RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13711
(580 letters)
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four helix
bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide sequences
such as N-box (5-CACGc/aG-3), those which have a COE
domain (Collier/Olf-1/EBF) which is involved in both in
dimerization and in DNA binding, and those which bind
pentanucleotides ACGTG or GCGTG and have a PAS domain
which allows the dimerization between PAS proteins, the
binding of small molecules (e.g., dioxin), and
interactions with non-PAS proteins.
Length = 60
Score = 62.6 bits (153), Expect = 1e-12
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 271 KRANKPLMEKRRRARINQSLALLKALILDSAKTENTKHSKLEKADILELTVRHLQRQKIL 330
+R L E+RRR RIN + L++L+ KL KA+IL V +++ + L
Sbjct: 4 RREAHNLRERRRRERINDAFDELRSLLP-----TLPPSKKLSKAEILRKAVDYIKSLQEL 58
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 61.7 bits (151), Expect = 2e-12
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 271 KRANKPLMEKRRRARINQSLALLKALILDSAKTENTKHSKLEKADILELTVRHLQ 325
+R E+RRR RIN + L+ L+ + KL KA+IL L + +++
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLP------TPPNKKLSKAEILRLAIEYIK 49
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 50.7 bits (122), Expect = 2e-08
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 5/53 (9%)
Query: 276 PLMEKRRRARINQSLALLKALILDSAKTENTKHSKLEKADILELTVRHLQRQK 328
E+RRR +IN++ L++L+ K+ KL KA+IL L + +++ +
Sbjct: 1 NARERRRRRKINEAFDELRSLL-----PTLPKNKKLSKAEILRLAIEYIKSLQ 48
>gnl|CDD|219453 pfam07527, Hairy_orange, Hairy Orange. The Orange domain is found
in the Drosophila proteins Hesr-1, Hairy, and Enhancer
of Split. The Orange domain is proposed to mediate
specific protein-protein interaction between Hairy and
Scute.
Length = 42
Score = 39.8 bits (94), Expect = 7e-05
Identities = 19/86 (22%), Positives = 29/86 (33%), Gaps = 44/86 (51%)
Query: 337 KYKAGYEECSREVSRFLETPELHLGLSSTTSSTPTPSGTGNKALPLPSKPTPSSLALASL 396
K++AG+ EC EV+RFL
Sbjct: 1 KFRAGFRECLNEVARFL------------------------------------------- 17
Query: 397 MSGEPVIDSGVRQRLFRHLENCMSEI 422
S +D VR RL HL +C++++
Sbjct: 18 -SSVEGVDPDVRARLLSHLASCLNQL 42
Score = 33.7 bits (78), Expect = 0.012
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 102 ASLMSGEPVIDSGVRQRLFRHLENCMSEI 130
A +S +D VR RL HL +C++++
Sbjct: 14 ARFLSSVEGVDPDVRARLLSHLASCLNQL 42
>gnl|CDD|128787 smart00511, ORANGE, Orange domain. This domain confers specificity
among members of the Hairy/E(SPL) family.
Length = 45
Score = 33.3 bits (77), Expect = 0.016
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 336 SKYKAGYEECSREVSRFL 353
S +++GY EC+ EVSRFL
Sbjct: 1 SSFRSGYRECANEVSRFL 18
>gnl|CDD|227899 COG5612, COG5612, Predicted integral membrane protein [Function
unknown].
Length = 148
Score = 31.1 bits (70), Expect = 0.85
Identities = 24/84 (28%), Positives = 35/84 (41%), Gaps = 12/84 (14%)
Query: 269 ALKRANKPLMEKRRRARIN--QSLALLKALILDSAKTENTKHSKLEKADILELTVRHLQR 326
AL+ A + E +RAR ++ ALL + LD+A LE+A E+ VR
Sbjct: 58 ALRAARQKNREITQRARQARREAAALLASPGLDTAALS----RALERARDAEIQVRGNVE 113
Query: 327 QKI------LSSDIRSKYKAGYEE 344
+ LS R+ G E
Sbjct: 114 TALATFAATLSPQERAALAEGLSE 137
>gnl|CDD|221532 pfam12328, Rpp20, Rpp20 subunit of nuclear RNase MRP and P. The
nuclear RNase P of Saccharomyces cerevisiae is made up
of at least nine protein subunits; Pop1, Pop3, Pop4,
Pop5, Pop6, Pop7, Pop8, Rpr2 and Rpp1. Many of these
subunits seem to be present also in the RNase MRP, with
the exception of Rpr2 (Rpp21) which is unique to RNase
P. Human nuclear RNase P and MRP appear to contain at
least 10 protein subunits, Rpp14, Rpp20, Rpp21, Rpp25,
Rpp29, Rpp30, Rpp38, Rpp40, hPop1 and hPop5, although
there is recent evidence that not all of these subunits
are shared between P and MRP. Archaeal RNase P has at
least four protein subunits homologous to eukaryotic
RNase P/MRP proteins. In the yeast RNase P, Pop6 and
Pop7 (the Rpp20 homologue) interact with each other and
they are both interaction partners of Pop4; in the human
MRP Rpp25 and Rpp20 interact with each other and Rpp25
binds to Rpp29 (Pop4).
Length = 108
Score = 30.3 bits (69), Expect = 0.89
Identities = 27/89 (30%), Positives = 40/89 (44%), Gaps = 17/89 (19%)
Query: 249 KTLVVMSSPPLVASSNSIPPALKRANKPLMEKRRRARINQSLALLKALILDSAKTENTKH 308
KT+ V S P ++ ALKR K L + +RA + L L + ++ K
Sbjct: 4 KTIYVKSKTPFIS-------ALKRVQKLLDKAEKRASKGEGLKLEEVVVKGMGKA----- 51
Query: 309 SKLEKADILELTVRHLQRQKILSSDIRSK 337
+EKA L L H QR+K D+R+
Sbjct: 52 --IEKA--LSL-ALHFQREKNYKVDVRTG 75
>gnl|CDD|222912 PHA02624, PHA02624, large T antigen; Provisional.
Length = 647
Score = 30.7 bits (70), Expect = 2.2
Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 10/48 (20%)
Query: 147 FSSEDDSAFPMLRVRPEPDSSTTTLLPVTHPTPTKPNVTPPKKKSKTK 194
SS+D+ P P + + + TPPKKK K
Sbjct: 111 SSSDDEDEPPPPSPPPSQEEES----------QSSSQATPPKKKKKNP 148
Score = 30.7 bits (70), Expect = 2.2
Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 10/48 (20%)
Query: 439 FSSEDDSAFPMLRVRPEPDSSTTTLLPVTHPTPTKPNVTPPKKKSKTK 486
SS+D+ P P + + + TPPKKK K
Sbjct: 111 SSSDDEDEPPPPSPPPSQEEES----------QSSSQATPPKKKKKNP 148
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 30.9 bits (70), Expect = 2.6
Identities = 33/197 (16%), Positives = 58/197 (29%), Gaps = 22/197 (11%)
Query: 363 SSTTSSTPTPSGTGNKALPLPSKPTPSSLALASLMSGEPVIDSGVRQRLFRHLENCMSEI 422
++ S+P + S P + S + P G +
Sbjct: 182 TARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASS----- 236
Query: 423 DLDFSASAEKLGITQDFSSE-DDSAFPMLRVRPEPDSSTTTLLPVTHPTPTKPNVTPPKK 481
S+S+E G +E + + ++ P + P P + +P ++
Sbjct: 237 --SDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRER 294
Query: 482 KSKTKMASVGGGGEKTASDISDSNSNQSSSAVESAMSVLQLIPSRLPDGQVVFILPNYMA 541
+S G G ++ S S+S+ S+ S S S G A
Sbjct: 295 SPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSS-----SESSRG---------AA 340
Query: 542 PSTSPPCKDDLKSSPPP 558
S P S PP
Sbjct: 341 VSPGPSPSRSPSPSRPP 357
>gnl|CDD|234307 TIGR03676, aRF1/eRF1, peptide chain release factor 1, archaeal and
eukaryotic forms. Directs the termination of nascent
peptide synthesis (translation) in response to the
termination codons UAA, UAG and UGA. This model
identifies both archaeal (aRF1) and eukaryotic (eRF1) of
the protein. Also known as translation termination
factor 1 [Protein synthesis, Translation factors].
Length = 357
Score = 29.9 bits (68), Expect = 3.6
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 497 TASDI-SDSNSNQSSSAVESAMSVLQLIPSRLPDGQVVF 534
A++I S SA+ES M L+L +G V+F
Sbjct: 46 QAANIKSKQTRKNVQSAIESIMQRLKLYKKPPENGLVLF 84
>gnl|CDD|237573 PRK13963, PRK13963, unkown domain/putative metalloprotease fusion
protein; Provisional.
Length = 258
Score = 29.4 bits (66), Expect = 5.2
Identities = 13/62 (20%), Positives = 17/62 (27%), Gaps = 14/62 (22%)
Query: 132 LDFSASAEKLGITQDFSSEDDSAFPMLRVRPE--------------PDSSTTTLLPVTHP 177
D S S+ + D + ML +RPE PD P P
Sbjct: 51 FDLSGSSGDAAVAIVAQHADPAMRAMLALRPEHYDSVTLRVGAEPAPDFVDDEDAPAREP 110
Query: 178 TP 179
Sbjct: 111 EL 112
Score = 29.4 bits (66), Expect = 5.2
Identities = 13/62 (20%), Positives = 17/62 (27%), Gaps = 14/62 (22%)
Query: 424 LDFSASAEKLGITQDFSSEDDSAFPMLRVRPE--------------PDSSTTTLLPVTHP 469
D S S+ + D + ML +RPE PD P P
Sbjct: 51 FDLSGSSGDAAVAIVAQHADPAMRAMLALRPEHYDSVTLRVGAEPAPDFVDDEDAPAREP 110
Query: 470 TP 471
Sbjct: 111 EL 112
>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase;
Provisional.
Length = 481
Score = 29.4 bits (65), Expect = 5.9
Identities = 14/59 (23%), Positives = 24/59 (40%)
Query: 454 PEPDSSTTTLLPVTHPTPTKPNVTPPKKKSKTKMASVGGGGEKTASDISDSNSNQSSSA 512
P +++ T+ N + P K + T S T ++ SN+N +SSA
Sbjct: 308 PSTNTNANKTNTNTNTNTNNTNTSTPSKNTNTNTNSNTNTNSNTNANQGSSNNNSNSSA 366
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 29.5 bits (66), Expect = 6.0
Identities = 41/281 (14%), Positives = 82/281 (29%), Gaps = 47/281 (16%)
Query: 54 PPQVSRFLETPELHLGLSSTTSSTPT----PSGTGNKALPLPSKPTPSSLALASLMSGEP 109
P + + L + +S+ T T P L + L G+
Sbjct: 202 PKEENHTLSVTDKEKSEASSKGLTSTKELVPVQNSGGNHSLSKSSNSQTPELEYSEKGKD 261
Query: 110 VIDSGVRQRLFRHLENCMSEIDLDFSASAEKLGITQDFSSEDDSAFPMLRV--------R 161
S + +GI S DS + V R
Sbjct: 262 HHHSH--------------------NHQHHSIGINNHHSKHADSKLQTIEVIENHSNKSR 301
Query: 162 PEPDSSTTTLLPVTHPTPTKPNVTPPKKKSKTKMATQQSLIMSTTSEHSGDGNNNIGTPD 221
P S+ + ++ + + + K SK+ + ++ S+ HS + N P
Sbjct: 302 PSSSSTNGSKETTSNSS-SAAAGSIGSKSSKSAKHSNRNKSNSSPKSHS---SANGSVPS 357
Query: 222 SSTGCQTKPRSTVKKDTHSPPLKRSLNKTLVVMSSPPLVASSNSIPPALKRANKPLMEKR 281
SS D S + S + + S S + +
Sbjct: 358 SSV-----------SDNESKQKRASKSSSGARDSKKDASGMSANGTVENCIPENKISTPS 406
Query: 282 RRARINQSLALLKALILDSAKTENTKHSKLEKADILELTVR 322
R+ Q + L+A + + + E+ +++ LE +++
Sbjct: 407 AIERLEQDIKKLQAELQQARQNESELRNQISLLTSLERSLK 447
>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 29.5 bits (66), Expect = 6.1
Identities = 22/78 (28%), Positives = 30/78 (38%), Gaps = 5/78 (6%)
Query: 48 KGFPLCPPQVSRFL-----ETPELHLGLSSTTSSTPTPSGTGNKALPLPSKPTPSSLALA 102
K PQ R E P + +S PTP A P P+P + A
Sbjct: 393 KAPEPDLPQPDRHPGPAKPEAPGARPAELPSPASAPTPEQQPPVARSAPLPPSPQASAPR 452
Query: 103 SLMSGEPVIDSGVRQRLF 120
++ SG+P +D G Q F
Sbjct: 453 NVASGKPGVDLGSWQGKF 470
Score = 29.1 bits (65), Expect = 8.0
Identities = 19/68 (27%), Positives = 27/68 (39%), Gaps = 1/68 (1%)
Query: 346 SREVSRF-LETPELHLGLSSTTSSTPTPSGTGNKALPLPSKPTPSSLALASLMSGEPVID 404
R E P + +S PTP A P P+P + A ++ SG+P +D
Sbjct: 403 DRHPGPAKPEAPGARPAELPSPASAPTPEQQPPVARSAPLPPSPQASAPRNVASGKPGVD 462
Query: 405 SGVRQRLF 412
G Q F
Sbjct: 463 LGSWQGKF 470
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 29.2 bits (65), Expect = 6.1
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 13/81 (16%)
Query: 283 RARINQSLALLKALILDSAKTENTKHSKLEKADILELTVRHLQRQKILSSDIRSKYKAGY 342
R +I + L LK L+ + TE + L+ T++ L + K A Y
Sbjct: 63 REKIERKLQDLKELLKQKSYTEPERKKTLQ-------TLKPLSERL------EEKESAIY 109
Query: 343 EECSREVSRFLETPELHLGLS 363
E S E+ + PE +GLS
Sbjct: 110 EIESFELEEVITEPERPVGLS 130
>gnl|CDD|218421 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein. This
family consists of REP proteins from Dictyostelium
(Slime molds). REP protein is likely involved in
transcription regulation and control of DNA replication,
specifically amplification of plasmid at low copy
numbers. The formation of homomultimers may be required
for their regulatory activity.
Length = 910
Score = 29.0 bits (65), Expect = 7.7
Identities = 18/73 (24%), Positives = 25/73 (34%), Gaps = 4/73 (5%)
Query: 451 RVRPEPDSSTTTLLPVTHPTPTKPNVTPPKKKSKTKMASVGGGGEKTASDISDSNS---- 506
R + + P TKP+ P S G + +IS S S
Sbjct: 274 RKSIDDHKLSLNQAPEKFKNNTKPDDDPQSDFSDKGSRKSGSLKDVRIDNISCSVSHNGV 333
Query: 507 NQSSSAVESAMSV 519
N S S E+ +SV
Sbjct: 334 NISISPTETIISV 346
>gnl|CDD|224420 COG1503, eRF1, Peptide chain release factor 1 (eRF1) [Translation,
ribosomal structure and biogenesis].
Length = 411
Score = 28.9 bits (65), Expect = 9.2
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 496 KTASDI-SDSNSNQSSSAVESAMSVLQLIPSRLPDGQVVF 534
TAS+I S SA+ESAM L+ +G V+F
Sbjct: 52 STASNIKSKVTRKNVLSAIESAMQRLKDYCKTPENGLVLF 91
>gnl|CDD|182644 PRK10681, PRK10681, DNA-binding transcriptional repressor DeoR;
Provisional.
Length = 252
Score = 28.5 bits (64), Expect = 9.4
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 12/48 (25%)
Query: 278 MEKRRRARINQSLALLKALILDSAKTENTKHSKLEKADIL---ELTVR 322
ME RR RI Q LL+AL K + H K + A +L E+T+R
Sbjct: 1 METRRDERIGQ---LLQAL-----KRSDKLHLK-DAAALLGVSEMTIR 39
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
0.310 0.127 0.361
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,614,351
Number of extensions: 2699128
Number of successful extensions: 2360
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2344
Number of HSP's successfully gapped: 61
Length of query: 580
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 478
Effective length of database: 6,413,494
Effective search space: 3065650132
Effective search space used: 3065650132
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 (21.8 bits)
S2: 62 (27.5 bits)