RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1090
(169 letters)
>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double
chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces
cerevisiae}
Length = 800
Score = 137 bits (346), Expect = 3e-38
Identities = 42/146 (28%), Positives = 64/146 (43%), Gaps = 13/146 (8%)
Query: 15 GK---VIAFFCKIIEEQALE-PNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKA 70
GK +AF +I + P++IV PLS + W F K+AP + + Y GN R
Sbjct: 267 GKTVQTVAFISWLIFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDT 326
Query: 71 LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGH 130
++ K K +L+TT + I D L I W + VDE H
Sbjct: 327 IREYEFYTNPRAKGKKTMKFN---------VLLTTYEYILKDRAELGSIKWQFMAVDEAH 377
Query: 131 SVKNKKSKLSIKLTALRATFKVLLTG 156
+KN +S L L + + ++L+TG
Sbjct: 378 RLKNAESSLYESLNSFKVANRMLITG 403
>1z3i_X Similar to RAD54-like; recombination ATPase helicase,
recombination-DNA binding COM; 3.00A {Danio rerio} SCOP:
c.37.1.19 c.37.1.19
Length = 644
Score = 101 bits (253), Expect = 1e-25
Identities = 26/128 (20%), Positives = 53/128 (41%), Gaps = 14/128 (10%)
Query: 30 LEPNLIVCPLSVLNNWEAEFRKFAP-FVRTVKYYGNAIERKALQSEALSLPTIKVPAKKG 88
++ ++V P S++ NW E K+ V+ V G + + + + +
Sbjct: 114 IDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVNF------ISQQGM 167
Query: 89 KTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRA 148
+ I L+ + + L K +I DEGH +KN ++ + L ++ A
Sbjct: 168 RIPTPI-------LIISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNA 220
Query: 149 TFKVLLTG 156
+VL++G
Sbjct: 221 QRRVLISG 228
>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex,
hydrolase/DNA complex complex; 3.00A {Sulfolobus
solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A
Length = 500
Score = 98.4 bits (246), Expect = 8e-25
Identities = 42/145 (28%), Positives = 71/145 (48%), Gaps = 30/145 (20%)
Query: 15 GK---VIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKAL 71
GK IA F +E L P+L++CPLSVL NWE E KFAP +R ++ + + K
Sbjct: 68 GKTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHLRFAVFHEDRSKIKLE 127
Query: 72 QSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHS 131
+ I++TT ++ D LK++ W I++DE +
Sbjct: 128 DYD--------------------------IILTTYAVLLRDTR-LKEVEWKYIVIDEAQN 160
Query: 132 VKNKKSKLSIKLTALRATFKVLLTG 156
+KN ++K+ + L++ +++ LTG
Sbjct: 161 IKNPQTKIFKAVKELKSKYRIALTG 185
>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
factor, RNA polymerase recycling, activator,
ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
Length = 968
Score = 68.2 bits (166), Expect = 4e-14
Identities = 25/153 (16%), Positives = 46/153 (30%), Gaps = 31/153 (20%)
Query: 15 GK---VIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF-RKFAPFVRTVKYYGNAIERKA 70
GK + + A E LI+ P ++ + W E R+F R +
Sbjct: 182 GKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNL--RFALFDDERYAEAQ 239
Query: 71 LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND--FGFLKKITWNCIIVDE 128
+ L++ + + L + W+ ++VDE
Sbjct: 240 HDAY------------------NPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDE 281
Query: 129 GHSVKNKKSKLS-----IKLTALRATFKVLLTG 156
H + + S I+ A +LLT
Sbjct: 282 AHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTA 314
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 35.8 bits (82), Expect = 0.005
Identities = 26/168 (15%), Positives = 48/168 (28%), Gaps = 53/168 (31%)
Query: 18 IAFFCKIIEEQALEPN--------L-----IVCPLSVLNNWEAEFRKFAPFVRTVKYYG- 63
A F + ++ + L P L + V++ V V Y G
Sbjct: 1741 KAAF-EDLKSKGLIPADATFAGHSLGEYAALASLADVMS--------IESLVEVVFYRGM 1791
Query: 64 ---NAIERKALQSEALSLPTIKVPAKKGKTKKQISLK--LPLILVTTPQIIE--NDFGFL 116
A+ R L + I P + + Q +L+ + + T ++E N
Sbjct: 1792 TMQVAVPRDELGRSNYGMIAI-NPGRVAASFSQEALQYVVERVGKRTGWLVEIVNY---- 1846
Query: 117 KKITWNC---IIVDEGHSV---------KNKKSKLSIKLTALRATFKV 152
N V G K + I + L+ + +
Sbjct: 1847 -----NVENQQYVAAGDLRALDTVTNVLNFIKLQ-KIDIIELQKSLSL 1888
Score = 30.0 bits (67), Expect = 0.44
Identities = 20/122 (16%), Positives = 39/122 (31%), Gaps = 43/122 (35%)
Query: 23 KIIEE--QALEPNLIVCPLSVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALSL 78
+ + L V +S++N V + G ++L L+L
Sbjct: 351 DYVNKTNSHLPAGKQVE-ISLVN---------GAKNLVVS----GPP---QSLYGLNLTL 393
Query: 79 PTIKVPAKKGKT-------KKQISLK-LPLILVTTP----------QIIENDFGFLKKIT 120
K P+ ++ K + S + LP V +P +I D ++
Sbjct: 394 RKAKAPSGLDQSRIPFSERKLKFSNRFLP---VASPFHSHLLVPASDLINKDLV-KNNVS 449
Query: 121 WN 122
+N
Sbjct: 450 FN 451
>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H
RNA-binding helicase, innate immunity, IFIH1, S
genomics; 1.60A {Homo sapiens}
Length = 216
Score = 34.4 bits (79), Expect = 0.009
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 8/38 (21%)
Query: 101 ILVTTPQIIEND--------FGFLKKITWNCIIVDEGH 130
I+++T QI+EN ++ ++ II+DE H
Sbjct: 135 IIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECH 172
>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA
repair, DNA recombina hydrolase; 2.90A {Pyrococcus
furiosus} SCOP: c.37.1.19 c.37.1.19
Length = 494
Score = 34.8 bits (79), Expect = 0.009
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 101 ILVTTPQIIENDF--GFLKKITWNCIIVDEGHSVKNKKSKLSI 141
++V TPQ IEND G + + I+ DE H + + I
Sbjct: 104 VIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFI 146
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 33.9 bits (78), Expect = 0.017
Identities = 19/122 (15%), Positives = 36/122 (29%), Gaps = 28/122 (22%)
Query: 14 SGKVIAFFCKIIEEQALEPN-LIVCPLSVLNNWEA-----EFRKFA-PFVRTVKYYGNAI 66
GK + +V P L +K A V+ +Y +
Sbjct: 47 VGKTTFGMMTALWLARKGKKSALVFPTVTL----VKQTLERLQKLADEKVKIFGFYSSMK 102
Query: 67 ERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIV 126
+ + K K +K ILV + Q + + L + ++ + V
Sbjct: 103 KEE-----------------KEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFV 145
Query: 127 DE 128
D+
Sbjct: 146 DD 147
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 32.2 bits (72), Expect = 0.082
Identities = 14/67 (20%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 76 LSLPTIKVPAKKGKTKKQISLKLPL----ILVTTPQIIENDF--GFLKKIT-WNCIIVDE 128
+ + G T +S++ + I++ TPQI+ N+ G + ++ + +I DE
Sbjct: 76 FERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDE 135
Query: 129 GHSVKNK 135
H+
Sbjct: 136 CHNTSKN 142
>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein;
HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19
c.37.1.19 PDB: 2fzl_A*
Length = 472
Score = 31.3 bits (71), Expect = 0.15
Identities = 17/113 (15%), Positives = 30/113 (26%), Gaps = 33/113 (29%)
Query: 34 LIVCPLSVLNN-WEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVPAKKGKTKK 92
LIV P L W+ F ++ G E K
Sbjct: 137 LIVVPTLALAEQWKERLGIF-GEEYVGEFSGRIKELKP---------------------- 173
Query: 93 QISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTA 145
+ V+T + L + +I DE H + + +++
Sbjct: 174 --------LTVSTYDSAYVNAEKLGN-RFMLLIFDEVHHLPAESYVQIAQMSI 217
>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.40A {Anas platyrhynchos}
Length = 797
Score = 30.7 bits (68), Expect = 0.27
Identities = 15/76 (19%), Positives = 26/76 (34%), Gaps = 7/76 (9%)
Query: 73 SEALSLPTIKVPAKKGKTKKQISLKLPL----ILVTTPQIIENDFG---FLKKITWNCII 125
V G+ +S++ + I+V TPQI+ N F + +I
Sbjct: 317 KHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMI 376
Query: 126 VDEGHSVKNKKSKLSI 141
DE H+ +
Sbjct: 377 FDECHNTTGNHPYNVL 392
>3hn7_A UDP-N-acetylmuramate-L-alanine ligase; ATP-binding,
nucleotide-binding, structural genomics, joint for
structural genomics, JCSG; HET: MSE; 1.65A
{Psychrobacter arcticus 273-4}
Length = 524
Score = 29.6 bits (67), Expect = 0.46
Identities = 14/59 (23%), Positives = 20/59 (33%), Gaps = 16/59 (27%)
Query: 19 AFFCKIIEEQALEPNLIVCPLSVLNNWEAE-----------FRKFAPFVRTVKYYGNAI 66
AFF K + P ++LNN E + +F VR + G I
Sbjct: 204 AFFDKRSKFVHYRPRT-----AILNNLEFDHADIFADLDAIQTQFHHMVRMIPSTGKII 257
>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*
Length = 556
Score = 29.1 bits (64), Expect = 0.66
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 101 ILVTTPQIIENDF--GFLKKI-TWNCIIVDEGHSVKNK 135
I+V TPQI+ N F G L + + +I DE H+
Sbjct: 108 IIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGN 145
>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.70A {Anas platyrhynchos}
Length = 936
Score = 28.4 bits (62), Expect = 1.3
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 101 ILVTTPQIIENDF--GFLKKI-TWNCIIVDEGHSVKNKK 136
I+V TPQI+ N F G L + + +I DE H+
Sbjct: 349 IIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNH 387
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 27.6 bits (60), Expect = 1.6
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 14/34 (41%)
Query: 128 EGHSVKNKKSKL--SIKL--------TALRATFK 151
E ++K KL S+KL A++AT +
Sbjct: 18 EKQALK----KLQASLKLYADDSAPALAIKATME 47
Score = 25.7 bits (55), Expect = 6.2
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 11/33 (33%)
Query: 86 KKGKTKK-QISLKL------P-LILVTTPQIIE 110
+K KK Q SLKL P L + T +E
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKAT---ME 47
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 28.0 bits (61), Expect = 1.7
Identities = 15/70 (21%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 73 SEALSLPTIKVPAKKGKTKKQISLKLPL----ILVTTPQIIENDF--GFLKKIT-WNCII 125
S+ +V G T + + ++ + I++ TPQI+ N+ G + ++ + +I
Sbjct: 82 SKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMI 141
Query: 126 VDEGHSVKNK 135
DE H+ +
Sbjct: 142 FDECHNTSKQ 151
>3eag_A UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-ME diaminopimelate
ligase; UDP-N-acetylmuramate:L-alanyl-G
glutamyl-MESO-diaminopimelate ligase; 2.55A {Neisseria
meningitidis MC58}
Length = 326
Score = 26.5 bits (59), Expect = 4.4
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 11/38 (28%)
Query: 40 SVLNNWEAE----F-------RKFAPFVRTVKYYGNAI 66
+VLNN E + F +F VRTV G +
Sbjct: 195 AVLNNLEFDHADIFADLGAIQTQFHYLVRTVPSEGLIV 232
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.321 0.136 0.413
Gapped
Lambda K H
0.267 0.0443 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,598,952
Number of extensions: 140280
Number of successful extensions: 226
Number of sequences better than 10.0: 1
Number of HSP's gapped: 219
Number of HSP's successfully gapped: 23
Length of query: 169
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 82
Effective length of database: 4,272,666
Effective search space: 350358612
Effective search space used: 350358612
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: 54 (25.3 bits)