RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2927
(123 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 = 133 bits (335), Expect = 5e-42
Identities = 60/85 (70%), Positives = 67/85 (78%)
Query: 38 EKMWEYLKLTRIYTKPKGQLPDYQSPVVLHTDRRSIEDFCNKLHRTIAKEFKYALVWGSS 97
YLKL RIYTKPKGQLPDY SPVVL R ++EDFC K+H+ + KEFKYALVWG S
Sbjct: 3 SGSSGYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTVEDFCMKIHKNLIKEFKYALVWGLS 62
Query: 98 VKHQPQKVGKEHVLNDEDVVQIVKK 122
VKH PQKVGK+H L DEDV+QIVKK
Sbjct: 63 VKHNPQKVGKDHTLEDEDVIQIVKK 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 = 32.2 bits (74), Expect = 0.030
Identities = 8/40 (20%), Positives = 19/40 (47%)
Query: 6 DQISIEELDIIYKIPHCVPLSAHHKWNFDDLLEKMWEYLK 45
D + ++ I +P+SA + N + L +K+++
Sbjct: 314 DLVEKLSKELYSPIFDVIPISALKRTNLELLRDKIYQLAT 353
>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 = 31.4 bits (70), Expect = 0.064
Identities = 22/151 (14%), Positives = 48/151 (31%), Gaps = 42/151 (27%)
Query: 2 QKVSDQ----ISIEELDIIYKIPHCVPLSAHHKWNF------------DDLLEKMWEYLK 45
+ V D +S EE+D I V + W +++L +++L
Sbjct: 36 KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFL- 94
Query: 46 LTRIYTKPKGQLPDYQSPV----VLHTDRRSIEDFCNKLHRTIAKEF---KYALVWGSSV 98
++ I T+ + + + L+ D + K + + + + + AL +
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA----KYNVSRLQPYLKLRQAL---LEL 147
Query: 99 KHQPQKV-------GKE----HVLNDEDVVQ 118
+ + GK V V
Sbjct: 148 RPAKNVLIDGVLGSGKTWVALDVCLSYKVQC 178
Score = 26.7 bits (58), Expect = 2.1
Identities = 15/103 (14%), Positives = 39/103 (37%), Gaps = 30/103 (29%)
Query: 28 HHKWNFDDLLEKMWEYLKLTRIYTKPKGQLPDYQSPVVLHTDRRSIEDFCNKLHRTIAKE 87
HH +F+ E ++Y + L ++ V + D + ++D + +E
Sbjct: 4 HHHMDFE-TGEHQYQYKDI----------LSVFEDAFVDNFDCKDVQDMPKSILSK--EE 50
Query: 88 FK------------YALVWGSSVKHQPQKVGKEHVLNDEDVVQ 118
L W ++ + +++ ++ V E+V++
Sbjct: 51 IDHIIMSKDAVSGTLRLFW--TLLSKQEEMVQKFV---EEVLR 88
>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA,
national P protein structural and functional analyses;
HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8
Length = 190
Score = 30.4 bits (69), Expect = 0.087
Identities = 9/45 (20%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 2 QKVSDQISIE-ELDIIYKIPHCVPLSAHHKWNFDDLLEKMWEYLK 45
Q+V + ++ + E+ + +P+SA N + L +++E ++
Sbjct: 139 QEVINFLAEKFEVPLSEIDKVFIPISAKFGDNIERLKNRIFEVIR 183
>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 = 29.2 bits (66), Expect = 0.31
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 23 VPLSAHHKWNFDDLLEKMWEYLKL-TRIYTKP 53
+P+SAHH+ N D LL+ + +++ R
Sbjct: 175 IPISAHHEANIDVLLKAIQDFIPTPKRDPDAT 206
>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation,
GTP-binding domain, maturation enzyme, oxidoreductase;
2.99A {Thermotoga neapolitana}
Length = 423
Score = 28.8 bits (65), Expect = 0.42
Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 1/51 (1%)
Query: 21 HCVPLSAHHKWNFDDLLEKMWEYLKLTRIYTKPKGQLPDYQSPVVLHTDRR 71
+ +SA K FDD+ + + E L G L D V+L
Sbjct: 171 KVLLVSALQKKGFDDIGKTISEILPGDEEIP-YLGDLIDGGDLVILVVPID 220
>3sjy_A Translation initiation factor 2 subunit gamma; zinc finger,
initiate translation, tRNA binding, mRNA bindin binding;
HET: GCP GDP; 2.00A {Sulfolobus solfataricus P2} PDB:
3pen_A* 3sjz_A* 2qn6_A* 2aho_A 2qmu_A* 2plf_A* 3v11_A*
3i1f_A* 3cw2_A 2pmd_A* 3p3m_A* 3qsy_A*
Length = 403
Score = 28.8 bits (65), Expect = 0.47
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 23 VPLSAHHKWNFDDLLEKMWEYLKL-TRIYTKP 53
+P+SA HK N D L+E + EY+K R ++
Sbjct: 169 IPVSALHKINIDSLIEGIEEYIKTPYRDLSQK 200
>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 = 28.5 bits (63), Expect = 0.65
Identities = 15/107 (14%), Positives = 28/107 (26%), Gaps = 42/107 (39%)
Query: 33 FDDLLEKMWEYLKLTRIYTKPKGQL--PDYQSPVVLHTDRRSIEDFCNKLHRTIAKEFK- 89
F ++ E Y + KG L + P + F + +
Sbjct: 1707 FKEINEHSTSY-----TFRSEKGLLSATQFTQPALTLM---EKAAF-----EDLKSKGLI 1753
Query: 90 -------------Y-ALVWGSSVKHQPQKVGKEHVLNDEDVVQIVKK 122
Y AL + V ++ E +V++V
Sbjct: 1754 PADATFAGHSLGEYAALASLADV------------MSIESLVEVVFY 1788
>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 = 0.99
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 23 VPLSAHHKWNFDDLLEKMWEYLKL-TRIYTKP 53
+P+SA H N D L++ + +++ R KP
Sbjct: 177 IPISALHGANIDVLVKAIEDFIPTPKRDPNKP 208
>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 = 27.4 bits (62), Expect = 1.0
Identities = 8/35 (22%), Positives = 15/35 (42%)
Query: 10 IEELDIIYKIPHCVPLSAHHKWNFDDLLEKMWEYL 44
++ L VP+SA N D + + ++L
Sbjct: 139 LQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHL 173
>3izy_P Translation initiation factor IF-2, mitochondrial; E coli, RNA,
ribosomal; 10.80A {Bos taurus}
Length = 537
Score = 27.5 bits (62), Expect = 1.2
Identities = 8/34 (23%), Positives = 12/34 (35%), Gaps = 7/34 (20%)
Query: 8 ISIEEL--DIIYKIPHCVPLSAHHKWNFDDLLEK 39
+ E+ D+ V +SA N L E
Sbjct: 133 VVCEDYGGDVQ-----AVHVSALTGENMMALAEA 161
>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 = 26.8 bits (60), Expect = 1.7
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 103 QKVGKEHVLNDEDVVQIV 120
++VG+++ L D+V+IV
Sbjct: 376 RRVGEDYELQFNDIVKIV 393
>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 = 27.1 bits (61), Expect = 1.7
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 23 VPLSAHHKWNFDDLLEKMWEYL 44
VP+SA N D+L++ + +YL
Sbjct: 159 VPISALKGANLDELVKTILKYL 180
>1zo1_I IF2, translation initiation factor 2; E. coli, ribosome, initiation
of protein synthesis, cryo-eletron microscopy,
translation/RNA complex; 13.80A {Escherichia coli}
Length = 501
Score = 26.7 bits (60), Expect = 2.2
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 22 CVPLSAHHKWNFDDLLEK 39
V +SA D+LL+
Sbjct: 143 FVHVSAKAGTGIDELLDA 160
>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 = 25.9 bits (58), Expect = 3.4
Identities = 4/39 (10%), Positives = 13/39 (33%)
Query: 6 DQISIEELDIIYKIPHCVPLSAHHKWNFDDLLEKMWEYL 44
+ +++ + LSA + +L + +
Sbjct: 133 PEEAMKAYHELLPEAEPRMLSALDERQVAELKADLLALM 171
>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural
genomics; HET: GDP; 1.96A {Thermus thermophilus}
Length = 161
Score = 25.5 bits (57), Expect = 4.0
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 23 VPLSAHHKWNFDDLLEKMWEYL 44
+P S+ H ++LLE +WE L
Sbjct: 139 IPTSSEHARGLEELLEAIWERL 160
>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus
stearothermophilus} PDB: 2lkd_A*
Length = 178
Score = 25.7 bits (57), Expect = 4.1
Identities = 8/17 (47%), Positives = 8/17 (47%)
Query: 22 CVPLSAHHKWNFDDLLE 38
LSA K D LLE
Sbjct: 147 FCKLSAKTKEGLDHLLE 163
>2ec4_A FAS-associated factor 1; UAS domain, protein FAF1, HFAF1, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 178
Score = 25.1 bits (54), Expect = 6.2
Identities = 8/50 (16%), Positives = 18/50 (36%)
Query: 72 SIEDFCNKLHRTIAKEFKYALVWGSSVKHQPQKVGKEHVLNDEDVVQIVK 121
S+E + A++ K ++ + V +L E +V +
Sbjct: 39 SLEAAFQEAFYVKARDRKLLAIYLHHDESVLTNVFCSQMLCAESIVSYLS 88
>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase,
cell division, cell cycle, SEP GTP-binding; 2.20A
{Burkholderia thailandensis}
Length = 223
Score = 25.3 bits (56), Expect = 6.2
Identities = 5/45 (11%), Positives = 12/45 (26%)
Query: 1 MQKVSDQISIEELDIIYKIPHCVPLSAHHKWNFDDLLEKMWEYLK 45
++ + SA + DD + +L+
Sbjct: 166 LRATQKSLDAYRDAGYAGKLTVQLFSALKRTGLDDAHALIESWLR 210
>3b1v_A Ferrous iron uptake transporter protein B; G protein, iron
transport, GTPase, transmembrane, potassium; HET: GGM;
1.85A {Streptococcus thermophilus} PDB: 3b1w_A* 3lx5_A*
3lx8_A* 3ss8_A* 3b1z_A 3b1y_A* 3b1x_A* 3tah_A*
Length = 272
Score = 25.0 bits (55), Expect = 7.3
Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 5/59 (8%)
Query: 6 DQISIEELDIIYKIPHCVPLSAHHKWNFDDLLEKMWEYLKLTRIYTKPKGQLPDYQSPV 64
+I++++L +P V SA + D +++K T P Y +
Sbjct: 125 KKINVDKLSYHLGVP-VVATSALKQTGVDQVVKKAAHTTT----STVGDLAFPIYDDRL 178
>3a1s_A Iron(II) transport protein B; FEOB, iron transporter, small GTPase,
G protein, GDI; HET: GDP; 1.50A {Thermotoga maritima}
PDB: 3a1t_A* 3a1u_A* 3a1v_A* 3a1w_A
Length = 258
Score = 24.9 bits (55), Expect = 7.4
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 4/59 (6%)
Query: 6 DQISIEELDIIYKIPHCVPLSAHHKWNFDDLLEKMWEYLKLTRIYTKPKGQLPDYQSPV 64
+I EL IP V S+ ++L EK+ EY + T + DY V
Sbjct: 128 MKIDRYELQKHLGIP-VVFTSSVTGEGLEELKEKIVEYAQKN---TILHRMILDYGEKV 182
>1mky_A Probable GTP-binding protein ENGA; GTPase, DER, KH-domain, tandem
G-domains, ligand binding protein; HET: GDP; 1.90A
{Thermotoga maritima} SCOP: c.37.1.8 c.37.1.8 d.52.5.1
Length = 439
Score = 25.2 bits (56), Expect = 7.7
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 23 VPLSAHHKWNFDDLLEKMWEYL 44
+P+SA H N D +LE + + L
Sbjct: 143 IPVSAEHNINLDTMLETIIKKL 164
>2ptz_A Enolase; lyase, glycolysis,His-TAG; 1.65A {Trypanosoma brucei}
SCOP: c.1.11.1 d.54.1.1 PDB: 2ptx_A 2pty_A* 2ptw_A
2pu0_A 2pu1_A* 1oep_A
Length = 432
Score = 25.2 bits (56), Expect = 8.4
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 85 AKEFKYALVWGSSVKHQPQKVGKEHVLND 113
A F AL GS V H + + K+ D
Sbjct: 176 ATSFSEALRMGSEVYHSLRGIIKKKYGQD 204
>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 = 24.8 bits (55), Expect = 8.9
Identities = 8/36 (22%), Positives = 13/36 (36%)
Query: 5 SDQISIEELDIIYKIPHCVPLSAHHKWNFDDLLEKM 40
++ I L+ I V +A K D L +
Sbjct: 343 VEKQLITSLEYPENITQIVHTAAAQKQGIDSLETAI 378
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 0.136 0.419
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,951,141
Number of extensions: 103341
Number of successful extensions: 310
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 50
Length of query: 123
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,412,271
Effective search space: 180903111
Effective search space used: 180903111
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: 51 (23.4 bits)