RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8220
(161 letters)
>1puj_A YLQF, conserved hypothetical protein YLQF; structural genomics,
nysgxrc T18, GTPase, PSI, protein structure initiative;
HET: GNP; 2.00A {Bacillus subtilis} SCOP: c.37.1.8
Length = 282
Score = 59.2 bits (144), Expect = 2e-11
Identities = 26/136 (19%), Positives = 57/136 (41%), Gaps = 31/136 (22%)
Query: 19 RSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKAGKPSTKIQSGSMAQ 78
++ D++ E+VDAR PM +R + ED++ K ++++NKA K +
Sbjct: 18 TEKLKLIDIVYELVDARIPMSSRNPMIEDIL---KNKPRIMLLNKADKADAAVT------ 68
Query: 79 IFQTWIPYNSIQSIYSSPRFSSRSQK----DAQTERDLKAINVSSCVGAELLMLLLGNYT 134
Q W + F ++ + ++ + L I + ++ ++ +
Sbjct: 69 --QQWKEH-----------FENQGIRSLSINSVNGQGLNQIVPA----SKEILQEKFDRM 111
Query: 135 RNKDIKT-SITVGVVG 149
R K +K +I ++G
Sbjct: 112 RAKGVKPRAIRALIIG 127
>3cnl_A YLQF, putative uncharacterized protein; circular permutation,
GNP, signaling protein; HET: GNP; 2.00A {Thermotoga
maritima} PDB: 3cnn_A* 3cno_A*
Length = 262
Score = 55.3 bits (134), Expect = 5e-10
Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 19 RSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKA 64
+ ++ + ++EV DAR P T + K+ +I++NK
Sbjct: 16 KDLLRLVNTVVEVRDARAPFATSAYGVD-----FSRKETIILLNKV 56
>3ec1_A YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase, signaling
protein; HET: GDP; 2.36A {Geobacillus
stearothermophilus}
Length = 369
Score = 47.2 bits (112), Expect = 4e-07
Identities = 9/46 (19%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 19 RSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKA 64
+ E+ +++ +VD D G+ +++V NKA
Sbjct: 66 HRIGESKALVVNIVDIFDFNGSFIPGLPRFA---ADNPILLVGNKA 108
>3h2y_A GTPase family protein; GTP-binding protein YQEH, possibly involved
in replication initiation, csgid, IDP90222; HET: DGI;
1.80A {Bacillus anthracis str}
Length = 368
Score = 45.7 bits (108), Expect = 2e-06
Identities = 10/46 (21%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 19 RSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKA 64
+ ++ +++++VD D G+ V K+++V NKA
Sbjct: 64 NGIGKSDALVVKIVDIFDFNGSWLPGLHRFV---GNNKVLLVGNKA 106
>3gee_A MNME, tRNA modification GTPase MNME; G protein, cytoplasm, GTP-
binding, hydrolase, magnesium, metal-binding,
nucleotide- binding, potassium; HET: GDP FON; 2.95A
{Chlorobium tepidum} PDB: 3gei_A*
Length = 476
Score = 41.4 bits (98), Expect = 4e-05
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 3/51 (5%)
Query: 17 IERS--VVEAADVILEVVDARDPMGTR-CKVAEDLVVGTPGKKLVIVINKA 64
I RS + AD+IL ++D +L P K + V NK
Sbjct: 303 IRRSRMKMAEADLILYLLDLGTERLDDELTEIRELKAAHPAAKFLTVANKL 353
>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 = 39.0 bits (92), Expect = 3e-04
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 9/52 (17%)
Query: 17 IERS--VVEAADVILEVVDARDPMGTRCKVAED--LVVGTPGKKLVIVINKA 64
+ERS AD++L +DA D + + L++V+NK
Sbjct: 294 VERSRQAANTADLVLLTIDAATGWT-----TGDQEIYEQVKHRPLILVMNKI 340
>1xzp_A Probable tRNA modification GTPase TRME; GTP-binding, THF-binding,
hydrolase; 2.30A {Thermotoga maritima} SCOP: a.24.25.1
c.37.1.8 d.250.1.2 PDB: 1xzq_A* 1xzp_B 1xzq_B*
Length = 482
Score = 38.7 bits (91), Expect = 4e-04
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 9/52 (17%)
Query: 17 IERS--VVEAADVILEVVDARDPMGTRCKVAED--LVVGTPGKKLVIVINKA 64
IER+ +E AD++L V+DA P+ ED ++ K+ ++VINK
Sbjct: 314 IERTLQEIEKADIVLFVLDASSPLD-----EEDRKILERIKNKRYLVVINKV 360
>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 = 36.8 bits (86), Expect = 0.001
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 17 IERS--VVEAADVILEVVDARDPMGT--RCKVAEDLVVGTPGKKLVIVINKA 64
IER+ +E AD +L +VD E + + +V NKA
Sbjct: 74 IERAWQEIEQADRVLFMVDGTTTDAVDPAEIWPEFIARLPAKLPITVVRNKA 125
>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET:
GDP; 2.50A {Bacillus subtilis}
Length = 436
Score = 32.8 bits (76), Expect = 0.038
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 16/65 (24%)
Query: 10 RGVVVQEIER-SVV------EAADVILEVVDARDPMGTRCKVAEDLVVGT----PGKKLV 58
+G V + E+ SV+ + ++V+ V+D + + + +D + GK +V
Sbjct: 236 KGKVYETTEKYSVLRALKAIDRSEVVAVVLDGEEGI-----IEQDKRIAGYAHEAGKAVV 290
Query: 59 IVINK 63
IV+NK
Sbjct: 291 IVVNK 295
Score = 29.8 bits (68), Expect = 0.42
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 9/47 (19%)
Query: 22 VEAADVILEVVDARDPMGTRCKVAEDLVVGT----PGKKLVIVINKA 64
++ ADVI+ +V+ R+ + A D V K +V+ +NK
Sbjct: 80 MDEADVIIFMVNGREGV-----TAADEEVAKILYRTKKPVVLAVNKL 121
>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 = 30.5 bits (70), Expect = 0.17
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 19 RSVVEAADVILEVVDARDPMGTR-CKVAEDLVVGTPGKKLVIVINK 63
+ + ++ VVD R P VA L +++V NK
Sbjct: 81 YEALADVNAVVWVVDLRHPPTPEDELVARALKPLVGKVPILLVGNK 126
>2qpt_A EH domain-containing protein-2; protein-nucleotide complex,
membrane protein, endocytosis; HET: ANP; 3.10A {Mus
musculus}
Length = 550
Score = 30.5 bits (68), Expect = 0.23
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 2/61 (3%)
Query: 5 KPMEMRGVVVQEIERSVVEAADVILEVVDARDP-MGTRCKVAEDLVVGTPGKKLVIVINK 63
K RG + R E D+I+ + DA + A + G K+ +V+NK
Sbjct: 169 KQRVSRGYDFPAVLRWFAERVDLIILLFDAHKLEISDEFSEAIGALRGH-EDKIRVVLNK 227
Query: 64 A 64
A
Sbjct: 228 A 228
>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural
genomics; HET: GDP; 1.96A {Thermus thermophilus}
Length = 161
Score = 29.4 bits (67), Expect = 0.33
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 9/47 (19%)
Query: 22 VEAADVILEVVDARDPMGTRCKVAEDLVVGT----PGKKLVIVINKA 64
+E A+V+L VD R + D V GK +++V K
Sbjct: 77 LEDAEVVLFAVDGRAEL-----TQADYEVAEYLRRKGKPVILVATKV 118
>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 = 29.8 bits (68), Expect = 0.33
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 9/46 (19%)
Query: 22 VEAADVILEVVDARDPMGTRCKVAEDL-VVGT---PGKKLVIVINK 63
+E ADV++ V+DA + +D + G G+ V+V NK
Sbjct: 261 IEKADVVVIVLDATQGI-----TRQDQRMAGLMERRGRASVVVFNK 301
Score = 29.4 bits (67), Expect = 0.54
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 9/47 (19%)
Query: 22 VEAADVILEVVDARDPMGTRCKVAEDLVVGT----PGKKLVIVINKA 64
+ AD++L VVD + + ED + ++V NKA
Sbjct: 79 IREADLVLFVVDGKRGI-----TKEDESLADFLRKSTVDTILVANKA 120
>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 = 30.0 bits (67), Expect = 0.37
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 1 MRSVKPMEMRGVVVQEIERSVVEAA----DVILEVV 32
M ++ P + QE + VVE ++E+V
Sbjct: 1809 MIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIV 1844
>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 = 29.0 bits (66), Expect = 0.68
Identities = 14/46 (30%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 19 RSVVEAADVILEVVDARDPMGTR-CKVAEDLVVGTPGKKLVIVINK 63
+ +E ADVIL ++DA + R ++ ++ + K +++VINK
Sbjct: 87 KQSLEEADVILFMIDATEGWRPRDEEIYQNFIKPL-NKPVIVVINK 131
>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation,
GTP-binding domain, maturation enzyme, oxidoreductase;
2.99A {Thermotoga neapolitana}
Length = 423
Score = 28.5 bits (64), Expect = 1.1
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 5/47 (10%)
Query: 19 RSVVEAADVILEVVDARDPMGTRCKVAEDL-VVGTPGKKLVIVINKA 64
R V AD + V D+ V + P V+V+NK
Sbjct: 108 RRVFYRADCGILVTDSAPTPYED-DVVNLFKEMEIP---FVVVVNKI 150
>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 = 28.0 bits (63), Expect = 1.3
Identities = 8/50 (16%), Positives = 24/50 (48%), Gaps = 9/50 (18%)
Query: 22 VEAADVILEVVDARDP-------MGTRCKVAEDLVVGTPGKKLVIVINKA 64
+ +D ++ V+D+ + + ++ ++ G GK +++ +NK
Sbjct: 255 AKYSDALILVIDSTFSENLLIETLQSSFEILREI--GVSGKPILVTLNKI 302
>1a3q_A Protein (nuclear factor kappa-B P52); transcription factor, immune
response, DNA-protein complex, transcription/DNA
complex; HET: DNA; 2.10A {Homo sapiens} SCOP: b.1.18.1
b.2.5.3 PDB: 3do7_B 3jv6_B 3jv5_A
Length = 285
Score = 27.4 bits (60), Expect = 1.9
Identities = 11/86 (12%), Positives = 29/86 (33%)
Query: 51 GTPGKKLVIVINKAGKPSTKIQSGSMAQIFQTWIPYNSIQSIYSSPRFSSRSQKDAQTER 110
G + + +A + + + F ++ ++ + S P S+S + +
Sbjct: 129 GLTEAEQRELEQEAKELKKVMDLSIVRLRFSAFLRSLPLKPVISQPIHDSKSPGASNLKI 188
Query: 111 DLKAINVSSCVGAELLMLLLGNYTRN 136
S G + + LL ++
Sbjct: 189 SRMDKTAGSVRGGDEVYLLCDKVQKD 214
>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 = 27.3 bits (61), Expect = 2.1
Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 13/76 (17%)
Query: 6 PMEMRGVVVQEIERSVVEA---ADVILEVVDAR------DPMGTRCKVAEDLVV----GT 52
P E++ + EI + + DV + VVD + R ++ D+
Sbjct: 61 PKEVQERIKDEIVHFIEDNAKNIDVAVLVVDGKAAPEIIKRWEKRGEIPIDVEFYQFLRE 120
Query: 53 PGKKLVIVINKAGKPS 68
++ +NK K
Sbjct: 121 LDIPTIVAVNKLDKIK 136
>2j69_A Bacterial dynamin-like protein; FZO, FZL, GTPase, hydrolase; 3.0A
{Nostoc punctiforme} PDB: 2j68_A 2w6d_A*
Length = 695
Score = 26.5 bits (57), Expect = 4.7
Identities = 12/95 (12%), Positives = 28/95 (29%)
Query: 16 EIERSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKAGKPSTKIQSGS 75
E+ V IL V+ A P + + + G + ++N + +
Sbjct: 192 ELSLGYVNNCHAILFVMRASQPCTLGERRYLENYIKGRGLTVFFLVNAWDQVRESLIDPD 251
Query: 76 MAQIFQTWIPYNSIQSIYSSPRFSSRSQKDAQTER 110
+ Q + + + ++ ER
Sbjct: 252 DVEELQASENRLRQVFNANLAEYCTVEGQNIYDER 286
>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport,
maltose uptake and regulation, sugar binding protein;
1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3
c.37.1.12 PDB: 2d62_A
Length = 372
Score = 26.0 bits (58), Expect = 5.8
Identities = 10/25 (40%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 6 PMEMRGVVVQEIERSVVEAADVILE 30
P+++R V QEI++ V E A+ +L
Sbjct: 105 PLKLRKVPRQEIDQRVREVAE-LLG 128
>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding
protein; structural genomics, NPPSFA; 1.94A {Pyrococcus
horikoshii}
Length = 362
Score = 26.0 bits (58), Expect = 5.9
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 6 PMEMRGVVVQEIERSVVEAADVILE 30
P+E+R +EI++ V E A +L
Sbjct: 99 PLELRKAPREEIDKKVREVAK-MLH 122
>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active
transport, sugar uptake and regulation, transport
protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3
b.40.6.3 c.37.1.12 PDB: 1vci_A*
Length = 372
Score = 26.0 bits (58), Expect = 6.7
Identities = 7/25 (28%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 6 PMEMRGVVVQEIERSVVEAADVILE 30
P++++ EI++ V AA+ +L+
Sbjct: 107 PLKIKKFPKDEIDKRVRWAAE-LLQ 130
>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 = 25.9 bits (58), Expect = 6.7
Identities = 8/46 (17%), Positives = 18/46 (39%), Gaps = 4/46 (8%)
Query: 19 RSVVEAADVILEVVDARDPMGTRCKVAEDLV-VGTPGKKLVIVINK 63
S + ++++ VV+ V L P +++ +NK
Sbjct: 83 SSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAP---VILAVNK 125
>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha
and beta proteins (A/B) TM0421, structural genomics,
NPPSFA; 2.11A {Thermotoga maritima}
Length = 359
Score = 25.6 bits (57), Expect = 9.6
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 6 PMEMRGVVVQEIERSVVEAADVILE 30
P+ R + E+E+ VVE A L
Sbjct: 99 PLRARRISKDEVEKRVVEIAR-KLL 122
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
0.316 0.131 0.361
Gapped
Lambda K H
0.267 0.0808 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,340,219
Number of extensions: 132895
Number of successful extensions: 359
Number of sequences better than 10.0: 1
Number of HSP's gapped: 346
Number of HSP's successfully gapped: 36
Length of query: 161
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 75
Effective length of database: 4,300,587
Effective search space: 322544025
Effective search space used: 322544025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.0 bits)