RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17052
(68 letters)
>3rrk_A V-type ATPase 116 kDa subunit; alpha beta fold, proton pump,
subunit I/A, V-ATPase, proton; HET: NHE; 2.64A
{Meiothermus ruber}
Length = 357
Score = 39.4 bits (91), Expect = 2e-05
Identities = 12/63 (19%), Positives = 19/63 (30%), Gaps = 4/63 (6%)
Query: 4 NLNPDVNAFQRKFVNEVRRCDEMERKLRYLEKEIKKDGIPMMDVGESPEAPQPREMIDLE 63
L PD R E E + E+ + G+ + P + + E
Sbjct: 43 PLRPDELGEYRLSPTEEAELKRWEAVVSQAEQSLTVVGLATVP----SSKPFTGSLEEAE 98
Query: 64 ASL 66
A L
Sbjct: 99 AVL 101
>3eh0_A UDP-3-O-[3-hydroxymyristoyl] glucosamine N- acyltransferase; LPXD,
LEFT-handed parallel beta helix, acyl carrier protein,
antibiotic resistance; 2.60A {Escherichia coli}
Length = 341
Score = 30.3 bits (69), Expect = 0.027
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 14 RKFVNEVRRCDEMERKLRYLEKEIKK 39
RK V D+M ++L+ LE+++ +
Sbjct: 314 RKTAALVMNIDDMSKRLKSLERKVNQ 339
>3pmo_A UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltr; lipid A
biosynthesis pathway, transferase; 1.30A {Pseudomonas
aeruginosa}
Length = 372
Score = 29.5 bits (67), Expect = 0.041
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 13 QRKFVNEVRRCDEMERKLRYLEKEIKK 39
+K +R+ D+M R+L+ LEK +
Sbjct: 335 WKKSAARIRQLDDMARRLQQLEKRLAA 361
>2iu8_A LPXD, UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase;
UDP-3- O-acyl-glucosamine N-acyltransferase, lipid A
biosynthesis; HET: PLM UD1; 2.2A {Chlamydia trachomatis}
PDB: 2iu9_A* 2iua_A*
Length = 374
Score = 29.6 bits (67), Expect = 0.043
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 14 RKFVNEVRRCDEMERKLRYLEKEIKK 39
+ V +VR +E ++ LEK ++K
Sbjct: 341 HRQVAKVRNLPRLEERIAALEKLVQK 366
>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 = 28.0 bits (61), Expect = 0.17
Identities = 7/30 (23%), Positives = 15/30 (50%), Gaps = 4/30 (13%)
Query: 27 ERK-LRYLEKEIKK---DGIPMMDVGESPE 52
E++ L+ L+ +K D P + + + E
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATME 47
>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 = 27.5 bits (60), Expect = 0.30
Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 14/50 (28%)
Query: 2 H-SNLNPD--VNAFQRKFVNEVRRCDEMERKLRYLEKEIKKDGIPMMDVG 48
H N+ + F+ F++ R+LE++I+ D G
Sbjct: 480 HLKNIEHPERMTLFRMVFLD-----------FRFLEQKIRHDSTAWNASG 518
Score = 26.0 bits (56), Expect = 1.1
Identities = 9/51 (17%), Positives = 21/51 (41%), Gaps = 4/51 (7%)
Query: 2 HSNLNPDVNAFQRKFVNEVRRCDEMERKLRYLEKE--IKKDGIPMMDVGES 50
L D F + V+ ++ ++ + L L + DG ++ G++
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDG--VLGSGKT 164
>1lw3_A Myotubularin-related protein 2; protein-phosphate complex,
hydrolase; 2.30A {Homo sapiens} SCOP: b.55.1.8 c.45.1.3
PDB: 1m7r_A
Length = 657
Score = 26.1 bits (56), Expect = 0.96
Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 1/62 (1%)
Query: 5 LNPDVNAFQRKFVNEVRRCDEMERKLRYLEKEIKKDGIPMMDVGESPEAPQPREMIDLEA 64
+ P R + + + E+++K+ L++EI + SP + A
Sbjct: 590 MKPQEPIHNR-YKELLAKRAELQKKVEELQREISNRSTSSSERASSPAQCVTPVQTVVAA 648
Query: 65 SL 66
+L
Sbjct: 649 AL 650
>1a92_A Delta antigen; leucine zipper, coiled-coil, oligomerization;
1.80A {Hepatitis delta virus} SCOP: h.4.6.1 PDB: 1by0_A
Length = 50
Score = 23.5 bits (50), Expect = 2.7
Identities = 11/25 (44%), Positives = 20/25 (80%)
Query: 15 KFVNEVRRCDEMERKLRYLEKEIKK 39
++V+ ++ +E+ER LR L+K+IKK
Sbjct: 8 QWVSGRKKLEELERDLRKLKKKIKK 32
>2w01_A Adenylate cyclase; guanylyl cyclase, class III nucleotidyl cyclase,
lyase; 2.31A {Synechocystis SP}
Length = 208
Score = 24.1 bits (53), Expect = 4.4
Identities = 6/24 (25%), Positives = 15/24 (62%)
Query: 25 EMERKLRYLEKEIKKDGIPMMDVG 48
EM+ LR + +++ G+ +++G
Sbjct: 90 EMQLALREVNQQVTGLGLQPLEMG 113
>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase;
RECA-like fold, PRE-mRNA processing protein; 1.90A
{Homo sapiens} SCOP: c.37.1.19
Length = 172
Score = 24.1 bits (53), Expect = 4.5
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 16 FVNEVRRCDEMERKLR 31
FV V+RC + + L
Sbjct: 37 FVKSVQRCIALAQLLV 52
>2ajg_A Leucyl-tRNA synthetase; editing domain, ligase; 2.00A
{Escherichia coli} PDB: 2ajh_A 2aji_A
Length = 196
Score = 23.6 bits (52), Expect = 5.1
Identities = 9/31 (29%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 6 NPDVNAFQRKFVNEVRRCDEMERKLRYLEKE 36
NP++ AF ++E R E ++ +EK+
Sbjct: 58 NPELAAF----IDECRNTKVAEAEMATMEKK 84
>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene
regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19
c.37.1.19 PDB: 1xtj_A* 1xtk_A
Length = 391
Score = 23.3 bits (51), Expect = 6.9
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 16 FVNEVRRCDEMERKLR 31
FV V+RC + + L
Sbjct: 256 FVKSVQRCIALAQLLV 271
>4arc_A Leucine--tRNA ligase; ligase-RNA complex, nucleotide-binding,
protein biosynthesis I aminoacyl-tRNA synthetase,
ATP-binding; 2.00A {Escherichia coli} PDB: 4aq7_A
4ari_A* 4as1_A*
Length = 880
Score = 23.3 bits (51), Expect = 7.5
Identities = 9/31 (29%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 6 NPDVNAFQRKFVNEVRRCDEMERKLRYLEKE 36
NP++ AF ++E R E ++ +EK+
Sbjct: 295 NPELAAF----IDECRNTKVAEAEMATMEKK 321
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_C*
Length = 1342
Score = 23.1 bits (50), Expect = 8.7
Identities = 10/34 (29%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 8 DVNAFQRKFVNEVRRCDEME-RKLRYLEKEIKKD 40
DV F R V + +R E+E +L+ +K++ ++
Sbjct: 930 DVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEE 963
>2v0c_A Aminoacyl-tRNA synthetase; ligase, nucleotide-binding, protein
biosynthesis; HET: LMS ANZ; 1.85A {Thermus thermophilus}
PDB: 1h3n_A* 1obc_A* 1obh_A* 2bte_A* 2byt_A 2v0g_A*
Length = 878
Score = 23.3 bits (51), Expect = 9.2
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 4/31 (12%)
Query: 6 NPDVNAFQRKFVNEVRRCDEMERKLRYLEKE 36
+V A+ V +R E+ER+ EK
Sbjct: 277 REEVLAY----VEAAKRKTEIERQAEGREKT 303
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
0.317 0.134 0.381
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,060,899
Number of extensions: 49814
Number of successful extensions: 203
Number of sequences better than 10.0: 1
Number of HSP's gapped: 203
Number of HSP's successfully gapped: 24
Length of query: 68
Length of database: 6,701,793
Length adjustment: 38
Effective length of query: 30
Effective length of database: 5,640,795
Effective search space: 169223850
Effective search space used: 169223850
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: 51 (23.3 bits)