RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13908
(149 letters)
>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 195
Score = 127 bits (321), Expect = 2e-38
Identities = 33/142 (23%), Positives = 67/142 (47%), Gaps = 1/142 (0%)
Query: 1 MVRKLKYHEQKLLKKVDFISWEADNNLHEVKIMRRFGIQKRQDYTTYNKLSRLIRTLAQK 60
M R + + + K +E + E+K++ +G++ +++ IR A+
Sbjct: 1 MPRAPRTYSKTYSTKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYALSRIRNNARH 60
Query: 61 IKDLDPKDPFRVESSAKLLEKLYLMGLIRT-KWDLENCNKVTASSFCKRRLPVVMYRNKM 119
+ LD K+P R+ LL ++ GL+ + L+ +T +F RRL ++++ M
Sbjct: 61 LLTLDEKNPRRIFEGEALLRRMNRYGLLADGQNKLDYVLALTVENFLARRLQTLVFKAGM 120
Query: 120 VQQLRLATQFIEQAHVRVGPEL 141
+ + A I Q H+RVG ++
Sbjct: 121 AKSIHHARVLIRQRHIRVGRQI 142
>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*
Length = 197
Score = 99.8 bits (248), Expect = 2e-27
Identities = 30/142 (21%), Positives = 62/142 (43%), Gaps = 3/142 (2%)
Query: 1 MVRKLKYHEQKLLKKVDFISWEADNNLHEVKIMRRFGIQKRQDYTTYNKLSRLIRTLAQK 60
M R + + + +E+ E+K+ FG++ +++ + IR A+
Sbjct: 1 MPRAPRTYSKTY--STPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARD 58
Query: 61 IKDLDPKDPFRVESSAKLLEKLYLMGLIRTK-WDLENCNKVTASSFCKRRLPVVMYRNKM 119
+ D KDP R+ L+ +L +G++ L+ + F +RRL +Y+ +
Sbjct: 59 LLTRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGL 118
Query: 120 VQQLRLATQFIEQAHVRVGPEL 141
+ + A I Q H+ VG ++
Sbjct: 119 AKSVHHARVLITQRHIAVGKQI 140
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_D
Length = 181
Score = 97.8 bits (243), Expect = 9e-27
Identities = 29/122 (23%), Positives = 62/122 (50%), Gaps = 1/122 (0%)
Query: 21 WEADNNLHEVKIMRRFGIQKRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLE 80
+E + +E+K++ FG++ +++ + R A+++ LDPKDP R+ + LL
Sbjct: 19 YEKERLDNEMKLIGTFGLKNKREVWRVQMILAKFRKAARELLTLDPKDPRRLFEGSALLR 78
Query: 81 KLYLMGLIRTK-WDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGP 139
+++ GL+ + L+ +T +RRL +++ + + + I Q H++VG
Sbjct: 79 RMFKYGLLSEQERKLDYVLGLTIHKLMERRLQTRVFKLNLANSIHHSRVLIRQRHIKVGK 138
Query: 140 EL 141
L
Sbjct: 139 NL 140
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog;
S4 domain, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 71
Score = 65.4 bits (160), Expect = 2e-15
Identities = 19/40 (47%), Positives = 27/40 (67%)
Query: 102 ASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPEL 141
+S RRLP V+ + +M Q L+ A F+EQ HVRVGP++
Sbjct: 2 SSGSSGRRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPDV 41
>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 = 34.8 bits (79), Expect = 0.008
Identities = 30/176 (17%), Positives = 51/176 (28%), Gaps = 47/176 (26%)
Query: 1 MVRKLKYHEQKLLKKVDFI----------SWEADNNL--HEVKIMRRFGI------QKRQ 42
KL+ +L + + +W A + ++V+ F I
Sbjct: 136 PYLKLRQALLEL-RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNS 194
Query: 43 DYTTYNKLSRLIRTLAQKIK---DLDPKDPFRVESSAK-----LLEKLYLMGLIRTKWDL 94
T L +L+ + D R+ S L K Y L+ L
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL----VL 250
Query: 95 EN-CNKVTASSF---CKRRLPVVMYRNKMVQQLRLATQFI---EQAHVRVGPELEG 143
N N ++F CK ++ R K V T F+ H+ +
Sbjct: 251 LNVQNAKAWNAFNLSCK---ILLTTRFKQV------TDFLSAATTTHISLDHHSMT 297
Score = 32.9 bits (74), Expect = 0.033
Identities = 11/83 (13%), Positives = 22/83 (26%), Gaps = 22/83 (26%)
Query: 41 RQDYTTYNKLSRLIRTLAQKIKDLDPKDP---------FR--VESSAKLLEKLYLMGLIR 89
D + +L + + L+P + F LL +
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLI------- 395
Query: 90 TKW--DLENCNKVTASSFCKRRL 110
W +++ V + K L
Sbjct: 396 --WFDVIKSDVMVVVNKLHKYSL 416
Score = 27.1 bits (59), Expect = 2.6
Identities = 19/106 (17%), Positives = 37/106 (34%), Gaps = 19/106 (17%)
Query: 42 QDYTTYNKLSRLIRTLAQK-IKDLDPKD----PFRVESSAK----LLEKLYLMGLIRTKW 92
Y Y + + + + D KD P + S + ++ K + G +R W
Sbjct: 14 HQYQ-YKDI---LSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW 69
Query: 93 DLENCNKVTASSFCKRRL----PVVM--YRNKMVQQLRLATQFIEQ 132
L + + F + L +M + + Q + +IEQ
Sbjct: 70 TLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ 115
>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 = 28.4 bits (62), Expect = 0.58
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 12/25 (48%)
Query: 59 QKIKDLDPKDPFRVESSAKLLEKLY 83
Q +K L ++S L KLY
Sbjct: 20 QALKKL--------QAS--L--KLY 32
>3rt3_C NS1, NS1B, non-structural protein 1; ubiquitin-like domain,
isgylation, antiviral protein-viral P complex; 2.01A
{Influenza b virus} PDB: 1xeq_A 3sdl_A 3r66_A
Length = 109
Score = 28.2 bits (62), Expect = 0.63
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 34 RRFGIQKRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGL 87
RF Q+ DY ++L RL R L +IK + +P E+ LE+ +G+
Sbjct: 32 ERFSWQRALDYPGQDRLHRLKRKLESRIKTHNKSEP---ENKRMSLEERKAIGV 82
>2xbu_A Hypoxanthine-guanine phosphoribosyltransferase;
glycosyltransferase, purine salvage, FLIP pepti; HET:
5GP; 1.80A {Saccharomyces cerevisiae} PDB: 2jkz_A*
2jky_A*
Length = 221
Score = 27.8 bits (61), Expect = 1.3
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 44 YTTYNKLSRLIRTLAQKIKDLDP 66
Y +YN + +L + A++IK+ P
Sbjct: 8 YISYNNVHQLCQVSAERIKNFKP 30
>1vdm_A Purine phosphoribosyltransferase; structural genomics, riken
structural genomics/proteomics initiative, RSGI; 2.50A
{Pyrococcus horikoshii} SCOP: c.61.1.1
Length = 153
Score = 25.7 bits (57), Expect = 5.3
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 44 YTTYNKLSRLIRTLAQKIKDLDP 66
Y T+ ++ R I LA+K+++ P
Sbjct: 5 YLTWWQVDRAIFALAEKLREYKP 27
>3sdb_A Glutamine-dependent NAD(+) synthetase; glutamine-amidotransferase,
glutaminase, glutamine-dependent synthetase, ligase;
2.00A {Mycobacterium tuberculosis} PDB: 3seq_A* 3sez_A*
3szg_A* 3dla_A* 3syt_A*
Length = 680
Score = 25.9 bits (57), Expect = 6.3
Identities = 6/27 (22%), Positives = 10/27 (37%), Gaps = 2/27 (7%)
Query: 116 RNKMVQQLRLATQFIEQAHVRVGPELE 142
++ R + A + V PEL
Sbjct: 31 AASVLDMARACHD--DGAALAVFPELT 55
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
0.322 0.136 0.394
Gapped
Lambda K H
0.267 0.0520 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,275,056
Number of extensions: 122691
Number of successful extensions: 264
Number of sequences better than 10.0: 1
Number of HSP's gapped: 260
Number of HSP's successfully gapped: 15
Length of query: 149
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 64
Effective length of database: 4,328,508
Effective search space: 277024512
Effective search space used: 277024512
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 (21.9 bits)
S2: 53 (24.7 bits)