RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17822
(91 letters)
>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 = 68.9 bits (168), Expect = 1e-15
Identities = 38/51 (74%), Positives = 44/51 (86%)
Query: 1 MDPKKGIEWLIQNNLLEPTEMGVAQFLYKGEGLNKTAIGDYLGERHDFNEK 51
MDPKKGI++LI+N+LL+ + VAQFLYKGEGLNKT IGDYLGER DFN K
Sbjct: 27 MDPKKGIQFLIENDLLQSSPEDVAQFLYKGEGLNKTVIGDYLGERDDFNIK 77
>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 = 66.7 bits (163), Expect = 2e-15
Identities = 34/51 (66%), Positives = 42/51 (82%)
Query: 1 MDPKKGIEWLIQNNLLEPTEMGVAQFLYKGEGLNKTAIGDYLGERHDFNEK 51
MDPKKGI++L++N LL+ T +A+FLYKGEGLNKTAIGDYLGER + N
Sbjct: 25 MDPKKGIQFLVENELLQNTPEEIARFLYKGEGLNKTAIGDYLGEREELNLA 75
Score = 48.2 bits (115), Expect = 2e-08
Identities = 28/53 (52%), Positives = 32/53 (60%), Gaps = 10/53 (18%)
Query: 48 FNEK----------NNLLEPTEMGVAQFLYKGEGLNKTAIGDYLGERHDFNEK 90
FN N LL+ T +A+FLYKGEGLNKTAIGDYLGER + N
Sbjct: 23 FNMDPKKGIQFLVENELLQNTPEEIARFLYKGEGLNKTAIGDYLGEREELNLA 75
>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 = 62.4 bits (152), Expect = 9e-14
Identities = 19/51 (37%), Positives = 34/51 (66%)
Query: 1 MDPKKGIEWLIQNNLLEPTEMGVAQFLYKGEGLNKTAIGDYLGERHDFNEK 51
PK+GI++L + +L T +AQFL++ E L+ T +G++LG+ FN++
Sbjct: 31 KKPKRGIQYLQEQGMLGTTPEDIAQFLHQEERLDSTQVGEFLGDNDKFNKE 81
Score = 45.1 bits (107), Expect = 3e-07
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 10/53 (18%)
Query: 48 FNEK----------NNLLEPTEMGVAQFLYKGEGLNKTAIGDYLGERHDFNEK 90
FN+K +L T +AQFL++ E L+ T +G++LG+ FN++
Sbjct: 29 FNKKPKRGIQYLQEQGMLGTTPEDIAQFLHQEERLDSTQVGEFLGDNDKFNKE 81
>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 = 56.2 bits (135), Expect = 4e-11
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 1 MDPKKGIEWLIQNNLLEPTE--MGVAQFLYKG-EGLNKTAIGDYLGERHDFNEK 51
PK GI + + +A+F ++ + L+ A+GDYL N++
Sbjct: 20 AKPKNGINKIKEICEQYKISPNEEIAEFFHQQRKNLDLEAVGDYLSSPEAENQQ 73
>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 = 50.6 bits (121), Expect = 3e-09
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 1 MDPKKGIEWLIQNNLL-EPTEMGVAQFLYKGEG-LNKTAIGDYLGERHDFN 49
PKKGI LI+ + ++ +A+FL+ +NK IG L +
Sbjct: 36 EKPKKGIPMLIEKGFIASDSDKDIAEFLFNNNNRMNKKTIGLLLCHPDKVS 86
>3hw5_A Polymerase acidic protein; avian influenza virus, PA_N, AMP,
phosphoprotein, hydrolase; HET: AMP; 1.81A {Influenza a
virus} PDB: 3hw4_A* 3hw3_A* 3hw6_A 3ebj_A 2w69_A
Length = 261
Score = 26.4 bits (57), Expect = 1.2
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 4/77 (5%)
Query: 4 KKGIEWLIQNNLLEPTEMGVAQFL---YKGEGLNKTAIGDYLGERHD-FNEKNNLLEPTE 59
+ + W + N++ T + +FL Y + IG E H + EK N ++ +
Sbjct: 88 DRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEK 147
Query: 60 MGVAQFLYKGEGLNKTA 76
+ F + GE + A
Sbjct: 148 THIHIFSFTGEEMATKA 164
>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain
III (ATPase domain), ATP-binding, cytoplasm, DNA
replication; HET: ADP; 3.00A {Thermotoga maritima} PDB:
2z4r_A*
Length = 440
Score = 25.7 bits (57), Expect = 2.1
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 4/25 (16%)
Query: 26 FLYKGEGLNKT----AIGDYLGERH 46
F+Y G GL KT +IG+Y+ +
Sbjct: 134 FIYGGVGLGKTHLLQSIGNYVVQNE 158
Score = 25.7 bits (57), Expect = 2.1
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 4/25 (16%)
Query: 65 FLYKGEGLNKT----AIGDYLGERH 85
F+Y G GL KT +IG+Y+ +
Sbjct: 134 FIYGGVGLGKTHLLQSIGNYVVQNE 158
>3bos_A Putative DNA replication factor; P-loop containing nucleoside
triphosphate hydrolases, struct genomics; HET: MSE CDP;
1.75A {Shewanella amazonensis} PDB: 3sc3_A
Length = 242
Score = 25.3 bits (56), Expect = 2.8
Identities = 4/27 (14%), Positives = 7/27 (25%), Gaps = 4/27 (14%)
Query: 26 FLYKGEGLNKT----AIGDYLGERHDF 48
+L+ +T A E
Sbjct: 56 YLWGPVKSGRTHLIHAACARANELERR 82
Score = 25.3 bits (56), Expect = 2.8
Identities = 4/27 (14%), Positives = 7/27 (25%), Gaps = 4/27 (14%)
Query: 65 FLYKGEGLNKT----AIGDYLGERHDF 87
+L+ +T A E
Sbjct: 56 YLWGPVKSGRTHLIHAACARANELERR 82
>3v68_A PF2050 protein, putative uncharacterized protein; DUF2666, double
stranded DNA, DNA binding protein; 1.56A {Pyrococcus
furiosus}
Length = 252
Score = 24.7 bits (53), Expect = 4.7
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 8 EWLIQNNLLEPTEMGVAQFLYKGEGLNKTAIGDYLGERHDFN 49
EW++ N+ + T +A FL + + I YLGE+ D N
Sbjct: 14 EWIVGENVEDFTNENIAMFLSRVSNTVSSKIPGYLGEKIDVN 55
>1l8q_A Chromosomal replication initiator protein DNAA; AAA+,
helix-turn-helix, nucleotide-binding, DNA binding, REP
initiation, DNA binding protein; HET: ADP; 2.70A
{Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB:
3r8f_A* 2hcb_A*
Length = 324
Score = 24.4 bits (54), Expect = 6.2
Identities = 7/21 (33%), Positives = 9/21 (42%), Gaps = 4/21 (19%)
Query: 26 FLYKGEGLNKT----AIGDYL 42
F+Y G KT A G+
Sbjct: 41 FIYGSVGTGKTHLLQAAGNEA 61
Score = 24.4 bits (54), Expect = 6.2
Identities = 7/21 (33%), Positives = 9/21 (42%), Gaps = 4/21 (19%)
Query: 65 FLYKGEGLNKT----AIGDYL 81
F+Y G KT A G+
Sbjct: 41 FIYGSVGTGKTHLLQAAGNEA 61
>3tdu_C Cullin-1, CUL-1; E2:E3, ligase-protein binding complex; 1.50A
{Homo sapiens} PDB: 3tdz_C
Length = 77
Score = 23.6 bits (51), Expect = 6.7
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 4 KKGIEWLIQNNLLEPTEMGVAQFLY 28
KK I+ LI+ LE + + Y
Sbjct: 51 KKCIDILIEKEYLERVDGEKDTYSY 75
>1iuy_A Cullin-3 homologue; winged helix, structural genomics, riken
structural genomics/proteomics initiative, RSGI,
unknown function; NMR {Mus musculus} SCOP: a.4.5.34
Length = 92
Score = 23.7 bits (51), Expect = 7.1
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 4 KKGIEWLIQNNLLEPTEMGVAQFLY 28
KK IE LI+ L T + Y
Sbjct: 66 KKRIEGLIEREYLARTPEDRKVYTY 90
>2hye_C Cullin-4A, CUL-4A; beta propeller, ring finger, zinc finger,
propeller cluster, helical repeats, cullin repeats,
protein binding; HET: DNA; 3.10A {Homo sapiens} SCOP:
a.4.5.34 a.118.17.1 e.40.1.1 PDB: 4a0k_A* 4a0c_C 4a0l_E*
Length = 759
Score = 24.4 bits (52), Expect = 7.3
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 4 KKGIEWLIQNNLLEPTEMGVAQFLY 28
KK IE LI + +E + Q+ Y
Sbjct: 733 KKRIESLIDRDYMERDKDNPNQYHY 757
>2fok_A R.FOKI, FOKI restriction endonuclease; nucleic acid recognition,
DNA-binding protein, type IIS restriction endonuclease;
2.30A {Planomicrobium okeanokoites} SCOP: a.4.5.12
a.4.5.12 a.4.5.12 c.52.1.12 PDB: 1fok_A*
Length = 579
Score = 24.3 bits (52), Expect = 8.4
Identities = 15/82 (18%), Positives = 27/82 (32%), Gaps = 7/82 (8%)
Query: 8 EWLIQNNLLEPTEMGVAQFLYKGEGLNKTAIGDYLGERHDFNEKNN-------LLEPTEM 60
W L +G +++ K + T +G + D + P +
Sbjct: 104 NWSSDGFLRWAHALGFIEYINKSDSFVITDVGLAYSKSADGSAIEKEILIEAISSYPPAI 163
Query: 61 GVAQFLYKGEGLNKTAIGDYLG 82
+ L G+ L K +G LG
Sbjct: 164 RILTLLEDGQHLTKFDLGKNLG 185
>2do7_A Cullin-4B, CUL-4B; helix-turn-helix motif, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 23.8 bits (51), Expect = 8.8
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 4 KKGIEWLIQNNLLEPTEMGVAQFLY 28
KK IE LI + +E + Q+ Y
Sbjct: 69 KKRIESLIDRDYMERDKENPNQYNY 93
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
0.313 0.138 0.408
Gapped
Lambda K H
0.267 0.0530 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,359,628
Number of extensions: 65912
Number of successful extensions: 107
Number of sequences better than 10.0: 1
Number of HSP's gapped: 105
Number of HSP's successfully gapped: 24
Length of query: 91
Length of database: 6,701,793
Length adjustment: 58
Effective length of query: 33
Effective length of database: 5,082,375
Effective search space: 167718375
Effective search space used: 167718375
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: 51 (23.9 bits)