RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17456
(203 letters)
>1ku1_A ARF guanine-nucleotide exchange factor 2; SEC7 domain, guanine
nucleotide exchange factor (GEF), ARF small GTP-binding
proteins; 1.93A {Saccharomyces cerevisiae} SCOP:
a.118.3.1 PDB: 1re0_B*
Length = 230
Score = 112 bits (282), Expect = 3e-31
Identities = 31/75 (41%), Positives = 44/75 (58%)
Query: 118 KTLINVAHTDDTAYVLAYSIIMLTTDLHSPQVKSKMTKEQYIRLNRGISDSQDLPEAYLS 177
+ V D+ ++L+YSIIML TDLH+PQVK M+ E Y +G + +D P YL
Sbjct: 150 DDISTVQPDADSVFILSYSIIMLNTDLHNPQVKEHMSFEDYSGNLKGCCNHKDFPFWYLD 209
Query: 178 KIYDEIADQEIKMKS 192
++Y I D+EI M
Sbjct: 210 RVYCSIRDKEIVMPE 224
Score = 89.5 bits (222), Expect = 2e-22
Identities = 24/62 (38%), Positives = 37/62 (59%)
Query: 1 MYAYVDQMQFAGRDLVSALRYFLEGFRLPGEAQKIDRLMEKFASRYCENNPNVGLQNCDD 60
+ Y+ F+G + A+R L FRLPGE+Q+I+R++E F+S YCEN + D+
Sbjct: 88 LNEYIRLFDFSGLRVDEAIRILLTKFRLPGESQQIERIIEAFSSAYCENQDYDPSKISDN 147
Query: 61 TE 62
E
Sbjct: 148 AE 149
>3ltl_A Brefeldin A-inhibited guanine nucleotide-exchange 1; all alpha,
guanine-nucleotide releasing factor, signaling PR; 2.20A
{Homo sapiens} PDB: 3l8n_A 3swv_A
Length = 211
Score = 111 bits (279), Expect = 6e-31
Identities = 53/73 (72%), Positives = 63/73 (86%)
Query: 125 HTDDTAYVLAYSIIMLTTDLHSPQVKSKMTKEQYIRLNRGISDSQDLPEAYLSKIYDEIA 184
+ DTAYVLAYSIIMLTTDLHSPQVK+KMTKEQYI++NRGI+DS+DLPE YLS IY+EIA
Sbjct: 139 ASADTAYVLAYSIIMLTTDLHSPQVKNKMTKEQYIKMNRGINDSKDLPEEYLSAIYNEIA 198
Query: 185 DQEIKMKSANKPG 197
++I MK + G
Sbjct: 199 GKKISMKETKETG 211
Score = 91.7 bits (228), Expect = 2e-23
Identities = 44/61 (72%), Positives = 47/61 (77%)
Query: 1 MYAYVDQMQFAGRDLVSALRYFLEGFRLPGEAQKIDRLMEKFASRYCENNPNVGLQNCDD 60
MYAYVDQ F+G+D VSALR FLEGFRLPGEAQKIDRLMEKFA+RY E N L D
Sbjct: 83 MYAYVDQHDFSGKDFVSALRMFLEGFRLPGEAQKIDRLMEKFAARYLECNQGQTLFASAD 142
Query: 61 T 61
T
Sbjct: 143 T 143
>1r8s_E ARNO; protein transport/exchange factor, protein transport-exchang
complex; HET: GDP; 1.46A {Homo sapiens} SCOP: a.118.3.1
PDB: 1r8m_E* 1r8q_E* 1s9d_E* 1pbv_A 1bc9_A
Length = 203
Score = 110 bits (276), Expect = 2e-30
Identities = 32/65 (49%), Positives = 46/65 (70%)
Query: 128 DTAYVLAYSIIMLTTDLHSPQVKSKMTKEQYIRLNRGISDSQDLPEAYLSKIYDEIADQE 187
DT YVL+YS+IML TDLH+P V+ KM E+++ +NRGI++ DLPE L +YD I ++
Sbjct: 134 DTCYVLSYSVIMLNTDLHNPNVRDKMGLERFVAMNRGINEGGDLPEELLRNLYDSIRNEP 193
Query: 188 IKMKS 192
K+
Sbjct: 194 FKIPE 198
Score = 84.4 bits (209), Expect = 1e-20
Identities = 32/53 (60%), Positives = 39/53 (73%)
Query: 1 MYAYVDQMQFAGRDLVSALRYFLEGFRLPGEAQKIDRLMEKFASRYCENNPNV 53
++A+VD +F +LV ALR FL FRLPG+AQKIDR+ME FA RYC NP V
Sbjct: 77 LHAFVDLHEFTDLNLVQALRQFLWSFRLPGKAQKIDRMMEAFAQRYCLCNPGV 129
>2r09_A Cytohesin-3; autoinhibition, GRP1, PIP3, ARF, 3-phosphoinositide,
pleckst homology domain, guanine-nucleotide releasing
factor, signa protein; HET: 4IP PGE PE5; 1.90A {Mus
musculus} SCOP: a.118.3.1 b.55.1.1 PDB: 2r0d_A*
Length = 347
Score = 96.2 bits (239), Expect = 4e-24
Identities = 29/65 (44%), Positives = 44/65 (67%)
Query: 128 DTAYVLAYSIIMLTTDLHSPQVKSKMTKEQYIRLNRGISDSQDLPEAYLSKIYDEIADQE 187
DT YVL+++IIML T LH+ V+ K T E++I +NRGI++ DLPE L +Y+ I ++
Sbjct: 136 DTCYVLSFAIIMLNTSLHNHNVRDKPTAERFITMNRGINEGGDLPEELLRNLYESIKNEP 195
Query: 188 IKMKS 192
K+
Sbjct: 196 FKIPE 200
Score = 85.5 bits (211), Expect = 4e-20
Identities = 34/53 (64%), Positives = 40/53 (75%)
Query: 1 MYAYVDQMQFAGRDLVSALRYFLEGFRLPGEAQKIDRLMEKFASRYCENNPNV 53
+ A+V+ +FA +LV ALR FL FRLPGEAQKIDR+ME FASRYC NP V
Sbjct: 79 LQAFVELHEFADLNLVQALRQFLWSFRLPGEAQKIDRMMEAFASRYCLCNPGV 131
Score = 28.5 bits (63), Expect = 1.4
Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 2/71 (2%)
Query: 51 PNVGLQNCDDTEIASLCLEGIRCAIRIACIFHLTLERNAYVQALARFTLLTANSPITEMK 110
N+ ++ +D + C E + + I E + V + ++P E K
Sbjct: 259 ENLSIREVEDPRKPN-CFELYNPSHKGQVIKACKTEADGRVVE-GNHVVYRISAPSPEEK 316
Query: 111 AKNIETIKTLI 121
+ +++IK I
Sbjct: 317 EEWMKSIKASI 327
>1xsz_A Guanine nucleotide exchange protein; ARF guanine nucleotide
exchange factor, signaling protein; 1.41A {Legionella
pneumophila} SCOP: a.118.3.1 d.129.9.1 PDB: 1xt0_B
Length = 356
Score = 96.7 bits (240), Expect = 4e-24
Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 122 NVAHTDDTAYVLAYSIIMLTTDLHSPQV--KSKMTKEQYIRLNRGISDSQDLPEAYLSKI 179
+V D AY+LA+ IML TDLH+P + K+KMT + R RG ++ D +L ++
Sbjct: 126 DVVSNADAAYLLAFQTIMLNTDLHNPSIPEKNKMTVDGLKRNLRGGNNGGDFDAKFLEEL 185
Query: 180 YDEIADQEIKMKS 192
Y EI + ++
Sbjct: 186 YSEIKAKPFELNF 198
Score = 82.4 bits (203), Expect = 6e-19
Identities = 27/53 (50%), Positives = 37/53 (69%)
Query: 1 MYAYVDQMQFAGRDLVSALRYFLEGFRLPGEAQKIDRLMEKFASRYCENNPNV 53
+ A+ QM F G+ V LR FL+ F+LPGEAQKIDRL++ F+ Y + NP+V
Sbjct: 75 LKAFTSQMNFNGQSFVEGLRTFLKTFKLPGEAQKIDRLVQSFSGAYFQQNPDV 127
Score = 63.1 bits (153), Expect = 3e-12
Identities = 12/77 (15%), Positives = 20/77 (25%), Gaps = 6/77 (7%)
Query: 52 NVGLQNCDDTEIASLCLEGIRCAIRIACIFHLTLER------NAYVQALARFTLLTANSP 105
+ D+ A ++ I +F LA +SP
Sbjct: 261 KGTITLTDNKTSAQATIQVYTPNIFSKWLFGEQPRVIIQPGQTKESIDLAAKAAADFSSP 320
Query: 106 ITEMKAKNIETIKTLIN 122
+ KA + LI
Sbjct: 321 VKNFKATYDYEVGDLIK 337
>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 = 44.8 bits (105), Expect = 8e-06
Identities = 32/186 (17%), Positives = 61/186 (32%), Gaps = 44/186 (23%)
Query: 10 FAGRDLVSALRYFLEG--FRLPGEAQKID--------RLMEKFASRYCENNPNVGLQNCD 59
++ S L +L+ LP E + + + + +N +V NCD
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW-DNWKHV---NCD 353
Query: 60 D-TEIASLCLEGIRCAIRIACIFHLTLERNAYVQALARFTLLTANSPITEMKAKNIETIK 118
T I L LE Y + R ++ ++ I +
Sbjct: 354 KLTTIIESSLN--------------VLEPAEYRKMFDRLSVFPPSAHIPT------ILLS 393
Query: 119 TLINVAHTDDTAYVLA----YSII-----MLTTDLHSPQVKSKMTKEQYIRLNRGISDSQ 169
+ D V+ YS++ T + S ++ K+ E L+R I D
Sbjct: 394 LIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHY 453
Query: 170 DLPEAY 175
++P+ +
Sbjct: 454 NIPKTF 459
Score = 37.5 bits (86), Expect = 0.002
Identities = 31/209 (14%), Positives = 71/209 (33%), Gaps = 69/209 (33%)
Query: 5 VDQMQFAGRDLVSALRYFLEGFRLPGEAQKIDRLMEKFASRYCENNPNVGLQNCDDTEIA 64
+ Q+ +D++S F + F ++ F +C D +
Sbjct: 11 TGEHQYQYKDILS---VFEDAF------------VDNF--------------DCKDVQ-- 39
Query: 65 SLCLEGIRCAIRIACIFHLTLERNAYVQALARFTLLTANSPITEMKAKNIETIKTLINVA 124
+ + + I H+ + ++A L F L +K E ++ +
Sbjct: 40 ----DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTL---------LSKQEEMVQKFVEEV 86
Query: 125 HTDDTAYVLAYSIIMLTTDLHSPQVKSKMTKEQYI-RLNRGISDSQDLPEAYLS--KIYD 181
+ Y +M + + + Q + M YI + +R +D+Q + +S + Y
Sbjct: 87 LRIN------YKFLM--SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYL 138
Query: 182 EI--ADQEIK---------MKSANKPGKQ 199
++ A E++ + + GK
Sbjct: 139 KLRQALLELRPAKNVLIDGVLGS---GKT 164
>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 = 38.9 bits (90), Expect = 7e-04
Identities = 25/130 (19%), Positives = 43/130 (33%), Gaps = 34/130 (26%)
Query: 3 AYVDQMQFAGRDLVSALRYFLEGFRLPGEAQKIDRLMEKFASRYCENNPNVGLQNCDDTE 62
+ D M LV + Y R G M+ R N G+ +
Sbjct: 1772 SLADVMSIE--SLVEVVFY-----R--G------MTMQVAVPRDELGRSNYGMIAINPGR 1816
Query: 63 I-ASLCLEGIRCAI-RIACIFHLTLE---RNA----YV-----QALARFTLLTANSPITE 108
+ AS E ++ + R+ +E N YV +AL T + +
Sbjct: 1817 VAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNV-----LNF 1871
Query: 109 MKAKNIETIK 118
+K + I+ I+
Sbjct: 1872 IKLQKIDIIE 1881
Score = 31.6 bits (71), Expect = 0.17
Identities = 18/97 (18%), Positives = 34/97 (35%), Gaps = 24/97 (24%)
Query: 100 LTANSPITEMKAKNI-ETIKTLINVAHTDDTAYVLAYSIIMLTTDLHSPQVKSKMTKEQY 158
L S A+++ H DT +SI+ + + +P
Sbjct: 1635 LYKTSKA----AQDVWNRAD-----NHFKDT---YGFSILDIVIN--NP-------VNLT 1673
Query: 159 IRLNRGISDSQDLPEAYLSKIYDEIADQEIKMKSANK 195
I G + + E Y + I++ I D ++K + K
Sbjct: 1674 I-HFGGEK-GKRIRENYSAMIFETIVDGKLKTEKIFK 1708
>3fk2_A Glucocorticoid receptor DNA-binding factor 1; structural genomics
consortium, GTPase-activating protein, SGC, alternative
splicing, anti-oncogene; 2.80A {Homo sapiens}
Length = 246
Score = 29.7 bits (67), Expect = 0.53
Identities = 8/45 (17%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 24 EG-FRLPGEAQKIDRLMEKFASRYCENNPNVGLQNCDDTEIASLC 67
EG +R+ G +++ L +F ++N ++ ++ +A
Sbjct: 87 EGIYRVSGNKSEMESLQRQFD---QDHNLDLAEKDFTVNTVAGAM 128
>3eap_A RHO GTPase-activating protein 11A; GAP, structural genomics
consortium, GTPase activation, phosphoprotein,
polymorphism hydrolase activator, SGC; 2.30A {Homo
sapiens}
Length = 271
Score = 28.5 bits (64), Expect = 1.5
Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 9/57 (15%)
Query: 13 RDLVSALRYFL--EG-FRLPGEAQKIDRLMEKFASRYCENNPNVGLQNCDDTEIASL 66
D ++L + EG FR G ++ L K ++ L + +IA L
Sbjct: 88 VDACTSLEDHIHTEGLFRKSGSVIRLKALKNKV-----DHGEGC-LSSAPPCDIAGL 138
>2ee4_A RHO GTPase activating protein 5 variant; all alpha protein,
GTPase-activating protein for RHO family members,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2ee5_A
Length = 209
Score = 27.6 bits (62), Expect = 2.3
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 24 EG-FRLPGEAQKIDRLMEKFASRYCENNPNVGLQNCDDTEIASLC 67
EG +R+ G D + ++F ++N N+ +A
Sbjct: 46 EGLYRVSGNKTDQDNIQKQFD---QDHNINLVSMEVTVNAVAGAL 87
>3msx_B RHO GTPase-activating protein 20; protein-proten complex,
transition state, protein BI; HET: GDP; 1.65A {Homo
sapiens}
Length = 201
Score = 27.2 bits (61), Expect = 2.7
Identities = 11/44 (25%), Positives = 15/44 (34%), Gaps = 6/44 (13%)
Query: 24 EG-FRLPGEAQKIDRLMEKFASRYCENNPNVGLQNCDDTEIASL 66
+G FR + L EK + V L IAS+
Sbjct: 45 KGIFRQSANVKSCRELKEKL-----NSGVEVHLDCESIFVIASV 83
>1tx4_A P50-rhogap; complex (GTPase activation/proto-oncogene), GTPase,
transition state, GAP; HET: GDP; 1.65A {Homo sapiens}
SCOP: a.116.1.1 PDB: 1am4_A* 1grn_B*
Length = 198
Score = 27.2 bits (61), Expect = 3.0
Identities = 8/46 (17%), Positives = 14/46 (30%), Gaps = 7/46 (15%)
Query: 24 EG-FRLPGEAQKIDRLMEKFASRYCENNPNVGLQNCDD-TEIASLC 67
EG FR Q + + +K+ V + A +
Sbjct: 45 EGIFRRSANTQVVREVQQKY-----NMGLPVDFDQYNALHLPAVIL 85
>1ow3_A RHO-GTPase-activating protein 1; complex, GTPase, GAP, transition
state, gene regulation/signaling protein complex; HET:
GDP; 1.80A {Homo sapiens} SCOP: a.116.1.1 PDB: 1rgp_A
2ngr_B*
Length = 242
Score = 27.3 bits (61), Expect = 3.5
Identities = 8/46 (17%), Positives = 15/46 (32%), Gaps = 7/46 (15%)
Query: 24 EG-FRLPGEAQKIDRLMEKFASRYCENNPNVGLQNCDD-TEIASLC 67
EG FR Q + + +K+ V ++ A +
Sbjct: 81 EGIFRRSANTQVVREVQQKY-----NMGLPVDFDQYNELHLPAVIL 121
>3ed3_A Protein disulfide-isomerase MPD1; thioredoxin-like domain, CXXC,
endoplasmic reticulum, glycoprotein, redox-active
center; 2.00A {Saccharomyces cerevisiae}
Length = 298
Score = 27.4 bits (60), Expect = 3.6
Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 2/34 (5%)
Query: 40 EKFASRYCENNPNVGLQNCDDTEIASLCLE-GIR 72
K A R + V NCD + +LC + +
Sbjct: 58 RKAAKRL-DGVVQVAAVNCDLNKNKALCAKYDVN 90
>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 = 26.5 bits (57), Expect = 5.5
Identities = 5/29 (17%), Positives = 15/29 (51%), Gaps = 6/29 (20%)
Query: 31 EAQKIDRL---MEKFASRYCENNPNVGLQ 56
E Q + +L ++ +A ++ P + ++
Sbjct: 18 EKQALKKLQASLKLYAD---DSAPALAIK 43
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
0.320 0.133 0.378
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,906,919
Number of extensions: 161118
Number of successful extensions: 325
Number of sequences better than 10.0: 1
Number of HSP's gapped: 322
Number of HSP's successfully gapped: 31
Length of query: 203
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 114
Effective length of database: 4,216,824
Effective search space: 480717936
Effective search space used: 480717936
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: 55 (24.8 bits)