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= psy8293
(124 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KUQ|A Chain A, Crystal Structure Of The Dlc1 Rhogap Domain
Length = 228
Score = 121 bits (304), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 58/103 (56%), Positives = 76/103 (73%), Gaps = 1/103 (0%)
Query: 15 SVFGVPLLVNIQKTGYALPKFIISSFEWLINNASDQIGIFRKPGVKTRIQKLREMADEVD 74
SVFGVPL VN+Q+TG LP+ I + +L N+ DQ+G+FRK GVK+RIQ LR+M +E
Sbjct: 19 SVFGVPLTVNVQRTGQPLPQSIQQAMRYLRNHCLDQVGLFRKSGVKSRIQALRQM-NEGA 77
Query: 75 FKLDEVDSQQAYDVADLVKQYFRELPEVLLTNKSSETFMSIFQ 117
+ Q AYDVAD++KQYFR+LPE L+TNK SETF+ I+Q
Sbjct: 78 IDCVNYEGQSAYDVADMLKQYFRDLPEPLMTNKLSETFLQIYQ 120
>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 = 48.9 bits (115), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 35/99 (35%), Positives = 48/99 (48%), Gaps = 3/99 (3%)
Query: 16 VFGVPLLVNIQKTGYALPKFIISSFEWLINNASDQIGIFRKPGVKTRIQKLREMAD--EV 73
VFG L ++ +G+ +P+ ++ S I GI+R GV + IQ+LR D V
Sbjct: 21 VFGCDLGEHLLNSGFEVPQ-VLQSCTAFIERYGIVDGIYRLSGVASNIQRLRHEFDSEHV 79
Query: 74 DFKLDEVDSQQAYDVADLVKQYFRELPEVLLTNKSSETF 112
E Q + V L K YFRELP LLT + E F
Sbjct: 80 PDLTKEPYVQDIHSVGSLCKLYFRELPNPLLTYQLYEKF 118
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 32/106 (30%), Positives = 55/106 (51%), Gaps = 9/106 (8%)
Query: 16 VFGVPLLV----NIQKTGYALPKFIISSFEWLINNASDQIGIFRKPGVKTRIQKLREMAD 71
+FGVP + + G+ +P F++ + L ++ + G+FRK G R++ L+ +
Sbjct: 64 IFGVPFNALPHSAVPEYGH-IPSFLVDACTSLEDHIHTE-GLFRKSGSVIRLKALK---N 118
Query: 72 EVDFKLDEVDSQQAYDVADLVKQYFRELPEVLLTNKSSETFMSIFQ 117
+VD + S D+A L+KQ+FRELPE +L E + Q
Sbjct: 119 KVDHGEGCLSSAPPCDIAGLLKQFFRELPEPILPADLHEALLKAQQ 164
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 42/89 (47%), Gaps = 1/89 (1%)
Query: 16 VFGVPLLVNIQKTGYALPKFIISSFEWLINNASDQIGIFRKPGVKTRIQKLREMAD-EVD 74
+FG L ++ +P F+ E + D GI+R G IQKLR + + E
Sbjct: 19 IFGSHLHKVCERENSTVPWFVKQCIEAVEKRGLDVDGIYRVSGNLATIQKLRFIVNQEEK 78
Query: 75 FKLDEVDSQQAYDVADLVKQYFRELPEVL 103
LD+ + + V +K +FRELPE L
Sbjct: 79 LNLDDSQWEDIHVVTGALKMFFRELPEPL 107
>pdb|2OVJ|A Chain A, The Crystal Structure Of The Human Rac Gtpase Activating
Protein 1 (Racgap1) Mgcracgap
Length = 201
Score = 32.0 bits (71), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 4/91 (4%)
Query: 25 IQKTGYALPKFIISSFEWLINNASDQIGIFRKPGVKTRIQKLREMADEVDFK--LDEVDS 82
+ +T +P ++ + + G++R G +++L+E V L +VD
Sbjct: 10 VSQTSPMIPSIVVHCVNEIEQRGLTETGLYRISGCDRTVKELKEKFLRVKTVPLLSKVDD 69
Query: 83 QQAYDVADLVKQYFRELPEVLLTNKSSETFM 113
A + L+K + R L E LLT + + FM
Sbjct: 70 IHA--ICSLLKDFLRNLKEPLLTFRLNRAFM 98
>pdb|2JZY|A Chain A, Solution Structure Of C-Terminal Effector Domain Of
Putative Two-Component-System Response Regulator
Involved In Copper Resistance From Klebsiella
Pneumoniae
Length = 112
Score = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 25 IQKTGYALPKFIISSFEWLINNASD 49
+Q+TG LP+ +ISS W +N SD
Sbjct: 41 LQRTGEVLPRSLISSLVWNMNFDSD 65
>pdb|1TX4|A Chain A, RhoRHOGAPGDP(DOT)ALF4 COMPLEX
Length = 198
Score = 28.9 bits (63), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 32 LPKFIISSFEWLINNASDQIGIFRKPG---VKTRIQKLREMADEVDFKLDEVDSQQAYDV 88
+P + + +L +A GIFR+ V +Q+ M VDF D A +
Sbjct: 26 IPIVLRETVAYLQAHALTTEGIFRRSANTQVVREVQQKYNMGLPVDF-----DQYNALHL 80
Query: 89 -ADLVKQYFRELPEVLLT 105
A ++K + RELPE LLT
Sbjct: 81 PAVILKTFLRELPEPLLT 98
>pdb|1GRN|B Chain B, Crystal Structure Of The Cdc42CDC42GAPALF3 COMPLEX
Length = 203
Score = 28.5 bits (62), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 32 LPKFIISSFEWLINNASDQIGIFRKPG---VKTRIQKLREMADEVDFKLDEVDSQQAYDV 88
+P + + +L +A GIFR+ V +Q+ M VDF D+ + + +
Sbjct: 23 IPIVLRETVAYLQAHALTTEGIFRRSANTQVVREVQQKYNMGLPVDF--DQYN--ELHLP 78
Query: 89 ADLVKQYFRELPEVLLT 105
A ++K + RELPE LLT
Sbjct: 79 AVILKTFLRELPEPLLT 95
>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 = 28.5 bits (62), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 32 LPKFIISSFEWLINNASDQIGIFRKPG---VKTRIQKLREMADEVDFKLDEVDSQQAYDV 88
+P + + +L +A GIFR+ V +Q+ M VDF D+ + + +
Sbjct: 27 IPIVLRETVAYLQAHALTTEGIFRRSANTQVVREVQQKYNMGLPVDF--DQYN--ELHLP 82
Query: 89 ADLVKQYFRELPEVLLT 105
A ++K + RELPE LLT
Sbjct: 83 AVILKTFLRELPEPLLT 99
>pdb|1XP4|A Chain A, Crystal Structure Of A Peptidoglycan Synthesis Regulatory
Factor (pbp3) From Streptococcus Pneumoniae
pdb|1XP4|B Chain B, Crystal Structure Of A Peptidoglycan Synthesis Regulatory
Factor (pbp3) From Streptococcus Pneumoniae
pdb|1XP4|C Chain C, Crystal Structure Of A Peptidoglycan Synthesis Regulatory
Factor (pbp3) From Streptococcus Pneumoniae
pdb|1XP4|D Chain D, Crystal Structure Of A Peptidoglycan Synthesis Regulatory
Factor (pbp3) From Streptococcus Pneumoniae
Length = 379
Score = 28.5 bits (62), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 76 KLDEVDSQQAYDVADLVKQYFRELPEVL-LTNKSSETFMS 114
K DE + AYDVA + + ++ P+VL +T K S TF
Sbjct: 161 KKDEENKLSAYDVAIVARNLIKKYPQVLEITKKPSSTFAG 200
>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 = 28.5 bits (62), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 32 LPKFIISSFEWLINNASDQIGIFRKPG---VKTRIQKLREMADEVDFKLDEVDSQQAYDV 88
+P + + +L +A GIFR+ V +Q+ M VDF D+ + + +
Sbjct: 62 IPIVLRETVAYLQAHALTTEGIFRRSANTQVVREVQQKYNMGLPVDF--DQYN--ELHLP 117
Query: 89 ADLVKQYFRELPEVLLT 105
A ++K + RELPE LLT
Sbjct: 118 AVILKTFLRELPEPLLT 134
>pdb|2QV2|A Chain A, A Role Of The Lowe Syndrome Protein Ocrl In Early Steps Of
The Endocytic Pathway
Length = 342
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 3/87 (3%)
Query: 19 VPLLVNIQKTGYALPKFIISSFEWLINNASDQIGIFRKPGVKTRIQKLREMADEVDFKLD 78
VPL + +PK I + L A Q +F+ PG++ ++L+++ D +D +
Sbjct: 162 VPLDEGASERPLQVPKEIWLLVDHLFKYACHQEDLFQTPGMQ---EELQQIIDCLDTSIP 218
Query: 79 EVDSQQAYDVADLVKQYFRELPEVLLT 105
E + VA+ + + LPE ++
Sbjct: 219 ETIPGSNHSVAEALLIFLEALPEPVIC 245
>pdb|3QIS|A Chain A, Recognition Of The F&h Motif By The Lowe Syndrome Protein
Ocrl
Length = 366
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 3/87 (3%)
Query: 19 VPLLVNIQKTGYALPKFIISSFEWLINNASDQIGIFRKPGVKTRIQKLREMADEVDFKLD 78
VPL + +PK I + L A Q +F+ PG++ ++L+++ D +D +
Sbjct: 186 VPLDEGASERPLQVPKEIWLLVDHLFKYACHQEDLFQTPGMQ---EELQQIIDCLDTSIP 242
Query: 79 EVDSQQAYDVADLVKQYFRELPEVLLT 105
E + VA+ + + LPE ++
Sbjct: 243 ETIPGSNHSVAEALLIFLEALPEPVIC 269
>pdb|2C46|A Chain A, Crystal Structure Of The Human Rna Guanylyltransferase And
5'-Phosphatase
pdb|2C46|B Chain B, Crystal Structure Of The Human Rna Guanylyltransferase And
5'-Phosphatase
pdb|2C46|C Chain C, Crystal Structure Of The Human Rna Guanylyltransferase And
5'-Phosphatase
pdb|2C46|D Chain D, Crystal Structure Of The Human Rna Guanylyltransferase And
5'-Phosphatase
Length = 241
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/44 (25%), Positives = 19/44 (43%)
Query: 16 VFGVPLLVNIQKTGYALPKFIISSFEWLINNASDQIGIFRKPGV 59
+ GV +TG+ + F++ +W I A R PG+
Sbjct: 143 LIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGI 186
>pdb|2XS6|A Chain A, Crystal Structure Of The Rhogap Domain Of Human Pik3r2
Length = 214
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 70 ADEVDFKLDEVDSQQAYDVADLVKQYFRELPEVLLTNKSS 109
A D+ L +VD +AD +K + LP L+T ++S
Sbjct: 68 APRTDWSLSDVDQWDTAALADGIKSFLLALPAPLVTPEAS 107
>pdb|1I9S|A Chain A, Crystal Structure Of The Rna Triphosphatase Domain Of
Mouse Mrna Capping Enzyme
Length = 210
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/44 (25%), Positives = 19/44 (43%)
Query: 16 VFGVPLLVNIQKTGYALPKFIISSFEWLINNASDQIGIFRKPGV 59
+ GV +TG+ + F++ +W I A R PG+
Sbjct: 121 LIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGI 164
>pdb|1I9T|A Chain A, Crystal Structure Of The Oxidized Rna Triphosphatase
Domain Of Mouse Mrna Capping Enzyme
Length = 210
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 11/44 (25%), Positives = 19/44 (43%)
Query: 16 VFGVPLLVNIQKTGYALPKFIISSFEWLINNASDQIGIFRKPGV 59
+ GV +TG+ + F++ +W I A R PG+
Sbjct: 121 LIGVHXTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGI 164
>pdb|2F7F|A Chain A, Crystal Structure Of Enterococcus Faecalis Putative
Nicotinate Phosphoribosyltransferase, New York
Structural Genomics Consortium
Length = 494
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 56 KPGVKTRIQKLREMADEVDFKLDEVDSQQAYDVADLVKQYFRELPEVLLT 105
K GV + I+ REM D+++F +DS D+A + K+ +L E T
Sbjct: 239 KAGVPSAIRVAREMGDKINFLGVRIDSG---DMAYISKRVREQLDEAGFT 285
>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 = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 32 LPKFIISSFEWLINNASDQIGIFRKPG---VKTRIQKLREMADEVDFKLDEVDSQQAYDV 88
+P + + +L +A GIF + V +Q+ M VDF D+ + + +
Sbjct: 54 IPIVLRETVAYLQAHALTTEGIFARSANTQVVREVQQKYNMGLPVDF--DQYN--ELHLP 109
Query: 89 ADLVKQYFRELPEVLLT 105
A ++K + RELPE LLT
Sbjct: 110 AVILKTFLRELPEPLLT 126
>pdb|1J8M|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens
Length = 297
Score = 25.4 bits (54), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 16 VFGVPL---LVNIQKTGYALPKFIISSFEWLINNASDQIGIFRKPGVKTRIQKLREM--A 70
V+G P +V I K G + KF+ E +I + + + G + + ++ + E
Sbjct: 156 VYGEPGEKDVVGIAKRG--VEKFLSEKMEIIIVDTAGRHGYGEEAALLEEMKNIYEAIKP 213
Query: 71 DEVDFKLDEVDSQQAYDVADLVKQ 94
DEV +D Q+AYD+A Q
Sbjct: 214 DEVTLVIDASIGQKAYDLASKFNQ 237
>pdb|1J8Y|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens T112a Mutant
Length = 297
Score = 25.4 bits (54), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 16 VFGVPL---LVNIQKTGYALPKFIISSFEWLINNASDQIGIFRKPGVKTRIQKLREM--A 70
V+G P +V I K G + KF+ E +I + + + G + + ++ + E
Sbjct: 156 VYGEPGEKDVVGIAKRG--VEKFLSEKMEIIIVDTAGRHGYGEEAALLEEMKNIYEAIKP 213
Query: 71 DEVDFKLDEVDSQQAYDVADLVKQ 94
DEV +D Q+AYD+A Q
Sbjct: 214 DEVTLVIDASIGQKAYDLASKFNQ 237
>pdb|1F7C|A Chain A, Crystal Structure Of The Bh Domain From Graf, The Gtpase
Regulator Associated With Focal Adhesion Kinase
Length = 231
Score = 25.4 bits (54), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 11/82 (13%)
Query: 29 GYALPKFIISSFEWLINNASDQIGIFRKPGVKTRIQKLREM------ADEVDFKLDEVDS 82
G+++ K I + E ++ G++R GV +R+QKL + A E + ++
Sbjct: 37 GFSIIKKCIHAVE---TRGINEQGLYRIVGVNSRVQKLLSILMDPKTATETETEI--CAE 91
Query: 83 QQAYDVADLVKQYFRELPEVLL 104
+ + +K Y R LP L+
Sbjct: 92 WEIKTITSALKTYLRMLPGPLM 113
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
0.322 0.138 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,996,987
Number of Sequences: 62578
Number of extensions: 107464
Number of successful extensions: 353
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 337
Number of HSP's gapped (non-prelim): 31
length of query: 124
length of database: 14,973,337
effective HSP length: 85
effective length of query: 39
effective length of database: 9,654,207
effective search space: 376514073
effective search space used: 376514073
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)