RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14657
(605 letters)
>gnl|CDD|214614 smart00317, SET, SET (Su(var)3-9, Enhancer-of-zeste, Trithorax)
domain. Putative methyl transferase, based on outlier
plant homologues.
Length = 124
Score = 116 bits (293), Expect = 6e-31
Identities = 46/124 (37%), Positives = 63/124 (50%), Gaps = 14/124 (11%)
Query: 453 PLTIFKTKNNRGWGVRTPDKIKAGTFVCEYVGEILTHENALQRTNQTYCFNLDFNQDSNS 512
L +FK+ +GWGVR + I G F+ EYVGEI+T E A +R D +
Sbjct: 2 KLEVFKSPG-KGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKA-----YDTDGAKAF 55
Query: 513 VAF------VLDAARYGNVSHFINHSCDPNLEVSRINNLNPDLHHVALFAKRDINKNEEL 566
F +DA R GN++ FINHSC+PN E+ + + +FA RDI EEL
Sbjct: 56 YLFDIDSDLCIDARRKGNLARFINHSCEPNCELLFVEVNGD--DRIVIFALRDIKPGEEL 113
Query: 567 SFCY 570
+ Y
Sbjct: 114 TIDY 117
>gnl|CDD|216155 pfam00856, SET, SET domain. SET domains are protein lysine
methyltransferase enzymes. SET domains appear to be
protein-protein interaction domains. It has been
demonstrated that SET domains mediate interactions with
a family of proteins that display similarity with
dual-specificity phosphatases (dsPTPases). A subset of
SET domains have been called PR domains. These domains
are divergent in sequence from other SET domains, but
also appear to mediate protein-protein interaction. The
SET domain consists of two regions known as SET-N and
SET-C. SET-C forms an unusual and conserved knot-like
structure of probably functional importance.
Additionally to SET-N and SET-C, an insert region
(SET-I) and flanking regions of high structural
variability form part of the overall structure.
Length = 113
Score = 107 bits (269), Expect = 7e-28
Identities = 37/114 (32%), Positives = 50/114 (43%), Gaps = 9/114 (7%)
Query: 464 GWGVRTPDKIKAGTFVCEYVGEILTHENALQRTNQTYCFNLDFNQDSNSVAF-------V 516
G G+ I G + EYVGE++T E A +R L +
Sbjct: 1 GRGLFATRDIPKGELIIEYVGELITPEEAEERELLYNKEELRGLLSDLELFLSRLDSEYD 60
Query: 517 LDAARYGNVSHFINHSCDPNLEVSRINNLNPDLHHVALFAKRDINKNEELSFCY 570
+DA GNV+ FINHSC+PN EV + + + A RDI EEL+ Y
Sbjct: 61 IDATGLGNVARFINHSCEPNCEVRFVF--VNGGDRIVVRALRDIKPGEELTIDY 112
>gnl|CDD|218393 pfam05033, Pre-SET, Pre-SET motif. This protein motif is a zinc
binding motif. It contains 9 conserved cysteines that
coordinate three zinc ions. It is thought that this
region plays a structural role in stabilising SET
domains.
Length = 103
Score = 102 bits (255), Expect = 5e-26
Identities = 38/95 (40%), Positives = 55/95 (57%), Gaps = 2/95 (2%)
Query: 88 RLTLENNFDLESPPMDFTYIPSSVPRDGVV-VTDDPVIWCECRGNCVSNRDACCSDLNDA 146
+ + N DLE PP +FTYI +P GV + ++ ++ C C+ C + + C LN
Sbjct: 10 PIPVVNEVDLEGPPPNFTYINEYIPGSGVSDIPNEFLVGCSCKDGCPDSSNCACLQLNGG 69
Query: 147 DFAYSRRTKRLKLEKGTPIYECNKKCACDETCLNR 181
FAY + RL++E G PIYECN +C CD +C NR
Sbjct: 70 GFAYDK-NGRLRVEPGPPIYECNSRCKCDPSCPNR 103
Score = 102 bits (255), Expect = 5e-26
Identities = 38/95 (40%), Positives = 55/95 (57%), Gaps = 2/95 (2%)
Query: 351 RLTLENNFDLESPPMDFTYIPSSVPRDGVV-VTDDPVIWCECRGNCVSNRDACCSDLNDA 409
+ + N DLE PP +FTYI +P GV + ++ ++ C C+ C + + C LN
Sbjct: 10 PIPVVNEVDLEGPPPNFTYINEYIPGSGVSDIPNEFLVGCSCKDGCPDSSNCACLQLNGG 69
Query: 410 DFAYSRRTKRLKLEKGTPIYECNKKCACDETCLNR 444
FAY + RL++E G PIYECN +C CD +C NR
Sbjct: 70 GFAYDK-NGRLRVEPGPPIYECNSRCKCDPSCPNR 103
>gnl|CDD|225491 COG2940, COG2940, Proteins containing SET domain [General function
prediction only].
Length = 480
Score = 94.5 bits (235), Expect = 2e-20
Identities = 60/243 (24%), Positives = 94/243 (38%), Gaps = 14/243 (5%)
Query: 368 TYIPSSVPRDGVVVTDDPVIWCECRGNCVSNRD-------ACCSDLNDADFAYSRRTKRL 420
+ PS +PR T D + G + C L A + R +
Sbjct: 241 STFPSPIPRLANTSTIDETKDSKPYGEIRISESLSPNFLEGCSPLLCSASPSAINRISKS 300
Query: 421 KLEKGTPIYECNKKCACDETCLNRVVQKGITLPLTIFKTKNNRGWGVRTPDKIKAGTFVC 480
+ + T + + LN K P + +++ +G+GV + IK G F+
Sbjct: 301 EEDSTTSSDFSKSNVSKLKELLNSNGCKKRREPNVVQESEI-KGYGVFALESIKKGEFII 359
Query: 481 EYVGEILTHENALQRTNQTYCFN--LDFNQDSNSVAFVLDAARYGNVSHFINHSCDPNLE 538
EY GEI+ + A +R F V D+ + G+V+ FINHSC PN E
Sbjct: 360 EYHGEIIRRKEAREREENYDLLGNEFSFGLLE-DKDKVRDSQKAGDVARFINHSCTPNCE 418
Query: 539 VSRINNLNPDLHHVALFAKRDINKNEELSFCYLDLTKAKFTSSKRKKLVRNECRCGSSNC 598
S I + ++++A RDI EEL++ Y + K+ R C CG C
Sbjct: 419 ASPIEVN--GIFKISIYAIRDIKAGEELTYDY-GPSLEDNRELKKLLEKRWGCACGEDRC 475
Query: 599 LGY 601
Sbjct: 476 SHT 478
>gnl|CDD|128744 smart00468, PreSET, N-terminal to some SET domains. A Cys-rich
putative Zn2+-binding domain that occurs N-terminal to
some SET domains. Function is unknown. Unpublished.
Length = 98
Score = 67.8 bits (166), Expect = 5e-14
Identities = 30/87 (34%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 88 RLTLENNFDLESPPMDFTYIPSSVPRDGVV--VTDDPVIWCECRGNCVSNRDACCSDLND 145
+ L N D + PP DF YI + GV + P++ C C G+C S+ C+ N
Sbjct: 12 PVPLVNEVDEDPPPPDFEYISEYIYGQGVPIDRSPSPLVGCSCSGDCSSSNKCECARKNG 71
Query: 146 ADFAYSRRTKRLKLEKGTPIYECNKKC 172
+FAY L+L++ IYECN +C
Sbjct: 72 GEFAYE-LNGGLRLKRKPLIYECNSRC 97
Score = 67.8 bits (166), Expect = 5e-14
Identities = 30/87 (34%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 351 RLTLENNFDLESPPMDFTYIPSSVPRDGVV--VTDDPVIWCECRGNCVSNRDACCSDLND 408
+ L N D + PP DF YI + GV + P++ C C G+C S+ C+ N
Sbjct: 12 PVPLVNEVDEDPPPPDFEYISEYIYGQGVPIDRSPSPLVGCSCSGDCSSSNKCECARKNG 71
Query: 409 ADFAYSRRTKRLKLEKGTPIYECNKKC 435
+FAY L+L++ IYECN +C
Sbjct: 72 GEFAYE-LNGGLRLKRKPLIYECNSRC 97
>gnl|CDD|237991 cd00024, CHROMO, Chromatin organization modifier (chromo) domain is
a conserved region of around 50 amino acids found in a
variety of chromosomal proteins, which appear to play a
role in the functional organization of the eukaryotic
nucleus. Experimental evidence implicates the chromo
domain in the binding activity of these proteins to
methylated histone tails and maybe RNA. May occur as
single instance, in a tandem arrangement or followd by a
related "chromo shadow" domain.
Length = 55
Score = 64.2 bits (157), Expect = 3e-13
Identities = 25/54 (46%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 222 TEYEVESVLDSLELTSDMTV-YLVKWKNYDPEYNTWEPIENLGNCAKKLAEFLK 274
EYEVE +LD + YLVKWK Y +TWEP ENL +C + + EF K
Sbjct: 1 EEYEVEKILDHRKKKDGGEYEYLVKWKGYSYSEDTWEPEENLEDCKELIDEFKK 54
>gnl|CDD|214605 smart00298, CHROMO, Chromatin organization modifier domain.
Length = 55
Score = 63.4 bits (155), Expect = 5e-13
Identities = 27/52 (51%), Positives = 31/52 (59%)
Query: 223 EYEVESVLDSLELTSDMTVYLVKWKNYDPEYNTWEPIENLGNCAKKLAEFLK 274
EYEVE +LD YLVKWK Y +TWEP ENL NC+KKL + K
Sbjct: 1 EYEVEKILDHRWKKKGELEYLVKWKGYSYSEDTWEPEENLLNCSKKLDNYKK 52
>gnl|CDD|215889 pfam00385, Chromo, Chromo (CHRromatin Organisation MOdifier)
domain.
Length = 52
Score = 59.1 bits (144), Expect = 2e-11
Identities = 21/47 (44%), Positives = 25/47 (53%)
Query: 225 EVESVLDSLELTSDMTVYLVKWKNYDPEYNTWEPIENLGNCAKKLAE 271
EVE +LD YLVKWK Y + TWEP ENL C +L +
Sbjct: 1 EVERILDHRLRKGGNKEYLVKWKGYPYDEATWEPEENLKACFPELIQ 47
>gnl|CDD|176962 CHL00019, atpF, ATP synthase CF0 B subunit.
Length = 184
Score = 32.1 bits (74), Expect = 0.42
Identities = 14/31 (45%), Positives = 15/31 (48%), Gaps = 3/31 (9%)
Query: 65 RKQQ-LANIREAEERYNAACE--TAARLTLE 92
RKQ L IR +EER A E AR L
Sbjct: 56 RKQTILNTIRNSEERREEAIEKLEKARARLR 86
Score = 32.1 bits (74), Expect = 0.42
Identities = 14/31 (45%), Positives = 15/31 (48%), Gaps = 3/31 (9%)
Query: 328 RKQQ-LANIREAEERYNAACE--TAARLTLE 355
RKQ L IR +EER A E AR L
Sbjct: 56 RKQTILNTIRNSEERREEAIEKLEKARARLR 86
>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Flap endonuclease-1 (FEN1) is
involved in multiple DNA metabolic pathways, including
DNA replication processes (5' flap DNA endonuclease
activity and double stranded DNA 5'-exonuclease
activity) and DNA repair processes (long-patch base
excision repair) in eukaryotes and archaea. Interaction
between FEN1 and PCNA (Proliferating cell nuclear
antigen) is an essential prerequisite to FEN1's DNA
replication functionality and stimulates FEN1 nuclease
activity by 10-50 fold. FEN1 belongs to the
FEN1-EXO1-like family of structure-specific, 5'
nucleases. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 45 residues in
FEN1 PIN domains) and a H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region.
Both the H3TH domain (not included here) and the helical
arch/clamp region are involved in DNA binding. Nucleases
within this group also have a carboxylate-rich active
site that is involved in binding essential divalent
metal ion cofactors (Mg2+/Mn2+). FEN1 has a C-terminal
extension containing residues forming the consensus
PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1
to PCNA.
Length = 261
Score = 30.9 bits (71), Expect = 1.6
Identities = 29/112 (25%), Positives = 40/112 (35%), Gaps = 45/112 (40%)
Query: 201 GSVVLLRVADINLTKFSSDTM--TEYEVESVLDSLELTSDMTVYLVKWKNYDPEYNTWEP 258
G+ L+R NLT + E E+E VL+ LEL KWK D E
Sbjct: 181 GAPRLVR----NLTISGKKKVPPEEIELEKVLEELEL---------KWKEPDEE------ 221
Query: 259 IENLGNCAKKLAEFLKAGPDQERTDFEKMKSFLSQHTEEEVESVLAKLRNKK 310
L +FL E DF +E+ V + +L+ K
Sbjct: 222 ---------GLIKFL-----VEEHDF----------SEDRVRKAIERLKKAK 249
>gnl|CDD|165114 PHA02747, PHA02747, protein tyrosine phosphatase; Provisional.
Length = 312
Score = 31.1 bits (70), Expect = 1.7
Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 435 CACDETCLNRVV-QKGITLPLTIFKTKNNRGWGVRTPDK---IKAGTFVCEY 482
CA D CLN++V +K I L T K + R G+ D I+ G V Y
Sbjct: 247 CAVD-ICLNQLVKRKAICLAKTAEKIREQRHAGIMNFDDYLFIQPGYEVLHY 297
>gnl|CDD|236875 PRK11189, PRK11189, lipoprotein NlpI; Provisional.
Length = 296
Score = 29.9 bits (68), Expect = 3.4
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 11/69 (15%)
Query: 290 FLSQHTEEEV-ESVLAKLRNKKDFAYAHMLLLTHFLHGKRKQQLANIREAEERYNAACET 348
+L + +EE + E + A + A L T+F K L ++ EA +
Sbjct: 208 YLGKISEETLMERLKAGATDNT--ELAERLCETYFYLAKYYLSLGDLDEAAALF------ 259
Query: 349 AARLTLENN 357
+L L NN
Sbjct: 260 --KLALANN 266
Score = 29.1 bits (66), Expect = 7.4
Identities = 15/58 (25%), Positives = 21/58 (36%), Gaps = 13/58 (22%)
Query: 42 LLSSAKDFA-----YAHMLLLTHFLHGKRKQQLANIREAEERYNAACETAARLTLENN 94
L+ K A A L T+F K L ++ EA + +L L NN
Sbjct: 217 LMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALF--------KLALANN 266
>gnl|CDD|130833 TIGR01772, MDH_euk_gproteo, malate dehydrogenase, NAD-dependent.
This model represents the NAD-dependent malate
dehydrogenase found in eukaryotes and certain gamma
proteobacteria. The enzyme is involved in the citric
acid cycle as well as the glyoxalate cycle. Several
isoforms exidt in eukaryotes. In S. cereviseae, for
example, there are cytoplasmic, mitochondrial and
peroxisomal forms. Although malate dehydrogenases have
in some cases been mistaken for lactate dehydrogenases
due to the similarity of these two substrates and the
apparent ease with which evolution can toggle these
activities, critical residues have been identified which
can discriminate between the two activities. At the time
of the creation of this model no hits above the trusted
cutoff contained critical residues typical of lactate
dehydrogenases [Energy metabolism, TCA cycle].
Length = 312
Score = 29.7 bits (67), Expect = 4.1
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 13/68 (19%)
Query: 436 ACDETCLNRVVQKGITLPL--------TIFKTKN----NRGWGVRTPDKIKAGTFVCEYV 483
A E+C ++ IT P+ + K K N+ +GV T D ++A TFV E
Sbjct: 102 AVAESCPKAMILV-ITNPVNSTVPIAAEVLKKKGVYDPNKLFGVTTLDIVRANTFVAELK 160
Query: 484 GEILTHEN 491
G+ N
Sbjct: 161 GKDPMEVN 168
>gnl|CDD|214703 smart00508, PostSET, Cysteine-rich motif following a subset of SET
domains.
Length = 17
Score = 25.8 bits (58), Expect = 5.9
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 590 ECRCGSSNCLGY 601
C CG+ NC G+
Sbjct: 4 PCLCGAPNCRGF 15
>gnl|CDD|236280 PRK08515, flgA, flagellar basal body P-ring biosynthesis protein
FlgA; Reviewed.
Length = 222
Score = 29.2 bits (66), Expect = 5.9
Identities = 15/67 (22%), Positives = 20/67 (29%), Gaps = 16/67 (23%)
Query: 502 FNLDFNQ-DSNSVAFVLDAARYGNVSHFINHSCDPNLEVSRINNLNPDLHHVALFAKRDI 560
FN A N F +S NLEV L + R I
Sbjct: 65 ELNAFNSLKGFGRASFKTPNNP-NKKLFFRYSIIANLEV--------------LKSIRAI 109
Query: 561 NKNEELS 567
K++ L+
Sbjct: 110 KKDDNLT 116
>gnl|CDD|153351 cd07667, BAR_SNX30, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 30. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. The specific function of SNX30 is
still unknown. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 240
Score = 28.8 bits (64), Expect = 7.0
Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 19/78 (24%)
Query: 242 YLVKWKNYDPEYNTW--------EPIENLGNCAKKLAEFLKAGPDQERTDF--------- 284
YLV+ + Y P Y+TW EP+E + C + L+ + DF
Sbjct: 84 YLVELREYGPVYSTWSGLEGELAEPLEGVSACIGNCSTALEELTEDMTEDFLPVLREYIL 143
Query: 285 --EKMKSFLSQHTEEEVE 300
E MK+ L + + + E
Sbjct: 144 YSESMKNVLKKRDQVQAE 161
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
0.319 0.133 0.407
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,812,530
Number of extensions: 2829587
Number of successful extensions: 2663
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2644
Number of HSP's successfully gapped: 28
Length of query: 605
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 502
Effective length of database: 6,369,140
Effective search space: 3197308280
Effective search space used: 3197308280
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 (21.8 bits)
S2: 62 (27.5 bits)