 KE 221
E
Sbjct: 1261 DE 1262
>gnl|CDD|168145 PRK05639, PRK05639, 4-aminobutyrate aminotransferase; Provisional.
Length = 457
Score = 27.6 bits (61), Expect = 9.5
Identities = 11/37 (29%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 84 NLLRVQVALIAAQEIGDEKLSIMQQ-VQDVIEGKTRQ 119
N++R+ L+ +EI ++ L IM++ ++D + GK +
Sbjct: 415 NVIRITPPLVITKEIAEKGLEIMERAIKDALAGKVER 451
>gnl|CDD|217884 pfam04086, SRP-alpha_N, Signal recognition particle, alpha subunit,
N-terminal. SRP is a complex of six distinct
polypeptides and a 7S RNA that is essential for
transferring nascent polypeptide chains that are
destined for export from the cell to the translocation
apparatus of the endoplasmic reticulum (ER) membrane.
SRP binds hydrophobic signal sequences as they emerge
from the ribosome, and arrests translation.
Length = 272
Score = 27.4 bits (61), Expect = 9.7
Identities = 18/108 (16%), Positives = 29/108 (26%), Gaps = 2/108 (1%)
Query: 104 SIMQQVQDVIEGKTRQIDGIFYNLPSVTSRREQEAVETSVKHDEAVSTEKTQQSETPVAP 163
M+ ++ + K I +R+Q S T S P P
Sbjct: 109 KAMRTFEESKKSKKTVDSMIERKPKEPGLKRKQRKKAQESATSPESSPSSTPNSSRPSTP 168
Query: 164 KKRQRKKNTEVDSEMIECSSTPLPRSSATIAVVKKPSTQSGGKKKKRK 211
+ K+ ++ SS K + KK RK
Sbjct: 169 HLLKAKEGPSRRAKKAA--KLSSTASSGDEKSPKSKAAPKKAGKKMRK 214
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 0.127 0.362
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,395,740
Number of extensions: 1422730
Number of successful extensions: 1594
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1572
Number of HSP's successfully gapped: 82
Length of query: 317
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 220
Effective length of database: 6,635,264
Effective search space: 1459758080
Effective search space used: 1459758080
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 (26.5 bits)