RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6883
(414 letters)
>gnl|CDD|189470 pfam00250, Fork_head, Fork head domain.
Length = 96
Score = 192 bits (490), Expect = 4e-61
Identities = 68/96 (70%), Positives = 79/96 (82%)
Query: 145 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 204
KPPYSYIALITMAI QSP K LTLS I ++IM FPYYR+ WQNSIRHNLSLN CF+
Sbjct: 1 KPPYSYIALITMAIQQSPEKMLTLSEIYQWIMDLFPYYRQNKQGWQNSIRHNLSLNKCFI 60
Query: 205 KIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 240
K+PR P PGKG+YWTLDP +E+MF+NG +L+RRKR
Sbjct: 61 KVPRSPDKPGKGSYWTLDPESENMFENGKYLKRRKR 96
>gnl|CDD|214627 smart00339, FH, FORKHEAD. FORKHEAD, also known as a "winged
helix".
Length = 89
Score = 169 bits (431), Expect = 2e-52
Identities = 65/89 (73%), Positives = 73/89 (82%)
Query: 145 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 204
KPPYSYIALI MAIL SP K+LTLS I ++I FPYYRE WQNSIRHNLSLNDCFV
Sbjct: 1 KPPYSYIALIAMAILSSPDKRLTLSEIYKWIEDNFPYYRENRAGWQNSIRHNLSLNDCFV 60
Query: 205 KIPREPGNPGKGNYWTLDPMAEDMFDNGS 233
K+PRE PGKG+YWTLDP AE+MF+NG+
Sbjct: 61 KVPREGDRPGKGSYWTLDPAAENMFENGN 89
>gnl|CDD|238016 cd00059, FH, Forkhead (FH), also known as a "winged helix". FH is
named for the Drosophila fork head protein, a
transcription factor which promotes terminal rather than
segmental development. This family of transcription
factor domains, which bind to B-DNA as monomers, are
also found in the Hepatocyte nuclear factor (HNF)
proteins, which provide tissue-specific gene regulation.
The structure contains 2 flexible loops or "wings" in
the C-terminal region, hence the term winged helix.
Length = 78
Score = 167 bits (426), Expect = 7e-52
Identities = 54/78 (69%), Positives = 61/78 (78%)
Query: 145 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 204
KPPYSY ALI MAI SP K+LTLS I ++I FPY+R+ WQNSIRHNLSLN CFV
Sbjct: 1 KPPYSYSALIAMAIQSSPEKRLTLSEIYKWISDNFPYFRDAPAGWQNSIRHNLSLNKCFV 60
Query: 205 KIPREPGNPGKGNYWTLD 222
K+PREP PGKG+YWTLD
Sbjct: 61 KVPREPDEPGKGSYWTLD 78
>gnl|CDD|227358 COG5025, COG5025, Transcription factor of the Forkhead/HNF3 family
[Transcription].
Length = 610
Score = 101 bits (252), Expect = 4e-23
Identities = 64/183 (34%), Positives = 82/183 (44%), Gaps = 10/183 (5%)
Query: 58 NLSSPSPSSEDDSDADINVESDDGDEQGMKSDDGDEQGMSNVRRNIAEFHKHFSNCESDV 117
L + S E+ S + + + D S S + N E K S
Sbjct: 258 VLDNHSSGEENISRINNSSQIDSPTPNYRMSSIDSSVNPSRLANNKDEGRK-----GSKS 312
Query: 118 NGCPTDGSISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMS 177
+ P D + P D + S KP +SY IT AIL SP K+TLS I +I S
Sbjct: 313 SPVPKDAA-PPSTLSDLSADVNRTS--KPAFSYANSITQAILSSPSGKMTLSEIYSWISS 369
Query: 178 RFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRR 237
PYYR K AWQNSIRHNLSLN F K+PR PGKG +W +D +++ S
Sbjct: 370 NLPYYRHKPTAWQNSIRHNLSLNKSFEKVPRSASQPGKGCFWKIDY--SYIYEKESKRNP 427
Query: 238 RKR 240
R
Sbjct: 428 RSP 430
Score = 76.0 bits (187), Expect = 8e-15
Identities = 43/85 (50%), Positives = 52/85 (61%)
Query: 145 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 204
PPYSY +AIL SP K LTLS I +I + F YY + WQNSIRHNLSLND F+
Sbjct: 86 VPPYSYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLNDAFI 145
Query: 205 KIPREPGNPGKGNYWTLDPMAEDMF 229
KI G KG++W++ P E F
Sbjct: 146 KIEGRNGAKVKGHFWSIGPGHETQF 170
>gnl|CDD|189050 cd09880, PIN_Smg5-Smg6-like, PIN domain. PIN (PilT N terminus)
domain of nonsense-mediated decay (NMD) factors, Smg5
and Smg6, and homologs are included in this family. Smg5
and Smg6 are essential factors in NMD, a
post-transcriptional regulatory pathway that recognizes
and rapidly degrades mRNAs containing premature
translation termination codons. In vivo, the Smg6 PIN
domain elicits degradation of bound mRNAs, as well as,
metal-ion dependent, degradation of single-stranded RNA,
in vitro. These PIN domains are structural homologs of
flap endonuclease-1 (FEN1)-like PIN domains, but lack
the extensive arch/clamp region and the H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like PIN
domains. Point mutation studies of the conserved
aspartate residues in the catalytic center of the Smg6
PIN domain revealed that Smg6 is the endonuclease
involved in human NMD. However, Smg5 lacks several of
these key catalytic residues and does not degrade
single-stranded RNA, in vivo. Eukaryotic Smg5 and
Smg6-like PIN domains are present at the C-terminal end
of telomerase activating proteins, Est1. Many of the
bacterial homologs in this group have an N-terminal PIN
domain and a C-terminal PhoH-like ATPase domain.
Length = 139
Score = 31.5 bits (72), Expect = 0.34
Identities = 12/61 (19%), Positives = 18/61 (29%), Gaps = 3/61 (4%)
Query: 85 GMKSDDGDEQGMSNVRRNIAEFHKHFSNCESDVNGCPTDGSISPGPEGDSDKQDGKNSIV 144
G+K E G RR I + + G S+ D D + I+
Sbjct: 39 GLKKSPRRELGH-LARRAIRFLEDALKKGDPRLRGQTLTESLLALDGFDKRSND--DRIL 95
Query: 145 K 145
Sbjct: 96 D 96
>gnl|CDD|223764 COG0692, Ung, Uracil DNA glycosylase [DNA replication,
recombination, and repair].
Length = 223
Score = 31.8 bits (73), Expect = 0.51
Identities = 23/64 (35%), Positives = 26/64 (40%), Gaps = 23/64 (35%)
Query: 262 LGSDPYH-----HGLLPHSLQHGGFSFMSPLPPAVPLLPPSELARIQLGLNLLSNQSLPC 316
LG DPYH HGL FS +PP V +PPS L I L L
Sbjct: 61 LGQDPYHGPGQAHGL--------SFS----VPPGVK-IPPS-LKNIYKEL----EADLGG 102
Query: 317 KPVP 320
P+P
Sbjct: 103 FPIP 106
>gnl|CDD|177447 PHA02664, PHA02664, hypothetical protein; Provisional.
Length = 534
Score = 31.9 bits (72), Expect = 0.67
Identities = 16/63 (25%), Positives = 24/63 (38%)
Query: 32 SPLDLRGAPHPGDMYLRGAPHPGDMCNLSSPSPSSEDDSDADINVESDDGDEQGMKSDDG 91
+ A P D + H + +P+ + DSD D E + GDE+ DD
Sbjct: 414 AAAAAAAANAPADQDVEAEAHDEFDQDPGAPAHADRADSDEDDMDEQESGDERADGEDDS 473
Query: 92 DEQ 94
D
Sbjct: 474 DSS 476
>gnl|CDD|131353 TIGR02300, FYDLN_acid, TIGR02300 family protein. Members of this
family are bacterial proteins with a conserved motif
[KR]FYDLN, sometimes flanked by a pair of CXXC motifs,
followed by a long region of low complexity sequence in
which roughly half the residues are Asp and Glu,
including multiple runs of five or more acidic residues.
The function of members of this family is unknown.
Length = 129
Score = 30.0 bits (67), Expect = 1.0
Identities = 9/42 (21%), Positives = 22/42 (52%)
Query: 58 NLSSPSPSSEDDSDADINVESDDGDEQGMKSDDGDEQGMSNV 99
+ +P+P+ DD D ++ DD D ++ ++ D+ ++
Sbjct: 82 DPGAPTPAGGDDLAEDEDIADDDDDVTFLEDEEDDDIDDEDI 123
>gnl|CDD|227326 COG4993, Gcd, Glucose dehydrogenase [Carbohydrate transport and
metabolism].
Length = 773
Score = 30.5 bits (69), Expect = 2.0
Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 13/83 (15%)
Query: 210 PGNPGKGNYWTL--DPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASFLGSDPY 267
PGN G N+ + DP+ + F N +L + P RDP M + D
Sbjct: 569 PGNHGMFNWGGVSVDPVRQVTFGNPYYLAFVSKL---VP----RDPV-GPMENGAAGDGT 620
Query: 268 HHGLLPHSLQHGGF---SFMSPL 287
G++P+ + G F+SP
Sbjct: 621 EGGVVPNYGEPYGVWMGPFLSPG 643
>gnl|CDD|223433 COG0356, AtpB, F0F1-type ATP synthase, subunit a [Energy production
and conversion].
Length = 246
Score = 29.9 bits (68), Expect = 2.2
Identities = 18/40 (45%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 279 GGF--SFMSPLPPAVPLLPP----SELAR-IQLGLNLLSN 311
GGF F P P PL+ P SELA+ I L L L N
Sbjct: 145 GGFFKEFAFPPFPLAPLMLPLEIVSELAKPISLSLRLFGN 184
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 30.3 bits (69), Expect = 2.2
Identities = 9/47 (19%), Positives = 15/47 (31%), Gaps = 1/47 (2%)
Query: 57 CNLSSPSPSSEDDSDADINVESDDGDEQGMKSDDGDEQGMSNVRRNI 103
+L E+ + D + DE DD D+ + R
Sbjct: 121 RDLEEDDDDDEESDEEDEESSKSEDDEDD-DDDDDDDDIATRERSLE 166
>gnl|CDD|182461 PRK10438, PRK10438, C-N hydrolase family amidase; Provisional.
Length = 256
Score = 28.9 bits (65), Expect = 3.9
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 182 YREKFPAWQNSIRHNL 197
YREKFPAW+++ L
Sbjct: 240 YREKFPAWRDADEFTL 255
>gnl|CDD|220610 pfam10165, Ric8, Guanine nucleotide exchange factor synembryn.
Ric8 is involved in the EGL-30 neurotransmitter
signalling pathway. It is a guanine nucleotide exchange
factor that regulates neurotransmitter secretion.
Length = 439
Score = 29.2 bits (66), Expect = 4.2
Identities = 15/43 (34%), Positives = 17/43 (39%), Gaps = 5/43 (11%)
Query: 286 PLPPAVPLLPPSELARIQLGLNLLSNQSLPCKPVPLTSSSSRN 328
P P PL P +NLLSN L C L+ S N
Sbjct: 187 PTIPEDPLDSPHSHL-----INLLSNLPLECLKSLLSKKFSPN 224
>gnl|CDD|185638 PTZ00459, PTZ00459, mucin-associated surface protein (MASP);
Provisional.
Length = 291
Score = 28.2 bits (62), Expect = 8.1
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 60 SSPSPSSEDDSDADINVESDDGDEQGMKSDDGDEQ 94
S P P+ EDD D D + E D D+ G + D+ +E+
Sbjct: 69 SPPLPTEEDDEDVDDDSEEGDDDDGGAE-DEEEEK 102
>gnl|CDD|227531 COG5206, GPI8, Glycosylphosphatidylinositol transamidase (GPIT),
subunit GPI8 [Posttranslational modification, protein
turnover, chaperones].
Length = 382
Score = 28.4 bits (63), Expect = 8.3
Identities = 34/133 (25%), Positives = 53/133 (39%), Gaps = 22/133 (16%)
Query: 141 NSIVKPPYS--YIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLS 198
N++ YS +A+ + I QS + + S I ++ RF Y+ KF + I L+
Sbjct: 193 NALYDKSYSPNVLAVGSSEIGQSSYSHHSDSLIGVAVIDRFTYFFLKFLE-KIDIGSKLT 251
Query: 199 LNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAM 258
L D + +EP + G + E +FD R P DFL+ D A
Sbjct: 252 LQDLLASLNKEPIHSHVG-------VRELVFD------------RRPSDFLITDFFANVQ 292
Query: 259 ASFLGSDPYHHGL 271
S L H+
Sbjct: 293 NSALELLKSHYHH 305
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
0.314 0.133 0.404
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,153,581
Number of extensions: 2039189
Number of successful extensions: 1370
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1350
Number of HSP's successfully gapped: 36
Length of query: 414
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 315
Effective length of database: 6,546,556
Effective search space: 2062165140
Effective search space used: 2062165140
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: 60 (26.8 bits)