RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7734
(349 letters)
>gnl|CDD|189470 pfam00250, Fork_head, Fork head domain.
Length = 96
Score = 93.5 bits (233), Expect = 7e-24
Identities = 30/50 (60%), Positives = 39/50 (78%)
Query: 103 NSIRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPGSEHKLIEQAFRRRRQR 152
NSIRHNLSLN+ FIKVPRS ++PGKGS+W +DP SE+ + +RR+R
Sbjct: 47 NSIRHNLSLNKCFIKVPRSPDKPGKGSYWTLDPESENMFENGKYLKRRKR 96
Score = 83.9 bits (208), Expect = 3e-20
Identities = 24/46 (52%), Positives = 30/46 (65%)
Query: 290 KPPYSYAQLIVQAVASAHDKQLTLSGIYSFITKNYPYYRTADKGWQ 335
KPPYSY LI A+ + +K LTLS IY +I +PYYR +GWQ
Sbjct: 1 KPPYSYIALITMAIQQSPEKMLTLSEIYQWIMDLFPYYRQNKQGWQ 46
>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 = 81.8 bits (203), Expect = 9e-20
Identities = 26/46 (56%), Positives = 35/46 (76%)
Query: 290 KPPYSYAQLIVQAVASAHDKQLTLSGIYSFITKNYPYYRTADKGWQ 335
KPPYSY+ LI A+ S+ +K+LTLS IY +I+ N+PY+R A GWQ
Sbjct: 1 KPPYSYSALIAMAIQSSPEKRLTLSEIYKWISDNFPYFRDAPAGWQ 46
Score = 68.7 bits (169), Expect = 6e-15
Identities = 23/32 (71%), Positives = 28/32 (87%)
Query: 103 NSIRHNLSLNRYFIKVPRSQEEPGKGSFWRID 134
NSIRHNLSLN+ F+KVPR +EPGKGS+W +D
Sbjct: 47 NSIRHNLSLNKCFVKVPREPDEPGKGSYWTLD 78
>gnl|CDD|214627 smart00339, FH, FORKHEAD. FORKHEAD, also known as a "winged
helix".
Length = 89
Score = 78.4 bits (194), Expect = 2e-18
Identities = 27/46 (58%), Positives = 32/46 (69%)
Query: 290 KPPYSYAQLIVQAVASAHDKQLTLSGIYSFITKNYPYYRTADKGWQ 335
KPPYSY LI A+ S+ DK+LTLS IY +I N+PYYR GWQ
Sbjct: 1 KPPYSYIALIAMAILSSPDKRLTLSEIYKWIEDNFPYYRENRAGWQ 46
Score = 64.6 bits (158), Expect = 2e-13
Identities = 24/41 (58%), Positives = 30/41 (73%)
Query: 103 NSIRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPGSEHKLIE 143
NSIRHNLSLN F+KVPR + PGKGS+W +DP +E+
Sbjct: 47 NSIRHNLSLNDCFVKVPREGDRPGKGSYWTLDPAAENMFEN 87
>gnl|CDD|227358 COG5025, COG5025, Transcription factor of the Forkhead/HNF3 family
[Transcription].
Length = 610
Score = 69.8 bits (171), Expect = 5e-13
Identities = 77/320 (24%), Positives = 108/320 (33%), Gaps = 29/320 (9%)
Query: 35 AIAKLQGREFEYMVRQKRITIGRN-SSRGDVDVNMGLSSFISRRHIEIFFEHPNFFMTCN 93
A AKL G + Y V GR + D + LS + H F+ +
Sbjct: 73 AYAKLAGSNWTYYVPPYSYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKV----VS 128
Query: 94 GKNGVFVDGNSIRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPGSEHKLIEQAFRR----- 148
NSIRHNLSLN FIK+ KG FW I PG E + ++ R
Sbjct: 129 RWQ------NSIRHNLSLNDAFIKIEGRNGAKVKGHFWSIGPGHETQFLKSGLRLDGGGK 182
Query: 149 -----------RRQRGVPCFRAPFGLSSRCTLRFPSTNIRLQFQSLVNESDPA--PTGQS 195
+ P S+ + +S PA +
Sbjct: 183 QMMFTLPSSTEIKITYSSTHSMPLLESNDSLNSNNERELLDIIKSSALIRIPADSSSNLD 242
Query: 196 VSSSGVGVMGNPATSSLLPPLRINIPDHPHTEISSSPFPSPTGTISAANSCPTSPRGLHN 255
VS + T L S P+P +S+ +S R +N
Sbjct: 243 VSLGHHISQPSTHTPVLDNHSSGEENISRINNSSQIDSPTPNYRMSSIDSSVNPSRLANN 302
Query: 256 RRNVSADLHMAAHYAAAHTNVVNHMSLSISQDDSKPPYSYAQLIVQAVASAHDKQLTLSG 315
+ + A + SKP +SYA I QA+ S+ ++TLS
Sbjct: 303 KDEGRKGSKSSPVPKDAAPPSTLSDLSADVNRTSKPAFSYANSITQAILSSPSGKMTLSE 362
Query: 316 IYSFITKNYPYYRTADKGWQ 335
IYS+I+ N PYYR WQ
Sbjct: 363 IYSWISSNLPYYRHKPTAWQ 382
Score = 54.4 bits (131), Expect = 4e-08
Identities = 49/226 (21%), Positives = 68/226 (30%), Gaps = 37/226 (16%)
Query: 103 NSIRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPGSEHKLIEQAFRRRRQRG--------- 153
NSIRHNLSLN+ F KVPRS +PGKG FW+ID ++ + R ++
Sbjct: 383 NSIRHNLSLNKSFEKVPRSASQPGKGCFWKIDYSYIYEKESKRNPRSPKKSPSAHSVHQK 442
Query: 154 ----------VPCFRAPFGLSSRCTLRFPSTNIRLQFQSLVNESDPAPTGQSVSSSGVGV 203
P SS+ I Q S + S
Sbjct: 443 LSLHVNDLYQSPATSDIASSSSQVNS--QPEFISTQIHSS-KGVSNVDLTEQDSQKEAS- 498
Query: 204 MGNPATSSLLPPLRINIPDHPHTEISSSPFPSPTGTISAANSCPTSPRGLHNRRNVSADL 263
GN S N EI+S + + S N
Sbjct: 499 KGNFLDDSGSLSPNTN-------EINSFSLNTTDSQQKQS----PSHNAPTNNSLNEMAS 547
Query: 264 HMAAHYAAAHTNVVNHMSLSISQDDSK---PPYSYAQLIVQAVASA 306
+ A + N ++ D S PY +Q A+
Sbjct: 548 KNSNSQTQASNSNENVAAVKAILDASAQMEKPYDLSQAATPTKATE 593
>gnl|CDD|238017 cd00060, FHA, Forkhead associated domain (FHA); found in eukaryotic
and prokaryotic proteins. Putative nuclear signalling
domain. FHA domains may bind phosphothreonine,
phosphoserine and sometimes phosphotyrosine. In
eukaryotes, many FHA domain-containing proteins localize
to the nucleus, where they participate in establishing
or maintaining cell cycle checkpoints, DNA repair, or
transcriptional regulation. Members of the FHA family
include: Dun1, Rad53, Cds1, Mek1,
KAPP(kinase-associated protein phosphatase),and Ki-67 (a
human nuclear protein related to cell proliferation).
Length = 102
Score = 54.3 bits (131), Expect = 2e-09
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 5/65 (7%)
Query: 46 YMVRQKRITIGRNSSRGDVDVNMGLSSFISRRHIEIFFEHPN--FFMTCNGKNGVFVDGN 103
Y+ TIGR+S D+ ++ +SRRH I ++ + NG FV+G
Sbjct: 17 YLDPGGTYTIGRDSDNCDIVLD---DPSVSRRHAVIRYDGDGGVVLIDLGSTNGTFVNGQ 73
Query: 104 SIRHN 108
+
Sbjct: 74 RVSPG 78
>gnl|CDD|214578 smart00240, FHA, Forkhead associated domain. Found in eukaryotic
and prokaryotic proteins. Putative nuclear signalling
domain.
Length = 52
Score = 43.7 bits (104), Expect = 3e-06
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 5/55 (9%)
Query: 53 ITIGRNSSRGDVDVNMGLSSFISRRHIEIFFE-HPNFFMTCNG-KNGVFVDGNSI 105
+TIGR+S D+ ++ ISRRH I ++ F++ G NG FV+G I
Sbjct: 1 VTIGRSSEDCDIQLD---GPSISRRHAVIVYDGGGRFYLIDLGSTNGTFVNGKRI 52
>gnl|CDD|215951 pfam00498, FHA, FHA domain. The FHA (Forkhead-associated) domain
is a phosphopeptide binding motif.
Length = 67
Score = 43.0 bits (102), Expect = 6e-06
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 53 ITIGRNSSRGDVDVNMGLSSFISRRHIEIFF-EHPNFFMT-CNGKNGVFVDGNSIRHN 108
+TIGR+ D D+ + +SRRH EI + F++ NG FV+G +
Sbjct: 1 VTIGRSP---DCDIVLD-DPSVSRRHAEIRYDGGGRFYLEDLGSTNGTFVNGQRLGPE 54
>gnl|CDD|224630 COG1716, COG1716, FOG: FHA domain [Signal transduction mechanisms].
Length = 191
Score = 33.4 bits (76), Expect = 0.090
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 53 ITIGRNSSRGDVDVNMGLSS-FISRRHIEIFFEHPNFFMTCNG-KNGVFVDGNSIRH 107
TIGR D D ++ L +SRRH E+ E F+ G NG +V+G +R
Sbjct: 91 TTIGR-----DPDNDIVLDDDVVSRRHAELRREGNEVFLEDLGSTNGTYVNGEKVRQ 142
>gnl|CDD|227907 COG5620, COG5620, Uncharacterized conserved protein [Function
unknown].
Length = 200
Score = 32.5 bits (74), Expect = 0.19
Identities = 11/37 (29%), Positives = 15/37 (40%)
Query: 126 GKGSFWRIDPGSEHKLIEQAFRRRRQRGVPCFRAPFG 162
G +W DP +IE ++ R VP FG
Sbjct: 59 SDGQYWICDPSIFQPVIEMSYFRDATVSVPIGYTAFG 95
>gnl|CDD|116868 pfam08284, RVP_2, Retroviral aspartyl protease. Single domain
aspartyl proteases from retroviruses, retrotransposons,
and badnaviruses (plant dsDNA viruses). These proteases
are generally part of a larger polyprotein; usually pol,
more rarely gag. Retroviral proteases appear to be
homologous to a single domain of the two-domain
eukaryotic aspartyl proteases.
Length = 135
Score = 29.7 bits (67), Expect = 0.94
Identities = 18/51 (35%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 134 DPGSEHKLIEQAFRRRRQRGVPCFRAPF-----GLSSRCTLRFPSTNIRLQ 179
D G+ H I QAF R + R P G T R PS NI +Q
Sbjct: 38 DSGASHSFISQAFVGRHGLPLEALRTPMLVHSPGGDMTATHRCPSVNIEIQ 88
>gnl|CDD|225987 COG3456, COG3456, Predicted component of the type VI protein
secretion system, contains a FHA domain [Intracellular
trafficking, secretion, and vesicular transport;
Signal transduction mechanisms].
Length = 430
Score = 30.5 bits (69), Expect = 1.3
Identities = 42/198 (21%), Positives = 72/198 (36%), Gaps = 31/198 (15%)
Query: 73 FISRRHIEIFFEHPNFFMTCNGKNGVFVDGNSIRHN-----------LSLNRYFIKVPRS 121
F+S++H I + F +T G+ V+G+ + + + RY I+V S
Sbjct: 46 FVSKQHCTISYRDGGFCLTDTSNGGLLVNGSDLPLGEGSARLQQGDEILIGRYIIRVHLS 105
Query: 122 QEEPGKG--------SFWRIDPGSEHKLIEQAFRRRRQRGVPCFRAPFGLSSRC-TLRFP 172
+ EP + S + L A R P P L+
Sbjct: 106 RAEPDESDPDTGSPQSAVSSTDMDDDFL---ADIEPEPRLPPGLTDPLQLADPVPNGFSA 162
Query: 173 STNIRLQFQSLVNESDPAPTGQSVSSSGVGVMGNPATSSLLPPLRINIP---DHPHTEIS 229
LQ +SL+ + DPA S+S + + +PA++ I+ P D I+
Sbjct: 163 DPLSALQSESLIAQPDPAGGAPSISRNSEAPLSDPASAG-----GIDTPFPDDLDVPPIA 217
Query: 230 SSPFPSPTGTISAANSCP 247
+SP G +A+
Sbjct: 218 ASPPGPQEGPTISASQPA 235
>gnl|CDD|179392 PRK02249, PRK02249, DNA primase large subunit; Validated.
Length = 343
Score = 29.9 bits (68), Expect = 2.1
Identities = 10/51 (19%), Positives = 17/51 (33%), Gaps = 1/51 (1%)
Query: 139 HKLIEQAFRRRRQRGVPCFRAPFGLSSRCTLRFPSTNIRLQFQSLVNESDP 189
+L+ +A R R G+P P ++ L+ L E
Sbjct: 167 ARLLREAIRERILDGLP-LAVPEEIAEALLPLLEEIREELEELDLETEFGT 216
>gnl|CDD|182236 PRK10093, PRK10093, primosomal replication protein N'';
Provisional.
Length = 171
Score = 28.7 bits (64), Expect = 2.8
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 10/58 (17%)
Query: 7 SNESDAWALLALKSTSPSPSKIQWKSGTAIAKLQGREFEY----MVRQKRITIGRNSS 60
+ E+ AW+L S P ++ Q K ++Q +EFE MV ++R + R +
Sbjct: 83 AREAAAWSLREWDSAPPGLARWQRK------RIQHQEFERRLLEMVAERRARLARATD 134
>gnl|CDD|234178 TIGR03354, VI_FHA, type VI secretion system FHA domain protein.
Members of this protein family are FHA
(forkhead-associated) domain-containing proteins that
are part of type VI secretion loci in a considerable
number of bacteria, most of which are known pathogens.
Species include Pseudomonas aeruginosa PAO1, Aeromonas
hydrophila, Yersinia pestis, Burkholderia mallei, etc
[Protein fate, Protein and peptide secretion and
trafficking, Cellular processes, Pathogenesis].
Length = 396
Score = 29.3 bits (66), Expect = 2.9
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 73 FISRRHIEIFFEHPNFFMTCNGKNGVFVDG 102
+S RH I + + +T NGVF++G
Sbjct: 44 HVSGRHARIRYRDGAYLLTDLSTNGVFLNG 73
>gnl|CDD|131728 TIGR02681, phage_pRha, phage regulatory protein, rha family.
Members of this protein family are found in temperate
phage and bacterial prophage regions. Members include
the product of the rha gene of the lambdoid phage
phi-80, a late operon gene. The presence of this gene
interferes with infection of bacterial strains that lack
integration host factor (IHF), which regulates the rha
gene. It is suggested that pRha is a phage regulatory
protein [Mobile and extrachromosomal element functions,
Prophage functions].
Length = 108
Score = 27.9 bits (62), Expect = 3.1
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 256 RRNVSADLHMAAHYAAAHTNVVNHM-SLSISQD 287
+ V+ L MA + H NV+ + L I +
Sbjct: 10 NQVVTDSLTMAQMFGKRHDNVIRDIKVLLIEAN 42
>gnl|CDD|113452 pfam04684, BAF1_ABF1, BAF1 / ABF1 chromatin reorganising factor.
ABF1 is a sequence-specific DNA binding protein involved
in transcription activation, gene silencing and
initiation of DNA replication. ABF1 is known to remodel
chromatin, and it is proposed that it mediates its
effects on transcription and gene expression by
modifying local chromatin architecture. These functions
require a conserved stretch of 20 amino acids in the
C-terminal region of ABF1 (amino acids 639 to 662 S.
cerevisiae). The N-terminal two thirds of the protein
are necessary for DNA binding, and the N-terminus (amino
acids 9 to 91 in S. cerevisiae) is thought to contain a
novel zinc-finger motif which may stabilise the protein
structure.
Length = 508
Score = 29.3 bits (65), Expect = 3.6
Identities = 30/115 (26%), Positives = 45/115 (39%), Gaps = 18/115 (15%)
Query: 228 ISSSPFP---SPTGTISAANSCPTSPRGL-------HNRRNVSADLHMAAHYAAAHTNVV 277
+ S PF S G ++ + SP G H+ N+ A H H+ HTN
Sbjct: 66 LKSCPFKILLSHQGANNSGQNEDGSPGGGSGDEGGHHHGHNMHA--HHHHHHHNGHTNGH 123
Query: 278 NHMSLSIS-----QDDSKPPYSYAQLIVQAVASAHDKQLTLSGIYSFITKNYPYY 327
+ DD + I AVA+ D Q T+ G ++ +TK PY+
Sbjct: 124 GLAEDDRAEDEAQDDDEDDDAAVTAAIAAAVAAVADSQETIKGPFA-VTKIEPYH 177
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 28.4 bits (63), Expect = 7.5
Identities = 17/82 (20%), Positives = 26/82 (31%), Gaps = 2/82 (2%)
Query: 158 RAPFGLSSRCTLRFPSTNIRLQFQSLVNESDPAPTGQSVSSSGVGVMGNPATSSLLPPLR 217
AP R R ++ +SL + DPA +V + + + + LPP
Sbjct: 2773 AAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPT 2832
Query: 218 INIPDHPHTEISSSPFPSPTGT 239
P P P P
Sbjct: 2833 SAQPTAPPP--PPGPPPPSLPL 2852
>gnl|CDD|199820 cd10495, MH2_R-SMAD, C-terminal Mad Homology 2 (MH2) domain in
receptor regulated SMADs. The MH2 domain is located at
the C-terminus of the SMAD (small mothers against
decapentaplegic) family of proteins, which are signal
transducers and transcriptional modulators that mediate
multiple signaling pathways. The MH2 domain is
responsible for type I receptor interaction,
phosphorylation-triggered homo- and
hetero-oligomerization, and transactivation. It is
negatively regulated by the N-terminal MH1 domain.
Receptor regulated SMADs (R-SMADs) include SMAD1, SMAD2,
SMAD3, SMAD5 and SMAD9. SMAD1 plays an essential role in
bone development and postnatal bone formation through
activation by bone morphogenetic protein (BMP) type 1
receptor kinase. SMAD2 regulates multiple cellular
processes, such as cell proliferation, apoptosis and
differentiation, while SMAD3 modulates signals of
activin and TGF-beta. SMAD5 is involved in BMP signal
modulation, possibly playing a role in the pathway
involving inhibition of hematopoietic progenitor cells
by TGF-beta. SMAD9 (also known as SMAD8) can mediate the
differentiation of mesenchymal stem cells into
tendon-like cells by inhibiting the osteogenic pathway.
Length = 182
Score = 27.7 bits (62), Expect = 7.6
Identities = 25/102 (24%), Positives = 41/102 (40%), Gaps = 20/102 (19%)
Query: 75 SRRHI----EIFFEHPNFFMTCNGKNGVFVDGNSIRHNLSLNRYFIKVPRSQEEPGKGSF 130
+RRHI +F+ + C + +FV S NL + V
Sbjct: 56 TRRHIGRGVHLFYVGGEVYAECLSDSAIFV--QSRNCNLRHGFHPATV------------ 101
Query: 131 WRIDPGSEHKLIE-QAFRRRRQRGVP-CFRAPFGLSSRCTLR 170
+I PG K+ Q+F + ++ V F A + L+ CT+R
Sbjct: 102 CKIPPGCSLKIFNNQSFAQLLEQSVNRGFEAVYELTKMCTIR 143
>gnl|CDD|215496 PLN02918, PLN02918, pyridoxine (pyridoxamine) 5'-phosphate oxidase.
Length = 544
Score = 28.0 bits (62), Expect = 8.6
Identities = 29/100 (29%), Positives = 40/100 (40%), Gaps = 14/100 (14%)
Query: 213 LPPLRINIPDHPHTEISSSPFPSPT-GTISAANSCPTSPRGLHNRRNVSADLHMAAHYAA 271
L PL I+ P + +SSSP P+ T S + P R L + A
Sbjct: 17 LLPLPISPPPPHSSSLSSSPSPTQRFLTPSQGSRLPPRRRAL-----CTKSQDPRWRRAM 71
Query: 272 AHTNVVNHMSLSISQDDSKPPYSYAQLIVQAVASAHDKQL 311
A V+ +M S S PP SY + Q A+ D+ L
Sbjct: 72 ASLAVIPNMQDSGS-----PPLSY---LTQREAAEIDETL 103
>gnl|CDD|223061 PHA03369, PHA03369, capsid maturational protease; Provisional.
Length = 663
Score = 28.0 bits (62), Expect = 9.3
Identities = 16/74 (21%), Positives = 24/74 (32%), Gaps = 2/74 (2%)
Query: 177 RLQFQSLVNESDPAPTGQSVSSSGVGVMGNPATSSLLPPLRINIPDHPHTEISSSPFPSP 236
+ + L S AP+ +++ V V+ P T + P P P S P SP
Sbjct: 342 KAHNEILKTASLTAPSRVLAAAAKVAVIAAPQTHTG--PADRQRPQRPDGIPYSVPARSP 399
Query: 237 TGTISAANSCPTSP 250
P
Sbjct: 400 MTAYPPVPQFCGDP 413
>gnl|CDD|222478 pfam13966, zf-RVT, zinc-binding in reverse transcriptase. This
domain would appear to be a zinc-binding region of a
putative reverse transcriptase.
Length = 86
Score = 26.0 bits (58), Expect = 9.4
Identities = 8/23 (34%), Positives = 9/23 (39%)
Query: 10 SDAWALLALKSTSPSPSKIQWKS 32
A+ LL S KI W S
Sbjct: 5 KSAYRLLRPTSPPVFWKKIIWFS 27
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
0.317 0.131 0.396
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: 17,362,668
Number of extensions: 1626925
Number of successful extensions: 1329
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1324
Number of HSP's successfully gapped: 30
Length of query: 349
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 251
Effective length of database: 6,590,910
Effective search space: 1654318410
Effective search space used: 1654318410
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.4 bits)