RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7550
(144 letters)
>2crw_A ARF GAP 3, ADP-ribosylation factor GTPase-activating protein 3;
arfgap domain, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 149
Score = 200 bits (509), Expect = 2e-67
Identities = 89/133 (66%), Positives = 111/133 (83%)
Query: 6 PNKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVR 65
P+K DI IFK+LR++PTNK CFDC AKNP+W+S+TYGVF+CIDCS HR LGVHLSF+R
Sbjct: 11 PSKQDILTIFKRLRSVPTNKVCFDCGAKNPSWASITYGVFLCIDCSGSHRSLGVHLSFIR 70
Query: 66 STQLDTNWTWVQLRQMQLGGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYREKLQHAAVQ 125
ST+LD+NW+W QLR MQ+GGNA+A SFF+QH C++ D KYNSRAAQLYREK++ A Q
Sbjct: 71 STELDSNWSWFQLRCMQVGGNASASSFFHQHGCSTNDTNAKYNSRAAQLYREKIKSLASQ 130
Query: 126 AMKIHGTKLFLDA 138
A + HGT L+LD+
Sbjct: 131 ATRKHGTDLWLDS 143
>2p57_A GTPase-activating protein ZNF289; zinc finger, GAP, structural
genomics, structural genomics consortium, SGC, metal
binding protein; 1.80A {Homo sapiens}
Length = 144
Score = 194 bits (493), Expect = 4e-65
Identities = 84/126 (66%), Positives = 103/126 (81%)
Query: 6 PNKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVR 65
PNK +I+ +FK+LR +PTNK CFDC AKNP+W+S+TYGVF+CIDCS VHR LGVHLSF+R
Sbjct: 19 PNKTEIQTLFKRLRAVPTNKACFDCGAKNPSWASITYGVFLCIDCSGVHRSLGVHLSFIR 78
Query: 66 STQLDTNWTWVQLRQMQLGGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYREKLQHAAVQ 125
ST+LD+NW W QLR MQ+GGNANA +FF QH CT+ DA KYNSRAAQ+YREK++
Sbjct: 79 STELDSNWNWFQLRCMQVGGNANATAFFRQHGCTANDANTKYNSRAAQMYREKIRQLGSA 138
Query: 126 AMKIHG 131
A+ HG
Sbjct: 139 ALARHG 144
>3sub_A ADP-ribosylation factor GTPase-activating protein; protein
trafficking, hydrolase AC; 2.40A {Plasmodium falciparum
3D7}
Length = 163
Score = 183 bits (466), Expect = 9e-61
Identities = 45/121 (37%), Positives = 70/121 (57%), Gaps = 1/121 (0%)
Query: 3 GEGPNKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLS 62
G N +E I + + +N +CFDC NP W SV +G+F+CI+CS VHR LGVH+S
Sbjct: 1 GSHMNAAAVEFINRLKKEDESNNKCFDCGISNPDWVSVNHGIFLCINCSGVHRSLGVHIS 60
Query: 63 FVRSTQLDTNWTWVQLRQMQLGGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYREKLQHA 122
VRS ++D +T QL+ + GGN ++ + + ++KY ++AA YR+ L+
Sbjct: 61 IVRSIKMDI-FTDEQLKYIDKGGNKKCQTYLENYGISDFIPERKYRTKAADHYRKILRSI 119
Query: 123 A 123
Sbjct: 120 V 120
>3dwd_A ADP-ribosylation factor GTPase-activating protein; GAP, structural
genomics consorti ER-golgi transport, golgi apparatus,
GTPase activation; 2.40A {Homo sapiens}
Length = 147
Score = 172 bits (437), Expect = 1e-56
Identities = 53/112 (47%), Positives = 70/112 (62%), Gaps = 3/112 (2%)
Query: 14 IFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNW 73
+ K++R N CF+C A NP W SVTYG++IC++CS HRGLGVHLSFVRS +D W
Sbjct: 28 VLKEVRVQDENNVCFECGAFNPQWVSVTYGIWICLECSGRHRGLGVHLSFVRSVTMDK-W 86
Query: 74 TWVQLRQMQLGGNANAVSFFNQHNCTSKDA--QQKYNSRAAQLYREKLQHAA 123
++L +M+ GGNA F Q+KYNSRAA L+R+K+ A
Sbjct: 87 KDIELEKMKAGGNAKFREFLESQEDYDPCWSLQEKYNSRAAALFRDKVVALA 138
>2owa_A Arfgap-like finger domain containing protein; zinc finger protein,
cysteine-rich motif, GTPase activation; 2.00A
{Cryptosporidium parvum iowa II}
Length = 138
Score = 168 bits (428), Expect = 3e-55
Identities = 46/128 (35%), Positives = 78/128 (60%), Gaps = 4/128 (3%)
Query: 1 MSGEGP-NKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGV 59
+ +G + + F+ +RN P N+ CFDC ++NPTW S+++ VFIC++CS+ HR +GV
Sbjct: 12 VDEKGFVSDKLRDNFFQIVRNRPENRTCFDCESRNPTWLSLSFAVFICLNCSSDHRKMGV 71
Query: 60 HLSFVRSTQLDTNWTWVQLRQMQLGGNANAVSFFNQHNCTS--KDAQQKYNSRAAQLYRE 117
H+SFVRS+ LD +T +QL +M +GGN A ++F Q + ++ +S + Y++
Sbjct: 72 HISFVRSSDLDK-FTPIQLVRMDIGGNGRARNYFKQVLGVNFSPKTKEYASSICGRQYKQ 130
Query: 118 KLQHAAVQ 125
L +
Sbjct: 131 ILDSEISE 138
>3o47_A ADP-ribosylation factor GTPase-activating protein ribosylation
factor 1; structural genomics consortium, GTPase
activation; HET: GDP; 2.80A {Homo sapiens}
Length = 329
Score = 146 bits (369), Expect = 6e-44
Identities = 52/109 (47%), Positives = 69/109 (63%), Gaps = 3/109 (2%)
Query: 14 IFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNW 73
+ K++R N CF+C A NP W SVTYG++IC++CS HRGLGVHLSFVRS +D W
Sbjct: 27 VLKEVRVQDENNVCFECGAFNPQWVSVTYGIWICLECSGRHRGLGVHLSFVRSVTMD-KW 85
Query: 74 TWVQLRQMQLGGNANAVSFFNQHNCTSKDA--QQKYNSRAAQLYREKLQ 120
++L +M+ GGNA F Q+KYNSRAA L+R+K+
Sbjct: 86 KDIELEKMKAGGNAKFREFLESQEDYDPCWSLQEKYNSRAAALFRDKVV 134
>2iqj_A Stromal membrane-associated protein 1-like; zinc, structural
genomics, structural genomics consortium, SGC, protein
transport; 1.90A {Homo sapiens}
Length = 134
Score = 129 bits (325), Expect = 1e-39
Identities = 41/119 (34%), Positives = 59/119 (49%), Gaps = 3/119 (2%)
Query: 1 MSGEGPNKND-IEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGV 59
M+G+ D + + L NK C DC +K P W+S GVFICI C+ +HR LGV
Sbjct: 3 MTGKSVKDVDRYQAVLANLLLEEDNKFCADCQSKGPRWASWNIGVFICIRCAGIHRNLGV 62
Query: 60 HLSFVRSTQLDTNWTWVQLRQMQLGGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYREK 118
H+S V+S LD WT Q++ MQ GN A + + + + + R+K
Sbjct: 63 HISRVKSVNLDQ-WTQEQIQCMQEMGNGKANRLYEAY-LPETFRRPQIDPAVEGFIRDK 119
>2crr_A Stromal membrane-associated protein SMAP1B; arfgap domain, zinc
finger, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 141
Score = 127 bits (320), Expect = 9e-39
Identities = 39/85 (45%), Positives = 50/85 (58%), Gaps = 1/85 (1%)
Query: 12 EVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDT 71
++I KL NK C DC AK P W+S GVFICI C+ +HR LGVH+S V+S LD
Sbjct: 17 QLILSKLLREEDNKYCADCEAKGPRWASWNIGVFICIRCAGIHRNLGVHISRVKSVNLDQ 76
Query: 72 NWTWVQLRQMQLGGNANAVSFFNQH 96
WT Q++ MQ GN A + +
Sbjct: 77 -WTAEQIQCMQDMGNTKARLLYEAN 100
>2b0o_E UPLC1; arfgap, structural genomics, structural genomics consortium,
SGC, metal binding protein; 2.06A {Homo sapiens}
Length = 301
Score = 122 bits (308), Expect = 3e-35
Identities = 31/115 (26%), Positives = 48/115 (41%), Gaps = 1/115 (0%)
Query: 2 SGEGPNKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHL 61
+G + +++ ++++ P N +C DC A +PTW S GV CI CS VHR LGV
Sbjct: 20 GHDGEPHDLTKLLIAEVKSRPGNSQCCDCGAADPTWLSTNLGVLTCIQCSGVHRELGVRF 79
Query: 62 SFVRSTQLDTNWTWVQLRQMQLGGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYR 116
S ++S LD +L GN + + + S
Sbjct: 80 SRMQSLTLDL-LGPSELLLALNMGNTSFNEVMEAQLPSHGGPKPSAESDMGTRRD 133
>3jue_A Arfgap with coiled-coil, ANK repeat and PH domain containing
protein 1; arfgap domain, zinc-binding module, GTPase
activ metal-binding, nitration; 2.30A {Homo sapiens}
Length = 368
Score = 120 bits (301), Expect = 9e-34
Identities = 32/105 (30%), Positives = 51/105 (48%), Gaps = 3/105 (2%)
Query: 14 IFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNW 73
+ +++++ N +C DC P W+S+ GV +CI CS +HR LGVH S VRS LD+ W
Sbjct: 35 VVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDS-W 93
Query: 74 TWVQLRQMQLGGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYREK 118
++ M GN + A +K ++ +E
Sbjct: 94 EPELVKLMCELGNVIINQIYEAR--VEAMAVKKPGPSCSRQEKEA 136
>2olm_A Nucleoporin-like protein RIP; arfgap, GTPase-activating protein,
REV-interacting protein, human immunodeficiency virus,
AIDS, structural genomics; 1.48A {Homo sapiens} PDB:
2d9l_A
Length = 140
Score = 113 bits (284), Expect = 2e-33
Identities = 29/108 (26%), Positives = 51/108 (47%), Gaps = 4/108 (3%)
Query: 14 IFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNW 73
+ + + +P N++CFDC+ + PT+ ++T G F+C CS RGL V+S + T +
Sbjct: 15 MLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLRGLNPP-HRVKSISMTT-F 72
Query: 74 TWVQLRQMQLGGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYREKLQH 121
T ++ +Q GN + + + R Q +E LQ
Sbjct: 73 TQQEIEFLQKHGNEVCKQIWLGL--FDDRSSAIPDFRDPQKVKEFLQE 118
>3lju_X ARF-GAP with dual PH domain-containing protein 1; structural
genomics consortium, GTPase activation, SGC, binding,
nucleus, phosphoprotein; HET: IP9; 1.70A {Homo sapiens}
PDB: 3feh_A* 3fm8_C 3mdb_C*
Length = 386
Score = 118 bits (297), Expect = 5e-33
Identities = 36/110 (32%), Positives = 50/110 (45%), Gaps = 5/110 (4%)
Query: 9 NDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQ 68
+ +L P N C DC A +P W+S T GVFIC+ CS +HR + +S V+S +
Sbjct: 19 KERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIP-QVSKVKSVR 77
Query: 69 LDTNWTWVQLRQMQLGGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYREK 118
LD W Q+ M GN A + F + QL RE+
Sbjct: 78 LDA-WEEAQVEFMASHGNDAARARFESKV---PSFYYRPTPSDCQLLREQ 123
>1dcq_A PYK2-associated protein beta; zinc-binding module, ankyrin
repeats, metal binding protein; 2.10A {Mus musculus}
SCOP: d.211.1.1 g.45.1.1
Length = 278
Score = 115 bits (288), Expect = 2e-32
Identities = 29/83 (34%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 14 IFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNW 73
I +++ + N C DC A +PTW S G+ CI+CS +HR LGVH S ++S LD
Sbjct: 7 IISEVQRMTGNDVCCDCGAPDPTWLSTNLGILTCIECSGIHRELGVHYSRMQSLTLDV-L 65
Query: 74 TWVQLRQMQLGGNANAVSFFNQH 96
+L + GNA
Sbjct: 66 GTSELLLAKNIGNAGFNEIMECC 88
>3lvq_E ARF-GAP with SH3 domain, ANK repeat and PH domain containing
protein 3, ADP-ribosylation...; GDP, ASAP3, UPLC1,
linkers, alternat splicing; HET: GDP; 3.38A {Homo
sapiens} PDB: 3lvr_E*
Length = 497
Score = 101 bits (252), Expect = 4e-26
Identities = 30/91 (32%), Positives = 45/91 (49%), Gaps = 1/91 (1%)
Query: 3 GEGPNKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLS 62
+G + +++ ++++ P N +C DC A +PTW S GV CI CS VHR LGV S
Sbjct: 2 HDGEPHDLTKLLIAEVKSRPGNSQCCDCGAADPTWLSTNLGVLTCIQCSGVHRELGVRFS 61
Query: 63 FVRSTQLDTNWTWVQLRQMQLGGNANAVSFF 93
++S LD +L GN +
Sbjct: 62 RMQSLTLD-LLGPSELLLALNMGNTSFNEVM 91
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 56.4 bits (135), Expect = 3e-10
Identities = 24/140 (17%), Positives = 49/140 (35%), Gaps = 19/140 (13%)
Query: 10 DIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICI---DCSAVHRGLGVHLSFVRS 66
D + + ++I + +E D + S T +F + V + FV
Sbjct: 34 DCKDVQDMPKSILSKEEI-DHIIMSKDAVSGTLRLFWTLLSKQEEMVQK-------FVEE 85
Query: 67 T-QLDTNWTWVQLRQMQLGGNANAVSFFNQHNCTSKDAQ--QKYN-SRAAQLYREKLQHA 122
+++ + ++ Q + + Q + D Q KYN SR KL+ A
Sbjct: 86 VLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPY--LKLRQA 143
Query: 123 AVQAMKIHGTKLFLDAMHGC 142
++ + +D + G
Sbjct: 144 LLEL--RPAKNVLIDGVLGS 161
Score = 29.4 bits (65), Expect = 0.42
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 9/61 (14%)
Query: 10 DIEVIFKKLRNIPTNKECFDCNAKNPTWSSVT----YGVFICIDCSAVHRGLGVHLSFVR 65
D + +K+R+ T NA +++ Y +IC + R + L F+
Sbjct: 499 DFRFLEQKIRHDSTA-----WNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLP 553
Query: 66 S 66
Sbjct: 554 K 554
>1u5k_A Hypothetical protein; OBD-fold, Zn-binding,
recombination,replication; 2.00A {Deinococcus
radiodurans} SCOP: b.40.4.13 g.45.1.2 PDB: 1w3s_A 2v1c_C
Length = 244
Score = 31.0 bits (70), Expect = 0.11
Identities = 8/27 (29%), Positives = 11/27 (40%)
Query: 26 ECFDCNAKNPTWSSVTYGVFICIDCSA 52
C C A +P G +C C+A
Sbjct: 152 RCARCGAPDPEHPDPLGGQLLCSKCAA 178
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 27.7 bits (61), Expect = 1.3
Identities = 9/38 (23%), Positives = 13/38 (34%), Gaps = 7/38 (18%)
Query: 20 NIPTNKECFDCNAKNPT----WSSVTYGVFICIDCSAV 53
N+ C +C P +S G +C C V
Sbjct: 17 NLNIVLTCPECKVYPPKIVERFSE---GDVVCALCGLV 51
>1muk_A Minor core protein lambda 3; single subunit polymerase fold,
fingers, PALM, thumb, right hand configuration, viral
protein; 2.50A {Reovirus SP} SCOP: e.8.1.4 PDB: 1mwh_A*
1n1h_A* 1n35_A* 1n38_A* 1uon_A* 2cse_1
Length = 1267
Score = 27.4 bits (60), Expect = 2.2
Identities = 6/23 (26%), Positives = 14/23 (60%)
Query: 38 SSVTYGVFICIDCSAVHRGLGVH 60
+S+T+ F+ + +A+H G+
Sbjct: 591 ASITWDFFLSVIMAAIHEGVASS 613
>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein,
neurite growth regulation; HET: NAG BMA; 2.00A {Mus
musculus}
Length = 361
Score = 26.0 bits (57), Expect = 5.3
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 16 KKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSA 52
KKL NI + + F+C+ + G + I C
Sbjct: 235 KKLHNI-FSLDFFNCSEYKESAWEAHLGDTLTIRCDT 270
>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET:
ADP; 3.90A {Thermus thermophilus}
Length = 499
Score = 25.6 bits (57), Expect = 6.3
Identities = 5/14 (35%), Positives = 8/14 (57%)
Query: 79 RQMQLGGNANAVSF 92
R + G + +A SF
Sbjct: 1 RNGRAGPSDSAFSF 14
>2wux_A Polyhedrin; microcrystals, polyhedra, viral protein, viral
occlusion BODY, viral capsid; 1.84A {Autographa
californica nuclearpolyhedrosis virus} PDB: 3jw6_A*
2wuy_A 3jvb_A
Length = 245
Score = 25.4 bits (55), Expect = 8.0
Identities = 11/43 (25%), Positives = 19/43 (44%)
Query: 5 GPNKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFIC 47
GP KN +FK++RN+ + K + T+ F+
Sbjct: 62 GPGKNQKLTLFKEIRNVKPDTMKLVVGWKGKEFYRETWTRFME 104
>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A
{Bacillus phage SPP1}
Length = 315
Score = 25.2 bits (56), Expect = 9.0
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 4 EGPNKNDIEVIFKKLRNIPT 23
E +KN +EVI K R+ P
Sbjct: 272 ESESKNIVEVIIAKHRDGPV 291
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 0.132 0.419
Gapped
Lambda K H
0.267 0.0574 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,121,138
Number of extensions: 103883
Number of successful extensions: 264
Number of sequences better than 10.0: 1
Number of HSP's gapped: 248
Number of HSP's successfully gapped: 26
Length of query: 144
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 59
Effective length of database: 4,328,508
Effective search space: 255381972
Effective search space used: 255381972
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 (21.9 bits)
S2: 52 (24.2 bits)