RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7063
(188 letters)
>2eki_A DRG 1, developmentally-regulated GTP-binding protein 1; protein
NEDD3, neural precursor cell expressed developmentally
DOWN-regulated protein 3; NMR {Homo sapiens}
Length = 93
Score = 84.9 bits (210), Expect = 3e-22
Identities = 29/82 (35%), Positives = 38/82 (46%), Gaps = 25/82 (30%)
Query: 132 WLYLSLIRVYTKKPGAPPDFDDGLILRKG-------------------------GTSTKY 166
YL L+R+YTK G PD+ ++L G S K+
Sbjct: 6 SGYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTVEDFCMKIHKNLIKEFKYALVWGLSVKH 65
Query: 167 SPQRVGLAHVMADEDVIQIVKK 188
+PQ+VG H + DEDVIQIVKK
Sbjct: 66 NPQKVGKDHTLEDEDVIQIVKK 87
>2qtf_A Protein HFLX, GTP-binding protein; beta-alpha-barrels,
nucleotide-binding, nucleotide binding protein; 2.00A
{Sulfolobus solfataricus P2} PDB: 2qth_A* 3kxi_A* 3kxl_A
3kxk_A
Length = 364
Score = 37.2 bits (87), Expect = 0.001
Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 13/78 (16%)
Query: 74 DELIDVINANRVYLPCIYAYNKIDQISIEEVDRI-----------ARQPNSVVVSCNMKL 122
E++ I + P + NKID+I+ + ++ + + + +S +
Sbjct: 282 FEILREIGVSGK--PILVTLNKIDKINGDLYKKLDLVEKLSKELYSPIFDVIPISALKRT 339
Query: 123 NLDYLLDIIWLYLSLIRV 140
NL+ L D I+ + + +
Sbjct: 340 NLELLRDKIYQLATQLSL 357
>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 = 36.6 bits (84), Expect = 0.004
Identities = 29/173 (16%), Positives = 56/173 (32%), Gaps = 66/173 (38%)
Query: 1 MGILEKISEIEKEIARTQKNKVLAYCWSKGTFQSYTSSINRH----YYYKSARAYEADTL 56
E + K + A G H Y +A A AD +
Sbjct: 1741 KAAFEDL----KSKGLIPADATFA-----G-----------HSLGEY---AALASLADVM 1777
Query: 57 PSKLTLKNVLFR-----EDCNADEL------IDVINANRVYLPCIYAYNKIDQISIEE-V 104
+ ++ V +R DEL + IN RV Q +++ V
Sbjct: 1778 SIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAA-------SFSQEALQYVV 1830
Query: 105 DRIARQ------------PNS-VVVSCNMKLNLDYLLDIIWLYLSLIRVYTKK 144
+R+ ++ N V + +++ LD + ++ L+ I++ +K
Sbjct: 1831 ERVGKRTGWLVEIVNYNVENQQYVAAGDLR-ALDTVTNV----LNFIKL--QK 1876
Score = 30.8 bits (69), Expect = 0.28
Identities = 31/164 (18%), Positives = 52/164 (31%), Gaps = 52/164 (31%)
Query: 27 WSKGTFQSYTSSINRHYYYKSARAYEA---DTLPSKLTLKNVLFRE----------DCNA 73
W +F ++ R YEA +LP + ++ E +
Sbjct: 289 WE--SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQ 346
Query: 74 DELIDVINANRVYLPCIYAYNKIDQISIEEVDRIARQPNSVVVS------CNMKLNLDYL 127
+++ D +N +LP K Q+ I V+ ++VVS + L L
Sbjct: 347 EQVQDYVNKTNSHLPA----GK--QVEISLVN----GAKNLVVSGPPQSLYGLNLTL--- 393
Query: 128 LDIIWLYLSLIRVYTKKPGAPPDFDDGLIL---RKGGTSTKYSP 168
+K AP D I RK S ++ P
Sbjct: 394 ---------------RKAKAPSGLDQSRIPFSERKLKFSNRFLP 422
Score = 28.1 bits (62), Expect = 1.9
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 171 VGLAHVMADEDVIQIVKK 188
LA VM+ E ++++V
Sbjct: 1771 ASLADVMSIESLVEVVFY 1788
>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation,
GTP-binding domain, maturation enzyme, oxidoreductase;
2.99A {Thermotoga neapolitana}
Length = 423
Score = 32.7 bits (75), Expect = 0.051
Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 7/67 (10%)
Query: 74 DELIDVINANRVYLPCIYAYNKIDQIS--IEEVDRIARQPNS---VVVSCNMKLNLDYLL 128
D+++++ + P + NKID + EE+ + ++VS K D +
Sbjct: 130 DDVVNLFKEMEI--PFVVVVNKIDVLGEKAEELKGLYESRYEAKVLLVSALQKKGFDDIG 187
Query: 129 DIIWLYL 135
I L
Sbjct: 188 KTISEIL 194
>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 = 29.8 bits (66), Expect = 0.55
Identities = 21/173 (12%), Positives = 52/173 (30%), Gaps = 54/173 (31%)
Query: 40 NRHYYYKSARAYEADTLPSKLTLKNVL--FREDCNAD-ELIDVINANRVYLPCIYAYNKI 96
+ H+++ + +T + K++L F + + + DV + + L
Sbjct: 1 HHHHHH-----MDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSIL--------- 46
Query: 97 DQISIEEVDRIARQPNSVVVSCNMKLNLDYLLDII---------------------WLYL 135
S EE+D I ++V L + +L
Sbjct: 47 ---SKEEIDHIIMSKDAV-------SGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM- 95
Query: 136 SLIRVYTKKPGAPPDFDDGLILRKGGTSTKYSPQRVGLAHVMADEDVIQIVKK 188
S I+ ++P R + ++ +V + +++ +
Sbjct: 96 SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY-----NVSRLQPYLKLRQA 143
>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA,
30S ribosome ASSE GTP-binding, nucleotide-binding; HET:
GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*
Length = 308
Score = 29.4 bits (67), Expect = 0.62
Identities = 25/93 (26%), Positives = 36/93 (38%), Gaps = 18/93 (19%)
Query: 73 ADELIDVINANRVYLPCIYAYNKIDQIS--------IEEVDRIARQPNSVV-VSCNMKLN 123
DE I + P I NKID+I I+E+ + + +V +S N
Sbjct: 109 RDEEIYQNFIKPLNKPVIVVINKIDKIGPAKNVLPLIDEIHKKHPELTEIVPISALKGAN 168
Query: 124 LDYLLDIIWLYLSLIRVYTKKPGAPPDFDDGLI 156
LD L+ I YL P P F + +I
Sbjct: 169 LDELVKTILKYL---------PEGEPLFPEDMI 192
>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 = 28.8 bits (63), Expect = 0.64
Identities = 7/35 (20%), Positives = 14/35 (40%), Gaps = 10/35 (28%)
Query: 29 KGTFQSYTSSINRHYYYKSARAYEADTLPSKLTLK 63
K + +S+ + Y D+ P+ L +K
Sbjct: 19 KQALKKLQASL---------KLYADDSAPA-LAIK 43
>1wxq_A GTP-binding protein; structural genomics, riken structural
genomics/proteomics initiative, RSGI, NPPSFA; 2.60A
{Pyrococcus horikoshii} SCOP: c.37.1.8 d.15.10.2
Length = 397
Score = 28.4 bits (64), Expect = 1.6
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 4/54 (7%)
Query: 69 EDCNADELIDVINANRVYL-PCIYAYNKIDQIS---IEEVDRIARQPNSVVVSC 118
+ D+L+ + R P + A NK D S I+ + R + +V+
Sbjct: 196 TKWSQDDLLAFASEIRRVNKPMVIAANKADAASDEQIKRLVREEEKRGYIVIPT 249
>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote
initiative, RSGI, structural genomics, hydrolase; HET:
GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8
d.52.3.1
Length = 301
Score = 27.8 bits (63), Expect = 2.1
Identities = 11/90 (12%), Positives = 28/90 (31%), Gaps = 15/90 (16%)
Query: 74 DELI-DVINANRVYLPCIYAYNKIDQIS-----IEEVDRIARQPNSVVVSCNMKLNLDYL 127
DEL+ + +P + NK+D ++ + + ++S + + L
Sbjct: 104 DELVARALKPLVGKVPILLVGNKLDAAKYPEEAMKAYHELLPEAEPRMLSALDERQVAEL 163
Query: 128 LDIIWLYLSLIRVYTKKPGAPPDFDDGLIL 157
+ + P P + +
Sbjct: 164 KADLLALM---------PEGPFFYPEDYAK 184
>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer,
alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A
{Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A*
2gja_A* 1rfl_A
Length = 172
Score = 27.1 bits (61), Expect = 2.7
Identities = 7/44 (15%), Positives = 12/44 (27%)
Query: 88 PCIYAYNKIDQISIEEVDRIARQPNSVVVSCNMKLNLDYLLDII 131
P NK D + +S +D L + +
Sbjct: 117 PITVVRNKADITGETLGMSEVNGHALIRLSARTGEGVDVLRNHL 160
>1kk1_A EIF2gamma; initiation of translation; HET: GNP; 1.80A {Pyrococcus
abyssi} SCOP: b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1kjz_A*
1kk2_A* 1kk3_A* 1kk0_A* 2d74_A 2dcu_A*
Length = 410
Score = 27.6 bits (62), Expect = 3.0
Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 28/95 (29%)
Query: 94 NKIDQIS----IEEVDRIARQPNS--------VVVSCNMKLNLDYLLDIIWLY------- 134
NKI+ + +E +I + +S N+D L+ I +
Sbjct: 145 NKIELVDKEKALENYRQIKEFIEGTVAENAPIIPISALHGANIDVLVKAIEDFIPTPKRD 204
Query: 135 ------LSLIRVYT-KKPGAPPDFDDGLILRKGGT 162
+ ++R + KPG PP+ G +L G+
Sbjct: 205 PNKPPKMLVLRSFDVNKPGTPPEKLVGGVL--DGS 237
>1yj8_A Glycerol-3-phosphate dehydrogenase; SGPP, structural genomics,
PSI; 2.85A {Plasmodium falciparum}
Length = 375
Score = 27.2 bits (61), Expect = 3.1
Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 67 FREDCNADELIDVINA---NRVYLP 88
E N + ++D+IN N YL
Sbjct: 59 RDEFVNGERMVDIINNKHENTKYLK 83
>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria,
structural genomics, structural genomics consortium,
SGC, unknown function; HET: GDP; 2.01A {Plasmodium
falciparum}
Length = 228
Score = 26.7 bits (59), Expect = 4.6
Identities = 7/68 (10%), Positives = 20/68 (29%), Gaps = 12/68 (17%)
Query: 88 PCIYAYNKIDQISIEEV------------DRIARQPNSVVVSCNMKLNLDYLLDIIWLYL 135
+ +NKID+ +++ + D + S + ++ L
Sbjct: 144 SIVIGFNKIDKCNMDSLSIDNKLLIKQILDNVKNPIKFSSFSTLTGVGVEQAKITACELL 203
Query: 136 SLIRVYTK 143
+ +
Sbjct: 204 KNDQAESI 211
>1lnz_A SPO0B-associated GTP-binding protein; GTPase, OBG, stringent
factor, stress response, sporulation, large G-protein,
structural genomics, PSI; HET: G4P; 2.60A {Bacillus
subtilis} SCOP: b.117.1.1 c.37.1.8
Length = 342
Score = 26.8 bits (60), Expect = 4.6
Identities = 11/57 (19%), Positives = 18/57 (31%), Gaps = 5/57 (8%)
Query: 88 PCIYAYNKIDQISIEE-----VDRIARQPNSVVVSCNMKLNLDYLLDIIWLYLSLIR 139
P I NK+D E +++ +S + L LL + L
Sbjct: 276 PQIIVANKMDMPEAAENLEAFKEKLTDDYPVFPISAVTREGLRELLFEVANQLENTP 332
>3geh_A MNME, tRNA modification GTPase MNME; G protein, U34, GTP-binding,
HYDR magnesium, metal-binding, nucleotide-binding,
potassium, TR processing; HET: GDP FON; 3.20A {Nostoc
SP}
Length = 462
Score = 26.7 bits (60), Expect = 5.2
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 3/47 (6%)
Query: 88 PCIYAYNKID---QISIEEVDRIARQPNSVVVSCNMKLNLDYLLDII 131
P I NKID + I ++ V + K +D L I
Sbjct: 332 PLILVMNKIDLVEKQLITSLEYPENITQIVHTAAAQKQGIDSLETAI 378
>1x0v_A GPD-C, GPDH-C, glycerol-3-phosphate dehydrogenase [NAD+],
cytoplasmic; two independent domains, GXGXXG motif,
oxidoreductase; 2.30A {Homo sapiens} PDB: 1x0x_A*
1wpq_A* 2pla_A*
Length = 354
Score = 26.8 bits (60), Expect = 5.4
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 67 FREDCNADELIDVINA---NRVYLP 88
F ED +L ++IN N YLP
Sbjct: 46 FEEDIGGKKLTEIINTQHENVKYLP 70
>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like,
hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8
d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X
Length = 301
Score = 26.3 bits (59), Expect = 6.9
Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 17/77 (22%)
Query: 88 PCIYAYNKIDQIS--------IEEVDRIARQPNSVVVSCNMKLNLDYLLDIIWLYLSLIR 139
P I A NK+D + ++ + + V +S LN+D + I+ +L
Sbjct: 118 PVILAVNKVDNVQEKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHL---- 173
Query: 140 VYTKKPGAPPDFDDGLI 156
P A F + I
Sbjct: 174 -----PEATHHFPEDYI 185
>1udx_A The GTP-binding protein OBG; TGS domain, riken structural
genomics/proteomics initiative, RSGI, structural
genomics; 2.07A {Thermus thermophilus} SCOP: b.117.1.1
c.37.1.8 d.242.1.1
Length = 416
Score = 26.4 bits (59), Expect = 7.2
Identities = 12/71 (16%), Positives = 20/71 (28%), Gaps = 5/71 (7%)
Query: 88 PCIYAYNKIDQISIEEVDRI-----ARQPNSVVVSCNMKLNLDYLLDIIWLYLSLIRVYT 142
P + A NK+D + E V + + VS L L + + +
Sbjct: 271 PSLVALNKVDLLEEEAVKALADALAREGLAVLPVSALTGAGLPALKEALHALVRSTPPPE 330
Query: 143 KKPGAPPDFDD 153
P
Sbjct: 331 MPKPVPRKEVQ 341
>1s0u_A EIF-2-gamma, translation initiation factor 2 gamma subunit; GTPase,
EF-1A, tRNA; 2.40A {Methanocaldococcus jannaschii} SCOP:
b.43.3.1 b.44.1.1 c.37.1.8
Length = 408
Score = 26.1 bits (58), Expect = 9.1
Identities = 20/95 (21%), Positives = 33/95 (34%), Gaps = 28/95 (29%)
Query: 94 NKIDQIS----IEEVDRIARQPNS--------VVVSCNMKLNLDYLLDIIWLY------- 134
NKID + E ++I + +S + + N+D LL I +
Sbjct: 143 NKIDLVDEKQAEENYEQIKEFVKGTIAENAPIIPISAHHEANIDVLLKAIQDFIPTPKRD 202
Query: 135 ------LSLIRVYT-KKPGAPPDFDDGLILRKGGT 162
+ + R + KPG G +L GG
Sbjct: 203 PDATPRMYVARSFDINKPGTEIKDLKGGVL--GGA 235
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
0.319 0.136 0.398
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,970,673
Number of extensions: 173461
Number of successful extensions: 362
Number of sequences better than 10.0: 1
Number of HSP's gapped: 359
Number of HSP's successfully gapped: 25
Length of query: 188
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 100
Effective length of database: 4,244,745
Effective search space: 424474500
Effective search space used: 424474500
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: 54 (24.5 bits)