RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 048058
(157 letters)
>3iz5_D 60S ribosomal protein L4 (L4P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_D
Length = 405
Score = 183 bits (464), Expect = 3e-57
Identities = 116/157 (73%), Positives = 140/157 (89%)
Query: 1 MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSR 60
MA RPL++V++LEGDMATD SS++ L +V +A +RPD+V FVH +S N RQPYAVSR
Sbjct: 1 MATQTRPLVSVKALEGDMATDNSSSLALAEVFRAPLRPDVVRFVHRLLSCNKRQPYAVSR 60
Query: 61 KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
+AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTK WR+WHR++N
Sbjct: 61 RAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRKWHRRVN 120
Query: 121 VNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
V+ +R A+ SA+AA++VPSLV+ARGH+IETVPE+PLV
Sbjct: 121 VHLRRVAVASALAATSVPSLVLARGHRIETVPELPLV 157
>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 421
Score = 178 bits (452), Expect = 2e-55
Identities = 110/155 (70%), Positives = 129/155 (83%), Gaps = 3/155 (1%)
Query: 3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
A ARPLI+V S +G+ + V LP V KA IRPDIV FVH+N+ KN+RQPYAVS A
Sbjct: 2 ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58
Query: 63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N
Sbjct: 59 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118
Query: 123 QKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
QKRYAI SA+A ++P+LVM++GH+IE VPE+PLV
Sbjct: 119 QKRYAICSALACLSLPALVMSKGHRIEEVPELPLV 153
>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel,
cotranslational protein translocation, protein
conducting channel; 6.48A {Triticum aestivum} PDB:
2wwa_H 2ww9_H 3izc_D 3izs_D 3o58_D 3o5h_D 3u5e_C 3u5i_C
1s1i_D 3jyw_D
Length = 362
Score = 169 bits (430), Expect = 1e-52
Identities = 103/153 (67%), Positives = 125/153 (81%), Gaps = 3/153 (1%)
Query: 5 ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGH 64
+RP +TV SL G+ ++ +PLP V A IRPDIV V ++++KN RQ YAVS KAGH
Sbjct: 2 SRPQVTVHSLTGE---ATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGH 58
Query: 65 QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQK 124
QTSAESWGTGRAV+RIPRV GGGT R+GQGAFGNMCRGGRMFAPTK WR+W+ K+N N+K
Sbjct: 59 QTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEK 118
Query: 125 RYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
RYA SAIAA+AV SLV+ARGH++E +PE+PLV
Sbjct: 119 RYATASAIAATAVASLVLARGHRVEKIPEIPLV 151
>4a17_C RPL4, ribosomal protein L3; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_C 4a1c_C 4a1e_C
Length = 410
Score = 168 bits (425), Expect = 2e-51
Identities = 83/158 (52%), Positives = 106/158 (67%), Gaps = 5/158 (3%)
Query: 4 AARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVS---- 59
+RP I V + + ++ + LP V A IR DIV V ++++KN +Q V
Sbjct: 2 TSRPQIHVHDAK-EANKQTATKLTLPAVFTAPIRTDIVHKVFTDLNKNRKQASGVKISTR 60
Query: 60 RKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKI 119
AG SAESWGTGRAV+RIPRV G GTHR+GQ AFGN CR GRMFAP K +RR HR++
Sbjct: 61 GTAGMGHSAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQCRKGRMFAPLKTYRRVHRRV 120
Query: 120 NVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
NVNQKR+A+ +A+AASA+ LV ARGH+I V E+P V
Sbjct: 121 NVNQKRHAVAAALAASALVPLVFARGHRISNVQELPYV 158
>1vq8_C 50S ribosomal protein L4E; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: c.22.1.1 PDB: 1k73_E*
1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E*
1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C
1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ...
Length = 246
Score = 138 bits (348), Expect = 1e-41
Identities = 46/149 (30%), Positives = 73/149 (48%), Gaps = 12/149 (8%)
Query: 9 ITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSA 68
T+ L+G+ V LPDV + +R D++G N +Q Y AG +T A
Sbjct: 3 ATIYDLDGN----TDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPA 58
Query: 69 ESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAI 128
ES+G+GR + +P++ G R Q GR P K + +N +++ A+
Sbjct: 59 ESFGSGRGQAHVPKLDGRA-RRVPQ------AVKGRSAHPPKTEKDRSLDLNDKERQLAV 111
Query: 129 VSAIAASAVPSLVMARGHKIETVPEMPLV 157
SA+AA+A LV RGH+ + E+P+V
Sbjct: 112 RSALAATADADLVADRGHEFDR-DEVPVV 139
>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 = 32.9 bits (74), Expect = 0.034
Identities = 20/120 (16%), Positives = 37/120 (30%), Gaps = 35/120 (29%)
Query: 32 MKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRA-----VSRIPRV--- 83
++ +R + F+ S I RQP ++R Q + + VSR+
Sbjct: 83 VEEVLRIN-YKFLMSPIKTEQRQPSMMTRMYIEQRD-RLYNDNQVFAKYNVSRLQPYLKL 140
Query: 84 --------PGGGT--HRAGQGAFG------NMCRGGRM--FAPTKIWRRWHRKINVNQKR 125
P G G ++C ++ KI+ W +N+
Sbjct: 141 RQALLELRPAKNVLID--GVLGSGKTWVALDVCLSYKVQCKMDFKIF--W---LNLKNCN 193
>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 = 29.1 bits (64), Expect = 0.39
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 10/34 (29%)
Query: 117 RKINVNQKRYAIVSAIAASAVPSLVM-ARGHKIE 149
+K+ + K YA SA P+L + A +E
Sbjct: 23 KKLQASLKLYADDSA------PALAIKA---TME 47
Score = 28.4 bits (62), Expect = 0.67
Identities = 6/28 (21%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 10 TVQSLEGDMATDASSTVP-LPDVMKASI 36
++ L+ + A + P L +KA++
Sbjct: 21 ALKKLQASLKLYADDSAPAL--AIKATM 46
>1mdl_A Mandelate racemase; isomerase, mandelate pathway, magnesium; HET:
RMN SMN; 1.85A {Pseudomonas aeruginosa} SCOP: c.1.11.2
d.54.1.1 PDB: 1mdr_A* 3uxk_A* 3uxl_A* 1dtn_A* 1mra_A*
2mnr_A 1mns_A
Length = 359
Score = 26.4 bits (59), Expect = 3.8
Identities = 5/33 (15%), Positives = 9/33 (27%)
Query: 102 GGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAA 134
AP + ++ + I A A
Sbjct: 74 VNEPLAPVSLEAMLAKRFCLAGYTGLIRMAAAG 106
>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 = 26.6 bits (58), Expect = 4.9
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 11/36 (30%)
Query: 126 YAIVSAIAASA-------VPSLVMARGHKI-ETVPE 153
Y +A+A+ A + +V RG + VP
Sbjct: 1767 Y---AALASLADVMSIESLVEVVFYRGMTMQVAVPR 1799
>1qcx_A Pectin lyase B; beta-helix protein, plant cell WALL; 1.70A
{Aspergillus niger} SCOP: b.80.1.2
Length = 359
Score = 25.9 bits (56), Expect = 7.7
Identities = 11/66 (16%), Positives = 19/66 (28%), Gaps = 1/66 (1%)
Query: 78 SRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAV 137
++ P T++ FG C+ F + I I +A A+
Sbjct: 289 GQLFSSPDANTNQQCASVFGRSCQLN-AFGNSGSMSGSDTSIISKFAGKTIAAAHPPGAI 347
Query: 138 PSLVMA 143
M
Sbjct: 348 AQWTMK 353
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 0.130 0.393
Gapped
Lambda K H
0.267 0.0485 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,375,295
Number of extensions: 129448
Number of successful extensions: 271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 264
Number of HSP's successfully gapped: 13
Length of query: 157
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 71
Effective length of database: 4,300,587
Effective search space: 305341677
Effective search space used: 305341677
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: 53 (24.8 bits)