RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1800
(81 letters)
>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 265
Score = 92.5 bits (229), Expect = 7e-25
Identities = 40/64 (62%), Positives = 48/64 (75%)
Query: 3 PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFC 62
GN+ M+TGGRN GRVG + NRE+H GSF+ +HV+D GH FATRL NVF IGKG K +
Sbjct: 177 VGNVVMVTGGRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWV 236
Query: 63 SKPK 66
S PK
Sbjct: 237 SLPK 240
>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena
thermophila} PDB: 2xzn_W
Length = 260
Score = 90.5 bits (224), Expect = 3e-24
Identities = 33/64 (51%), Positives = 45/64 (70%)
Query: 3 PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFC 62
GN+C I G N+GRVG + + E+H GSFDI HVKD G+ FATRL N+F++G+G K++
Sbjct: 179 SGNVCYIQQGNNIGRVGIIQHIEKHQGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWI 238
Query: 63 SKPK 66
P
Sbjct: 239 ELPS 242
>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_D 3u5g_E
Length = 261
Score = 90.5 bits (224), Expect = 4e-24
Identities = 37/64 (57%), Positives = 48/64 (75%)
Query: 3 PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFC 62
G L +TGGRNLGR+GT+V++ERH G FD+VH+KD + F TRLNNVF+IG+ K +
Sbjct: 177 AGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYI 236
Query: 63 SKPK 66
S PK
Sbjct: 237 SLPK 240
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG,
structural genomics, PSI-2, protein structure
initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}
Length = 213
Score = 74.8 bits (183), Expect = 2e-18
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 3 PGNLCMITGGRNLGRVGTVVNRERHPGS-FDIVHVKDGNGHVFATRLNNVFIIGKGTKAF 61
PGN IT G ++ + GT+ E GS ++VH ++G F+T ++VF+IG +F
Sbjct: 141 PGNKAYITAGSHVNQTGTISKIEAKEGSSANLVHFQEG----FSTIKDHVFMIGSSKFSF 196
Query: 62 CSKPK 66
P+
Sbjct: 197 VLSPE 201
>1coz_A Protein (glycerol-3-phosphate cytidylyltransferase); HET: CTP;
2.00A {Bacillus subtilis} SCOP: c.26.1.2 PDB: 1n1d_A*
Length = 129
Score = 26.7 bits (60), Expect = 0.66
Identities = 10/44 (22%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 29 GSFDIVHVKDGNGHV----FATRLNNVFIIGKGTKAFCSKPKRN 68
G+FD++H GH+ A +L + ++ T F + ++
Sbjct: 8 GTFDLLHW----GHIKLLERAKQLGDYLVVAISTDEFNLQKQKK 47
>2rh8_A Anthocyanidin reductase; flavonoids, rossmann fold, short chain
dehydrogenase/reductase, oxidoreductase; 2.22A {Vitis
vinifera} PDB: 3hfs_A
Length = 338
Score = 26.1 bits (58), Expect = 1.1
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 6 LCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD-GNGHVFA 45
+ +ITG N + + + GS I HV+D H+F
Sbjct: 215 MSLITG--NEFLINGMKGMQMLSGSVSIAHVEDVCRAHIFV 253
>2b7l_A Glycerol-3-phosphate cytidylyltransferase; rossmann fold; 3.00A
{Staphylococcus aureus}
Length = 132
Score = 25.9 bits (58), Expect = 1.2
Identities = 9/43 (20%), Positives = 18/43 (41%), Gaps = 8/43 (18%)
Query: 29 GSFDIVHVKDGNGHV----FATRLNNVFIIGKGTKAFCSKPKR 67
G++D++H GH+ A + + I+ T F +
Sbjct: 8 GTYDLLHY----GHIELLRRAREMGDYLIVALSTDEFNQIKHK 46
>1pxf_A Hypothetical protein YGJH; oligonucleotide-oligosaccharide
binding fold, OB fold, beta- barrel; 1.87A {Escherichia
coli} SCOP: b.40.4.4 PDB: 3ers_X
Length = 111
Score = 25.7 bits (57), Expect = 1.3
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 17 RVGTVVNRERHPGS 30
RVG +V +RH +
Sbjct: 15 RVGKIVEVKRHENA 28
>3l23_A Sugar phosphate isomerase/epimerase; structural genomics, JO center
for structural genomics, JCSG, protein structure INI
PSI-2; HET: MSE; 1.70A {Parabacteroides distasonis}
Length = 303
Score = 25.9 bits (56), Expect = 1.3
Identities = 6/24 (25%), Positives = 13/24 (54%), Gaps = 5/24 (20%)
Query: 25 ERHPGSFDIVHVKD-----GNGHV 43
++HP ++H+KD +G +
Sbjct: 232 QKHPDRIKVLHIKDRAVFGQSGMM 255
>3obe_A Sugar phosphate isomerase/epimerase; structural genomics, joint
center for structural genomics, J protein structure
initiative; HET: MSE; 1.70A {Parabacteroides distasonis}
Length = 305
Score = 26.2 bits (57), Expect = 1.3
Identities = 7/24 (29%), Positives = 13/24 (54%), Gaps = 5/24 (20%)
Query: 25 ERHPGSFDIVHVKD-----GNGHV 43
E +P F ++H+KD +G +
Sbjct: 234 ENYPNRFKLLHIKDRWIIGDSGMM 257
>1f9a_A Hypothetical protein MJ0541; alpha/beta, transferase, structural
genomics; HET: ATP; 2.00A {Methanocaldococcus
jannaschii} SCOP: c.26.1.3
Length = 168
Score = 25.9 bits (57), Expect = 1.4
Identities = 12/49 (24%), Positives = 16/49 (32%), Gaps = 9/49 (18%)
Query: 28 PGSFDIVHVKDGNGHV----FATRLNNVFIIGKGTKAFCSKPKRNFVSP 72
G F H GH+ + IIG G+ A S N +
Sbjct: 6 IGRFQPFH----KGHLEVIKKIAEEVDEIIIGIGS-AQKSHTLENPFTA 49
>1mkh_A Metrs;, C-terminal domain of methionyl-tRNA synthetase; beta
barrel, dimerization domain, ligase; 2.01A {Pyrococcus
abyssi} SCOP: b.40.4.4
Length = 107
Score = 25.2 bits (56), Expect = 1.7
Identities = 5/14 (35%), Positives = 9/14 (64%)
Query: 17 RVGTVVNRERHPGS 30
RVG ++ + HP +
Sbjct: 14 RVGKIIEVKDHPNA 27
>1ntg_A Tyrrs, tyrosyl-tRNA synthetase; beta barrel, ligase; 2.21A {Homo
sapiens} SCOP: b.40.4.4
Length = 172
Score = 25.5 bits (56), Expect = 1.9
Identities = 6/14 (42%), Positives = 10/14 (71%)
Query: 17 RVGTVVNRERHPGS 30
RVG ++ E+HP +
Sbjct: 13 RVGKIITVEKHPDA 26
>1fl0_A Endothelial-monocyte activating polypeptide II; RNA-binding
domain, OB-fold, tRNA synthetase complex, RNA binding
protein; 1.50A {Homo sapiens} SCOP: b.40.4.4 PDB:
1e7z_A 1euj_A
Length = 171
Score = 25.0 bits (55), Expect = 2.4
Identities = 4/14 (28%), Positives = 9/14 (64%)
Query: 17 RVGTVVNRERHPGS 30
R+G ++ +HP +
Sbjct: 9 RIGCIITARKHPDA 22
>2iv2_X Formate dehydrogenase H; oxidoreductase, 4Fe-4S, anaerobic,
complete proteome, direct protein sequencing, Fe4S4,
iron, iron sulfur cluster; HET: 2MD MGD; 2.27A
{Escherichia coli} SCOP: b.52.2.2 c.81.1.1 PDB: 1fdi_A*
1fdo_A* 1aa6_A*
Length = 715
Score = 25.2 bits (56), Expect = 2.9
Identities = 9/19 (47%), Positives = 12/19 (63%), Gaps = 2/19 (10%)
Query: 5 NLCMITGGRNLGRVGTVVN 23
+L M+TG NLG+ VN
Sbjct: 314 SLAMLTG--NLGKPHAGVN 330
>3izc_n 60S ribosomal protein RPL38 (L38E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins; NMR {Saccharomyces cerevisiae} PDB:
3izs_n 3u5e_k 3u5i_k
Length = 78
Score = 24.6 bits (53), Expect = 3.3
Identities = 2/21 (9%), Positives = 4/21 (19%)
Query: 3 PGNLCMITGGRNLGRVGTVVN 23
++ T N
Sbjct: 17 RADVKTATVKINKKLNKAGKP 37
>1pyb_A Methionyl-tRNA synthetase beta subunit; oligonucleotide,
oligosaccharide-binding fold, OB-fold, beta-barrel, RNA
binding protein; 2.50A {Aquifex aeolicus} SCOP:
b.40.4.4
Length = 111
Score = 24.1 bits (53), Expect = 4.2
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 17 RVGTVVNRERHPGS 30
RV V++ ER GS
Sbjct: 18 RVAKVLSAERVEGS 31
>3p6l_A Sugar phosphate isomerase/epimerase; TIM barrel, structural
genomics, joint center for structural genomics, JCSG;
HET: CIT; 1.85A {Parabacteroides distasonis}
Length = 262
Score = 24.4 bits (53), Expect = 4.7
Identities = 7/33 (21%), Positives = 11/33 (33%)
Query: 25 ERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKG 57
++ G +H KD + I G G
Sbjct: 180 KQLKGRIISLHFKDIAPKKAGENEQHDVIWGTG 212
>2cwp_A Metrs related protein; structural GEN riken structural
genomics/proteomics initiative, RSGI; 2.10A {Pyrococcus
horikoshii}
Length = 112
Score = 24.1 bits (53), Expect = 4.7
Identities = 4/14 (28%), Positives = 7/14 (50%)
Query: 17 RVGTVVNRERHPGS 30
+VG V E+ +
Sbjct: 18 KVGLVKKAEKIKRT 31
>3iz5_N 60S ribosomal protein L14 (L14E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
PDB: 3izr_N
Length = 134
Score = 24.1 bits (52), Expect = 4.8
Identities = 5/21 (23%), Positives = 13/21 (61%)
Query: 3 PGNLCMITGGRNLGRVGTVVN 23
G + ++ G++ GR+ +V+
Sbjct: 9 IGRVALVNYGKDYGRLVVIVD 29
>3glv_A Lipopolysaccharide core biosynthesis protein; structural GEN PSI,
MCSG, protein structure initiative; HET: AMP; 1.99A
{Thermoplasma volcanium GSS1}
Length = 143
Score = 23.7 bits (52), Expect = 6.8
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 9/44 (20%)
Query: 29 GSFDIVHVKDGNGHVF----ATRLNNVFIIGKGTKAFCSK-PKR 67
G FDI+H+ GH+ + +L + ++ + K
Sbjct: 9 GVFDILHL----GHIHYLKESKKLGDELVVVVARDSTARNNGKI 48
>2jyc_A Uncharacterized protein C6ORF130; macro domain, A1PP domain,
BC011709, protein structure initiative, PSI-2; NMR
{Homo sapiens} PDB: 2lgr_A
Length = 160
Score = 23.8 bits (51), Expect = 7.7
Identities = 7/42 (16%), Positives = 19/42 (45%)
Query: 24 RERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKP 65
+++ G ++++ + +G V + + +I TK S
Sbjct: 57 KKKFGGVQELLNQQKKSGEVAVLKRDGRYIYYLITKKRASHK 98
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
0.325 0.142 0.454
Gapped
Lambda K H
0.267 0.0581 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,273,952
Number of extensions: 64585
Number of successful extensions: 183
Number of sequences better than 10.0: 1
Number of HSP's gapped: 182
Number of HSP's successfully gapped: 32
Length of query: 81
Length of database: 6,701,793
Length adjustment: 50
Effective length of query: 31
Effective length of database: 5,305,743
Effective search space: 164478033
Effective search space used: 164478033
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.8 bits)