BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy5715
(107 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XA6|A Chain A, Crystal Structure Of The Human Beta2-Chimaerin
Length = 466
Score = 57.8 bits (138), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/61 (47%), Positives = 40/61 (65%), Gaps = 4/61 (6%)
Query: 14 VVHE----LPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGDDRSWTC 69
VHE LP H++TL+Y++ HLK+V N + N M A NL I+FGPTL+R +D + T
Sbjct: 385 AVHEVLMLLPPAHYETLRYLMIHLKKVTMNEKDNFMNAENLGIVFGPTLMRPPEDSTLTT 444
Query: 70 L 70
L
Sbjct: 445 L 445
>pdb|2OSA|A Chain A, The Rho-Gap Domain Of Human N-Chimaerin
Length = 202
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 35/53 (66%)
Query: 18 LPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGDDRSWTCL 70
LP H +TL+Y++ HLKRV + + N M A NL I+FGPTL+R+ + + L
Sbjct: 129 LPPAHCETLRYLMAHLKRVTLHEKENLMNAENLGIVFGPTLMRSPELDAMAAL 181
>pdb|3CXL|A Chain A, Crystal Structure Of Human Chimerin 1 (Chn1)
Length = 463
Score = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/46 (50%), Positives = 33/46 (71%)
Query: 18 LPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGD 63
LP H +TL+Y++ HLKRV + + N M A NL I+FGPTL+R+ +
Sbjct: 390 LPPAHCETLRYLMAHLKRVTLHEKENLMNAENLGIVFGPTLMRSPE 435
>pdb|1F7C|A Chain A, Crystal Structure Of The Bh Domain From Graf, The Gtpase
Regulator Associated With Focal Adhesion Kinase
Length = 231
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 37/65 (56%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGDDRSWTCLVFG 73
+VH LPE + Q L ++ HL +V DN + N M NL ++FGPTL+R ++ +
Sbjct: 140 LVHRLPEKNRQMLHLLMNHLAKVADNHKQNLMTVANLGVVFGPTLLRPQEETVAAIMDIK 199
Query: 74 FYKLL 78
F ++
Sbjct: 200 FQNIV 204
>pdb|3IUG|A Chain A, Crystal Structure Of The Rhogap Domain Of Rics
pdb|3IUG|B Chain B, Crystal Structure Of The Rhogap Domain Of Rics
Length = 229
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 37/53 (69%)
Query: 9 LKLVLVVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRA 61
+K+ V+ +LP H++TL+++++HL + D + M A+NLAI++ P L+R+
Sbjct: 132 IKIHDVIQQLPPPHYRTLEFLMRHLSLLADYCSITNMHAKNLAIVWAPNLLRS 184
>pdb|2NGR|B Chain B, Transition State Complex For Gtp Hydrolysis By Cdc42:
Comparisons Of The High Resolution Structures For Cdc42
Bound To The Active And Catalytically Compromised Forms
Of The Cdc42-gap
Length = 234
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 33/50 (66%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGD 63
V+ LPE ++Q L+++ L ++ +S+ NKM NLA++FGP L+ A D
Sbjct: 151 VLQTLPEENYQVLRFLTAFLVQISAHSDQNKMTNTNLAVVFGPNLLWAKD 200
>pdb|3FK2|A Chain A, Crystal Structure Of The Rhogap Domain Of Human
Glucocorticoid Receptor Dna-Binding Factor 1
pdb|3FK2|B Chain B, Crystal Structure Of The Rhogap Domain Of Human
Glucocorticoid Receptor Dna-Binding Factor 1
pdb|3FK2|C Chain C, Crystal Structure Of The Rhogap Domain Of Human
Glucocorticoid Receptor Dna-Binding Factor 1
pdb|3FK2|D Chain D, Crystal Structure Of The Rhogap Domain Of Human
Glucocorticoid Receptor Dna-Binding Factor 1
Length = 246
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 32/47 (68%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVR 60
V+ + P+ + + KY++ HL +V N++VN M + NL+I F PTL+R
Sbjct: 167 VLKKFPKENHEVFKYVISHLNKVSHNNKVNLMTSENLSICFWPTLMR 213
>pdb|1TX4|A Chain A, RhoRHOGAPGDP(DOT)ALF4 COMPLEX
Length = 198
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 33/50 (66%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGD 63
V+ LPE ++Q L+++ L ++ +S+ NKM NLA++FGP L+ A D
Sbjct: 123 VLQTLPEENYQVLRFLTAFLVQISAHSDQNKMTNTNLAVVFGPNLLWAKD 172
>pdb|1GRN|B Chain B, Crystal Structure Of The Cdc42CDC42GAPALF3 COMPLEX
Length = 203
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 33/50 (66%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGD 63
V+ LPE ++Q L+++ L ++ +S+ NKM NLA++FGP L+ A D
Sbjct: 120 VLQTLPEENYQVLRFLTAFLVQISAHSDQNKMTNTNLAVVFGPNLLWAKD 169
>pdb|1OW3|A Chain A, Crystal Structure Of Rhoa.Gdp.Mgf3-In Complex With Rhogap
pdb|1RGP|A Chain A, Gtpase-Activation Domain From Rhogap
Length = 242
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 33/50 (66%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGD 63
V+ LPE ++Q L+++ L ++ +S+ NKM NLA++FGP L+ A D
Sbjct: 159 VLQTLPEENYQVLRFLTAFLVQISAHSDQNKMTNTNLAVVFGPNLLWAKD 208
>pdb|1AM4|A Chain A, Complex Between Cdc42hs.Gmppnp And P50 Rhogap (H. Sapiens)
pdb|1AM4|B Chain B, Complex Between Cdc42hs.Gmppnp And P50 Rhogap (H. Sapiens)
pdb|1AM4|C Chain C, Complex Between Cdc42hs.Gmppnp And P50 Rhogap (H. Sapiens)
Length = 199
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 33/50 (66%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGD 63
V+ LPE ++Q L+++ L ++ +S+ NKM NLA++FGP L+ A D
Sbjct: 124 VLQTLPEENYQVLRFLTAFLVQISAHSDQNKMTNTNLAVVFGPNLLWAKD 173
>pdb|3BYI|A Chain A, Crystal Structure Of Human Rho Gtpase Activating Protein
15 (arhgap15)
pdb|3BYI|B Chain B, Crystal Structure Of Human Rho Gtpase Activating Protein
15 (arhgap15)
pdb|3BYI|C Chain C, Crystal Structure Of Human Rho Gtpase Activating Protein
15 (arhgap15)
pdb|3BYI|D Chain D, Crystal Structure Of Human Rho Gtpase Activating Protein
15 (arhgap15)
Length = 214
Score = 43.1 bits (100), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 33/51 (64%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGDD 64
+V +LP + T+K + HL ++V + N M ++L I+FGPTL+RA ++
Sbjct: 135 LVQKLPPPNRDTMKVLFGHLTKIVAKASKNLMSTQSLGIVFGPTLLRAENE 185
>pdb|2OVJ|A Chain A, The Crystal Structure Of The Human Rac Gtpase Activating
Protein 1 (Racgap1) Mgcracgap
Length = 201
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLV 59
V ELP+ + TL +++ HL+RV S KM+ NLA +FGPT+V
Sbjct: 116 AVGELPQANRDTLAFLMIHLQRVA-QSPHTKMDVANLAKVFGPTIV 160
>pdb|2EE4|A Chain A, Solution Structure Of The Rhogap Domain From Human Rho
Gtpase Activating Protein 5 Variant
Length = 209
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 25/39 (64%)
Query: 22 HFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVR 60
++ +Y++ HL RV ++N M A NL+I F PTL+R
Sbjct: 134 NYDVFRYVITHLNRVSQQHKINLMTADNLSICFWPTLMR 172
>pdb|2EE5|A Chain A, Solution Structure Of The N-Teruminus Extended Rhogap
Domain From Human Rho Gtpase Activating Protein 5
Variant
Length = 219
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 25/39 (64%)
Query: 22 HFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVR 60
++ +Y++ HL RV ++N M A NL+I F PTL+R
Sbjct: 144 NYDVFRYVITHLNRVSQQHKINLMTADNLSICFWPTLMR 182
>pdb|3EAP|A Chain A, Crystal Structure Of The Rhogap Domain Of Arhgap11a
pdb|3EAP|B Chain B, Crystal Structure Of The Rhogap Domain Of Arhgap11a
pdb|3EAP|C Chain C, Crystal Structure Of The Rhogap Domain Of Arhgap11a
pdb|3EAP|D Chain D, Crystal Structure Of The Rhogap Domain Of Arhgap11a
Length = 271
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%)
Query: 18 LPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGD 63
L +H L+Y L+ V S NKM++ NLA++F P L++ +
Sbjct: 181 LADHTVHVLRYFFNFLRNVSLRSSENKMDSSNLAVIFAPNLLQTSE 226
>pdb|1PBW|A Chain A, Structure Of Bcr-Homology (Bh) Domain
pdb|1PBW|B Chain B, Structure Of Bcr-Homology (Bh) Domain
Length = 216
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 30/52 (57%)
Query: 9 LKLVLVVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVR 60
LK ++ +P ++ TL+Y+L+H ++ S N + AR L+ +F P L R
Sbjct: 120 LKKLIRSPSIPHQYWLTLQYLLKHFFKLSQTSSKNLLNARVLSEIFSPMLFR 171
>pdb|2QV2|A Chain A, A Role Of The Lowe Syndrome Protein Ocrl In Early Steps Of
The Endocytic Pathway
Length = 342
Score = 33.1 bits (74), Expect = 0.042, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 26/47 (55%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVR 60
V+ +LP H +Y++ L+ ++ SE N + A +A +F L+R
Sbjct: 265 VISQLPRCHRNVFRYLMAFLRELLKFSEYNSVNANMIATLFTSLLLR 311
>pdb|3QIS|A Chain A, Recognition Of The F&h Motif By The Lowe Syndrome Protein
Ocrl
Length = 366
Score = 32.7 bits (73), Expect = 0.047, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 26/47 (55%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVR 60
V+ +LP H +Y++ L+ ++ SE N + A +A +F L+R
Sbjct: 289 VISQLPRCHRNVFRYLMAFLRELLKFSEYNSVNANMIATLFTSLLLR 335
>pdb|2XS6|A Chain A, Crystal Structure Of The Rhogap Domain Of Human Pik3r2
Length = 214
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 18 LPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFG 55
LP H TL+++LQHL RV + R L FG
Sbjct: 130 LPLHRALTLRFLLQHLGRVARRAPALGPAVRALGATFG 167
>pdb|3MSX|B Chain B, Crystal Structure Of Rhoa.Gdp.Mgf3 In Complex With Gap
Domain Of Arhgap20
Length = 201
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 26/46 (56%)
Query: 14 VVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLV 59
++ +LP + L+Y+ L + +S N+M A NLA+ P+++
Sbjct: 123 LLDQLPRANVVLLRYLFGVLHNIEQHSSSNQMTAFNLAVCVAPSIL 168
>pdb|3KUQ|A Chain A, Crystal Structure Of The Dlc1 Rhogap Domain
Length = 228
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 2 YCVQDFQLKLV-LVVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTL 58
Y +D +L+ + + LP+ + + L+ +L L V + N+M NLA+ P+L
Sbjct: 121 YVPKDQRLQAIKAAIMLLPDENREVLQTLLYFLSDVTAAVKENQMTPTNLAVCLAPSL 178
>pdb|2HYI|A Chain A, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|G Chain G, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2J0Q|C Chain C, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|F Chain F, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0S|C Chain C, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
pdb|3EX7|A Chain A, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|E Chain E, The Crystal Structure Of Ejc In Its Transition State
pdb|2XB2|C Chain C, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Y Chain Y, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 146
Score = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 27 KYILQHLKRVVDNSEVNKME 46
K +++ LKR++D+SE+ K +
Sbjct: 54 KSVMEELKRIIDDSEITKED 73
>pdb|1P27|A Chain A, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|C Chain C, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 144
Score = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 27 KYILQHLKRVVDNSEVNKME 46
K +++ LKR++D+SE+ K +
Sbjct: 53 KSVMEELKRIIDDSEITKED 72
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.329 0.142 0.449
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,279,028
Number of Sequences: 62578
Number of extensions: 112758
Number of successful extensions: 526
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 501
Number of HSP's gapped (non-prelim): 24
length of query: 107
length of database: 14,973,337
effective HSP length: 72
effective length of query: 35
effective length of database: 10,467,721
effective search space: 366370235
effective search space used: 366370235
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)