RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15650
(211 letters)
>2xzm_2 40S ribosomal protein S8; ribosome, translation; 3.93A {Tetrahymena
thermophila} PDB: 2xzn_2
Length = 208
Score = 126 bits (316), Expect = 2e-36
Identities = 70/171 (40%), Positives = 91/171 (53%), Gaps = 48/171 (28%)
Query: 2 TRGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIVVIDAT 61
RGG+ K+RALR+ +GNFSWGSE TRKT+I+DV YNA+NNELVRTKTLVKN+IV ID+T
Sbjct: 56 VRGGHLKFRALRLCEGNFSWGSENITRKTKILDVKYNATNNELVRTKTLVKNSIVEIDST 115
Query: 62 PFRQWYETYYALPIGRRKTGKLDVQQLTPSLDPEEYTLYVPVVVTRSTELSVLTRAISHG 121
PFR+WY+ +Y + +G +K
Sbjct: 116 PFREWYKLHYGIDLGLKK------------------------------------------ 133
Query: 122 DLNTEAEEAVLNKKRSKKVVKKYKSRQKHAKVEQAIEEQFQTGRILVSILS 172
+ VL K + V+K R K +E+ IEEQF + RIL I S
Sbjct: 134 ------DRTVLGNKEKSRHVQKRVKRTKAQALEKNIEEQFVSQRILACITS 178
>3u5c_I RP19, S14, YS9, 40S ribosomal protein S8-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3u5g_I
Length = 200
Score = 119 bits (300), Expect = 3e-34
Identities = 69/171 (40%), Positives = 87/171 (50%), Gaps = 47/171 (27%)
Query: 2 TRGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIVVIDAT 61
TRGGNKKYRALRI+ GNFSW SE ++KTRI VVY+ SNNELVRT TL K AIV IDAT
Sbjct: 48 TRGGNKKYRALRIETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDAT 107
Query: 62 PFRQWYETYYALPIGRRKTGKLDVQQLTPSLDPEEYTLYVPVVVTRSTELSVLTRAISHG 121
PFRQW+E +Y +G++K K +
Sbjct: 108 PFRQWFEAHYGQTLGKKKNVKEEET----------------------------------- 132
Query: 122 DLNTEAEEAVLNKKRSKKVVKKYKSRQKHAKVEQAIEEQFQTGRILVSILS 172
+SK +K+ +R AK+E ++E QF GR+ I S
Sbjct: 133 ------------VAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISS 171
>2kcp_A 30S ribosomal protein S8E; RPS8E, beta, NESG, ribonucleoprotein,
structural genomics, PSI-2; NMR {Methanothermobacter
thermautotrophicusstr} PDB: 2kcy_A
Length = 98
Score = 92.9 bits (231), Expect = 6e-25
Identities = 18/63 (28%), Positives = 25/63 (39%)
Query: 2 TRGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIVVIDAT 61
TRGGN K R + N I +VV N +N VR + + A+V +
Sbjct: 10 TRGGNTKVRLASDTRINVVDPETGKVEIAEIRNVVENTANPHFVRRNIITRGAVVETNLG 69
Query: 62 PFR 64
R
Sbjct: 70 NVR 72
>2kco_A 30S ribosomal protein S8E; ribosomal protein of unknown function,
ribonucleoprotein, PSI-2, protein structure initiative;
NMR {Sulfolobus solfataricus P2}
Length = 133
Score = 88.4 bits (219), Expect = 7e-23
Identities = 15/63 (23%), Positives = 28/63 (44%)
Query: 2 TRGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIVVIDAT 61
T GGN K R N + +K +I++++ +N EL R +++ A + +A
Sbjct: 48 TLGGNFKVRLKYTTTANVLDPATNTAKKVKILEILETPANKELARRGIIIRGAKIRTEAG 107
Query: 62 PFR 64
Sbjct: 108 LAV 110
>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 = 35.6 bits (81), Expect = 0.011
Identities = 32/228 (14%), Positives = 71/228 (31%), Gaps = 82/228 (35%)
Query: 6 NKKY-RALRI-DQGNFSWGSEC-------C-----TRKTRIIDVVYNASNNELV---RTK 48
+K Y L + N ++ C TR ++ D + A+ + +
Sbjct: 240 SKPYENCLLVLL--NV-QNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSM 296
Query: 49 TLVKNAIVVIDATPFRQWYET-YYALP-------------IGRRKTG---------KLDV 85
TL + + + ++ + LP I ++
Sbjct: 297 TLTPDEVKSL----LLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNC 352
Query: 86 QQLTP-------SLDPEEY-TLY-----------VPVVVTRSTELSVLTRAISHGDLNTE 126
+LT L+P EY ++ +P ++ LS++ D+
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL-----LSLI-----WFDVIKS 402
Query: 127 AEEAVLNKKRSKKVVKKYKSRQK------HAKVEQAIEEQFQTGRILV 168
V+NK +V+K + +++ +E ++ R +V
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIV 450
Score = 27.9 bits (61), Expect = 2.7
Identities = 38/205 (18%), Positives = 68/205 (33%), Gaps = 68/205 (33%)
Query: 42 NELVRTKTLVKNAIVVIDATPFRQWYETYYALP-IGRRKTGKLD---------VQQ---- 87
N+L + +LV+ +Q E+ ++P I KL+ V
Sbjct: 409 NKLHK-YSLVE-----------KQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIP 456
Query: 88 --------LTPSLD----------------PEEYTLYVPVVVTRSTELSVLTRAISHGDL 123
+ P LD PE TL+ V + + L + I H
Sbjct: 457 KTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFL----DFRFLEQKIRHDST 512
Query: 124 NTEAEEAVLNKKRSKKVVKKYKS--RQKHAKVEQAIE--EQF--QTGRILVSILSERTAV 177
A ++LN + + +K YK K E+ + F + L I S+ T +
Sbjct: 513 AWNASGSILN---TLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENL--ICSKYTDL 567
Query: 178 RQAKFHAVDSGSGGWWFESKSSSER 202
+ A+ + + E+ +R
Sbjct: 568 LRI---ALMAEDEAIFEEAHKQVQR 589
>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 = 35.0 bits (80), Expect = 0.018
Identities = 24/122 (19%), Positives = 45/122 (36%), Gaps = 39/122 (31%)
Query: 4 GGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRT--KTLVKNAIVVIDAT 61
GG QGN ++ + R + Y+ +L++ +TL + +DA
Sbjct: 161 GG----------QGN----TDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAE 206
Query: 62 PFRQWYETYYALPIGRRKTGKLDVQQ-LT-PSLDP-EEYTLYVPVVVTRSTELSVLTRAI 118
G L++ + L PS P ++Y L +P+ S L + +
Sbjct: 207 KV---------FTQG------LNILEWLENPSNTPDKDYLLSIPI----SCPLIGVI-QL 246
Query: 119 SH 120
+H
Sbjct: 247 AH 248
Score = 31.2 bits (70), Expect = 0.30
Identities = 30/207 (14%), Positives = 61/207 (29%), Gaps = 58/207 (28%)
Query: 3 RGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIVVIDATP 62
++ +++ N + ++ I + N + N +V+ P
Sbjct: 342 SNLTQEQVQDYVNKTNSHLPAG---KQVEI--SLVNGAKN-------------LVVSGPP 383
Query: 63 FRQWYETYYALPIGRRK---TGKLDVQQLTPSLDPEEYTLYVPVVVTRSTELSVLTRAIS 119
++ Y L + RK LD Q P ++ R L ++
Sbjct: 384 -----QSLYGLNLTLRKAKAPSGLD-QSRIP------FSERKLKFSNR-----FLP--VA 424
Query: 120 ---HGDLNTEAEEAVLNKKRSKKVVKKYKSRQKHAKVE--------QAIEEQFQTGRILV 168
H L A + + V + ++ V + + + RI+
Sbjct: 425 SPFHSHLLVPASDLINKDLVKNNV--SFNAKDIQIPVYDTFDGSDLRVLSGSI-SERIVD 481
Query: 169 SILSER----TAVRQAKFHAVDSGSGG 191
I+ T + H +D G GG
Sbjct: 482 CIIRLPVKWETTTQFKATHILDFGPGG 508
Score = 30.4 bits (68), Expect = 0.49
Identities = 30/172 (17%), Positives = 56/172 (32%), Gaps = 52/172 (30%)
Query: 3 RGGNKKYRALR----IDQGN--FSWGSECCTRKTRI------IDVVYNASNNELVRTKTL 50
G N R + +DQ FS RK + + +++ LV L
Sbjct: 387 YGLNLTLRKAKAPSGLDQSRIPFS------ERKLKFSNRFLPVASPFHSH--LLVPASDL 438
Query: 51 VKNAIVVIDATPFRQWYETYYALPIGRRKTGKLDVQQLTPSLDPE--EYTLYVPV----- 103
+ +V + + +P+ G D++ L+ S+ + + +PV
Sbjct: 439 INKDLVKNNV----SFNAKDIQIPVYDTFDGS-DLRVLSGSISERIVDCIIRLPVKWETT 493
Query: 104 VVTRST-----------ELSVLT---------RAISHGDLNTEAEEAVLNKK 135
++T L VLT R I G L+ ++ K+
Sbjct: 494 TQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPDDDYGFKQ 545
Score = 30.0 bits (67), Expect = 0.62
Identities = 20/118 (16%), Positives = 44/118 (37%), Gaps = 24/118 (20%)
Query: 88 LTPSLDPEEYTLYVPVVVTRSTELSVLTRAISHG-DLNTEA------EEAVLNKKRSKKV 140
++ ++P + + V+ + L+ G D++ A + L K K++
Sbjct: 68 VSSLVEPSKVGQFDQVL---NLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKT--KEL 122
Query: 141 VKKY-KSRQKHAKVEQAIEEQFQTGRILVSILSERTAVRQAKFHAVDSGSG--GWWFE 195
+K Y +R ++ +++ S L A+ A+ G G +FE
Sbjct: 123 IKNYITAR---IMAKRPFDKKSN------SALFRAVGEGNAQLVAIFGGQGNTDDYFE 171
Score = 29.2 bits (65), Expect = 1.1
Identities = 22/119 (18%), Positives = 36/119 (30%), Gaps = 42/119 (35%)
Query: 3 RG------------GNKKYRALRIDQGNFSWG----------SECCTRKTRIIDVV-YNA 39
RG G Y + I+ G + R ++++V YN
Sbjct: 1789 RGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNV 1848
Query: 40 SNNELVRTKTL--VKNAIVVIDATPFRQWYETYYALPIGRRKTGKLDVQQLTPSLDPEE 96
N + V L + V++ K K+D+ +L SL EE
Sbjct: 1849 ENQQYVAAGDLRALDTVTNVLNFI-----------------KLQKIDIIELQKSLSLEE 1890
>3up9_A Putative uncharacterized protein; membrane lipoprotein,
L-methionine binding protein, NLPA LIP structural
genomics; HET: PG4 PE4; 2.35A {Actinomyces
odontolyticus}
Length = 245
Score = 29.5 bits (67), Expect = 0.67
Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 4/35 (11%)
Query: 133 NKKRSKKVVKKYKSRQKHAKVEQAIEEQFQTGRIL 167
K+ K S +V+Q IE+ + G ++
Sbjct: 212 KVDAIAKLEKLLHS----DEVKQYIEKTWSDGSVI 242
>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 = 28.8 bits (63), Expect = 0.84
Identities = 7/34 (20%), Positives = 13/34 (38%), Gaps = 10/34 (29%)
Query: 82 KLDVQQLTPSLDPEEYTLYVP-----VVVTRSTE 110
K +++L SL LY + + + E
Sbjct: 19 KQALKKLQASL-----KLYADDSAPALAIKATME 47
Score = 27.6 bits (60), Expect = 2.0
Identities = 6/29 (20%), Positives = 14/29 (48%), Gaps = 8/29 (27%)
Query: 138 KKVVKKYKSRQK-HA-------KVEQAIE 158
K+ +KK ++ K +A ++ +E
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKATME 47
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 28.9 bits (64), Expect = 1.0
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 7/44 (15%)
Query: 24 ECCTRKTRIIDVVYNASNNELVRTKT-LVKNAIVVIDATPFRQW 66
EC K +V S ++V LV + ++D +W
Sbjct: 26 EC---KVYPPKIVERFSEGDVVCALCGLVLSD-KLVDTRS--EW 63
>3rcn_A Beta-N-acetylhexosaminidase; structural genomics, PSI-biology,
midwest center for structu genomics, MCSG, alpha-beta
half sandwich; HET: MSE; 2.51A {Arthrobacter aurescens}
Length = 543
Score = 27.7 bits (62), Expect = 3.1
Identities = 11/54 (20%), Positives = 18/54 (33%), Gaps = 3/54 (5%)
Query: 60 ATPFRQWYETYYALPIGRRKTGKLDVQ-QLTPSLDPEEYTLYVP--VVVTRSTE 110
+ + + ++ L PSLD E Y L V VV++
Sbjct: 42 RRWLTRALGGATGWDLAPAPAREAGIRLLLDPSLDAEAYRLEVSDAVVISAGGA 95
>3k2d_A ABC-type metal ION transport system, periplasmic; alpha/beta
domain, immune system; 2.60A {Vibrio vulnificus}
Length = 237
Score = 27.2 bits (61), Expect = 3.6
Identities = 7/30 (23%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 133 NKKRSKKVVKKYKSRQKHAKVEQAIEEQFQ 162
+ + VK Y++ +V A +E F+
Sbjct: 212 QNENVQNFVKAYQT----EEVYTAAKEIFK 237
>3gxa_A Outer membrane lipoprotein GNA1946; periplasmic, L-methionine
bingding, protein binding; 2.25A {Neisseria
meningitidis}
Length = 275
Score = 27.3 bits (61), Expect = 3.7
Identities = 5/30 (16%), Positives = 12/30 (40%), Gaps = 4/30 (13%)
Query: 133 NKKRSKKVVKKYKSRQKHAKVEQAIEEQFQ 162
+ + K V + Y S + ++F+
Sbjct: 228 DSQWLKDVTEAYNS----DAFKAYAHKRFE 253
>3ir1_A Outer membrane lipoprotein GNA1946; D-methionine cultured, protein
binding; 2.15A {Neisseria meningitidis}
Length = 245
Score = 26.8 bits (60), Expect = 4.2
Identities = 5/30 (16%), Positives = 12/30 (40%), Gaps = 4/30 (13%)
Query: 133 NKKRSKKVVKKYKSRQKHAKVEQAIEEQFQ 162
+ + K V + Y S + ++F+
Sbjct: 206 DSQWLKDVTEAYNS----DAFKAYAHKRFE 231
>1p99_A Hypothetical protein PG110; structural genomics, PSI, protein
structure initiative, midwest center for structural
genomics, MCSG; 1.70A {Staphylococcus aureus subsp}
SCOP: c.94.1.1
Length = 295
Score = 26.5 bits (59), Expect = 5.7
Identities = 7/30 (23%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 133 NKKRSKKVVKKYKSRQKHAKVEQAIEEQFQ 162
+ K K+V+ Y S + ++A++E +
Sbjct: 248 DNKTYAKIVELYHS----KEAQKALQEDVK 273
>1ozj_A SMAD 3; MAD homology domain 1, DNA recognition, TGF-beta signaling,
zinc-binding module, transcription/DNA complex; 2.40A
{Homo sapiens} SCOP: d.164.1.1 PDB: 1mhd_A*
Length = 144
Score = 26.1 bits (57), Expect = 5.7
Identities = 12/49 (24%), Positives = 22/49 (44%)
Query: 112 SVLTRAISHGDLNTEAEEAVLNKKRSKKVVKKYKSRQKHAKVEQAIEEQ 160
++ R + +E +K K +VKK K + ++E+AI Q
Sbjct: 10 PIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQ 58
>3tqw_A Methionine-binding protein; transport and binding proteins,
transport protein; HET: MSE; 2.00A {Coxiella burnetii}
Length = 240
Score = 26.4 bits (59), Expect = 6.1
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 4/30 (13%)
Query: 133 NKKRSKKVVKKYKSRQKHAKVEQAIEEQFQ 162
N R K++V S V A ++ F
Sbjct: 209 NDPRLKQLVSALHS----PAVLSAAKKIFG 234
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 26.3 bits (57), Expect = 7.0
Identities = 6/52 (11%), Positives = 19/52 (36%), Gaps = 4/52 (7%)
Query: 118 ISHGDLNTEAEEAVLNKKRSKKVVKKYKSR----QKHAKVEQAIEEQFQTGR 165
+ D ++ E +K K + + + + +K+ + ++ F
Sbjct: 98 LQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQP 149
>1jal_A YCHF protein; nucleotide-binding fold, structural genomics,
structure 2 function project, S2F, unknown function;
2.40A {Haemophilus influenzae} SCOP: c.37.1.8 d.15.10.2
Length = 363
Score = 26.6 bits (60), Expect = 7.3
Identities = 9/48 (18%), Positives = 21/48 (43%), Gaps = 6/48 (12%)
Query: 135 KRSKKVVKKYKSRQKHAKVEQAIEEQFQTGRILVSILSERTAVRQAKF 182
+ +++ K+ K K AK E ++ E+ ++ +L +R
Sbjct: 142 RAIQRLQKRAKGGDKEAKFELSVMEK------ILPVLENAGMIRSVGL 183
>2b3t_A Protein methyltransferase HEMK; translation termination,
methylation, conformational changes; HET: SAH; 3.10A
{Escherichia coli} SCOP: c.66.1.30 PDB: 1t43_A*
Length = 276
Score = 25.9 bits (58), Expect = 9.5
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 14/45 (31%)
Query: 153 VEQAIEEQFQ-----------TGRILVSILSERTAVRQAKFHAVD 186
VEQA+ + TG I +++ SER + AVD
Sbjct: 99 VEQALARLPEQPCRILDLGTGTGAIALALASER---PDCEIIAVD 140
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
0.315 0.128 0.366
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,119,863
Number of extensions: 176258
Number of successful extensions: 493
Number of sequences better than 10.0: 1
Number of HSP's gapped: 487
Number of HSP's successfully gapped: 32
Length of query: 211
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 122
Effective length of database: 4,216,824
Effective search space: 514452528
Effective search space used: 514452528
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: 55 (24.9 bits)