RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4496
(228 letters)
>1mp1_A Ser/Arg-related nuclear matrix protein; four helix bundle, RNA
binding protein; NMR {Homo sapiens} SCOP: a.188.1.1
Length = 111
Score = 67.3 bits (164), Expect = 7e-15
Identities = 25/49 (51%), Positives = 40/49 (81%)
Query: 12 PQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKV 60
+ +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE +
Sbjct: 9 ECLEKKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVKNP 57
>2ftc_E L12MT, MRP-L12, 39S ribosomal protein L12, mitochondrial;
mitochondrial ribosome, large ribosomal subunit,
ribosomal R ribosome; 12.10A {Bos taurus}
Length = 137
Score = 51.0 bits (122), Expect = 1e-08
Identities = 24/45 (53%), Positives = 30/45 (66%)
Query: 161 PKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
PKI +L DI+SLTLLE +DL+ LLKK L + D +M MG G
Sbjct: 1 PKIQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLMPMGGMVPG 45
>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 = 50.4 bits (120), Expect = 2e-07
Identities = 33/198 (16%), Positives = 58/198 (29%), Gaps = 73/198 (36%)
Query: 92 VLAILMQEVEGRRKILRG--------------------RKTITRTYYSKIYLTCKPTKVS 131
VL + + E E L G K + + Y + + +P
Sbjct: 83 VLNLCLTEFE--NCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKK 140
Query: 132 AQTA-TEAVSSSSEQPFPI-----PTPDGAD------KTYSPKITKLANDISSLTLLECA 179
+ +A AV + Q I T D + +TY + L S+ TL E
Sbjct: 141 SNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLI-KFSAETLSELI 199
Query: 180 --------------DLSSLLKKQLNLPDA----------PMMAMGAFAQGRYLRTIFDAT 215
++ L+ N PD P++ + A Y+ T
Sbjct: 200 RTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAH--YVVT----- 252
Query: 216 SCEI------KLFPSIPG 227
++ +L + G
Sbjct: 253 -AKLLGFTPGELRSYLKG 269
Score = 36.6 bits (84), Expect = 0.005
Identities = 31/146 (21%), Positives = 54/146 (36%), Gaps = 33/146 (22%)
Query: 67 DLAKKVPVCKEI-GKGD------LG--LMQVVT---VVLAILMQEVEGRRKILRGRKTIT 114
DL K +++ + D G ++ +V V L I +G+R I
Sbjct: 1634 DLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKR--------IR 1685
Query: 115 RTYYSKIYLTCKPTKVSAQTATEAVS-SSSEQPFPIPTPDGA-DKTYSPKITKLANDISS 172
Y + I+ T K+ + + ++ S+ F + G T + T+ A
Sbjct: 1686 ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTF--RSEKGLLSAT---QFTQPA----- 1735
Query: 173 LTLLECADLSSLLKKQLNLPDAPMMA 198
LTL+E A LK + +P A
Sbjct: 1736 LTLMEKA-AFEDLKSKGLIPADATFA 1760
Score = 28.1 bits (62), Expect = 3.0
Identities = 18/107 (16%), Positives = 39/107 (36%), Gaps = 24/107 (22%)
Query: 40 LGMEDDVVVAFVYNQLEAEKVSTIFEFDLAKKVPVCKEIGKGDLGLMQVV-------TVV 92
LG + ++A + +V+ F + + V + +GK L+++V V
Sbjct: 1802 LGRSNYGMIA-----INPGRVAASFSQEALQYV--VERVGKRTGWLVEIVNYNVENQQYV 1854
Query: 93 LAILMQEVEGRRKILRGRKTITRTYYSKIYLTCKPTKVSAQTATEAV 139
A ++ ++ +L K KI ++ + E V
Sbjct: 1855 AAGDLRALDTVTNVLNFIKL------QKI----DIIELQKSLSLEEV 1891
>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 = 38.7 bits (89), Expect = 0.001
Identities = 39/287 (13%), Positives = 83/287 (28%), Gaps = 85/287 (29%)
Query: 3 WAVFALTSK-------PQVVQKVDMTKVK----------------LDILKPWITQKITQL 39
W F L+ K QV + +L ++ + L
Sbjct: 259 WNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL 318
Query: 40 -----------LGMEDDVVVAFV---------YNQLEAEKVSTIFEFDLAKKVPVCKEIG 79
L + + + + + +K++TI E L P E
Sbjct: 319 PREVLTTNPRRLSI----IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP--AEYR 372
Query: 80 K--GDLGLMQ----VVTVVLAIL------------MQEVEGRRKILRGRKTITRTYYSKI 121
K L + + T++L+++ + ++ + + K T + S I
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS-I 431
Query: 122 YL--TCKPTKVSA--QTATEAVSSSSEQPFPIPTPDGADK------TYSPKITKLANDIS 171
YL K A ++ + + P D+ + K + ++
Sbjct: 432 YLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMT 491
Query: 172 SLTLLECADLSSLLKKQLNLPDAPMMAMGA----FAQGR-YLRTIFD 213
++ D L++++ A G+ Q + Y I D
Sbjct: 492 LFRMV-FLDF-RFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICD 536
Score = 29.4 bits (65), Expect = 1.2
Identities = 32/210 (15%), Positives = 69/210 (32%), Gaps = 61/210 (29%)
Query: 12 PQVVQKVDMTKVKLDILKPWITQK-ITQLLGMEDDVV-VAFVYNQLEAEKVSTIFEFDLA 69
V D V D+ K ++++ I ++ +D V ++ L +++ + +F
Sbjct: 27 DAFVDNFDCKDV-QDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKF--- 82
Query: 70 KKVPVCKEIGKGDLGLMQVVTVVLAILMQEVEGRRKILRGRKTITRTY------------ 117
+E+ + + LM + + R +TR Y
Sbjct: 83 -----VEEVLRINYKF----------LMSPI---KTEQRQPSMMTRMYIEQRDRLYNDNQ 124
Query: 118 -YSKIYLTCKPTKVSAQTATEAVSSSSEQPFPIPTPD-------GADKTY-------SPK 162
++K ++ + + A + P + G+ KT+ S K
Sbjct: 125 VFAKYNVSRLQPYLKLRQALLELR---------PAKNVLIDGVLGSGKTWVALDVCLSYK 175
Query: 163 I-TKLANDISSLTLLECADLSSLLKKQLNL 191
+ K+ I L L C ++L+ L
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLEMLQKL 205
>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 = 34.9 bits (79), Expect = 0.009
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 8/31 (25%)
Query: 172 SLTLLECADLSSLLKKQLNLPD-APMMAMGA 201
+L L+ +SL +L D AP +A+ A
Sbjct: 21 ALKKLQ----ASL---KLYADDSAPALAIKA 44
>3sgf_J 50S ribosomal protein L7/L12; typeii release factor binding with
ribosome, ribosome-antibi complex; 3.20A {Escherichia
coli} PDB: 2xtg_L 2xux_L 3uos_J 1rqu_A 1rqv_A 2gya_3
2gyc_3 1rqt_A
Length = 121
Score = 33.1 bits (76), Expect = 0.023
Identities = 7/55 (12%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 160 SPKITKLANDISSLTLLECADLSSLLKKQLNL-PDAPMMAMGAFAQGRYLRTIFD 213
S ++ ++++++++ +L S ++++ + A + + +T FD
Sbjct: 2 SITKDQIIEAVAAMSVMDVVELISAMEEKFGVSAAAAVAVAAGPVEAAEEKTEFD 56
>2zjq_5 50S ribosomal protein L7/L12; ribosome, ribosomal subunit,
thiopeptide antibiotics, complex, translational
regulation, molecular switch; 3.30A {Deinococcus
radiodurans} SCOP: d.45.1.1
Length = 122
Score = 31.6 bits (72), Expect = 0.072
Identities = 11/46 (23%), Positives = 20/46 (43%)
Query: 160 SPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
+ L + + LT++E ADL LK+ + A ++ G
Sbjct: 2 AYDKQALIDQLGQLTIMELADLIDGLKETWGVTAAVAVSGGGAGAA 47
>2j01_L 50S ribosomal protein L7; ribosome, tRNA, paromomycin, mRNA,
translation; 2.8A {Thermus thermophilus} PDB: 2j03_L
3i8i_I
Length = 125
Score = 31.6 bits (72), Expect = 0.075
Identities = 11/46 (23%), Positives = 21/46 (45%)
Query: 160 SPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
+ I ++ ++S T+LE L LK+ + A +A+ A
Sbjct: 2 ALDIERIKEELSQATVLELKQLIDALKEAWGVTAAAPVAVAAAPAA 47
>3cw1_L U1 small nuclear ribonucleoprotein C; PRE-mRNA splicing,
spliceosome, RNA-binding domain, SM fold, finger, RNA
recognition motif, 5' splice site; 5.49A {Homo sapiens}
PDB: 1uw2_A 2vrd_A
Length = 77
Score = 30.0 bits (67), Expect = 0.14
Identities = 15/56 (26%), Positives = 19/56 (33%), Gaps = 2/56 (3%)
Query: 102 GRRKILRGRK--TITRTYYSKIYLTCKPTKVSAQTATEAVSSSSEQPFPIPTPDGA 155
R+ GRK + YY K + + TA PF P P GA
Sbjct: 20 VRKTHCSGRKHKENVKDYYCKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAPPPAGA 75
>1dd3_A 50S ribosomal protein L7/L12; dimer formation, flexibility, hinge
region, four-helix-bundl helix- bundle, alpha-beta
structure; 2.00A {Thermotoga maritima} SCOP: a.108.1.1
d.45.1.1 PDB: 1dd4_A* 1giy_I 1yl3_I
Length = 128
Score = 29.0 bits (65), Expect = 0.62
Identities = 11/43 (25%), Positives = 20/43 (46%)
Query: 163 ITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
I ++ I LT+ E A+L L+ + + A +A+ A
Sbjct: 3 IDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVAAAPVA 45
>1khi_A HEX1; membrane sealing, peroxisomal target, structural protein;
1.78A {Neurospora crassa} SCOP: b.34.5.2 b.40.4.5
Length = 176
Score = 29.3 bits (65), Expect = 0.65
Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 11/87 (12%)
Query: 30 PWITQKITQLLGMEDDVVVAFVYNQLEAEKVSTIFEFDLAKKVPVCKEIGKGDLGLMQVV 89
K ++L M+D +VA + + I + L ++ E G+G + V
Sbjct: 99 LGPVFKQYRVLDMQDGSIVAMTETGDVKQNLPVIDQSSLWNRLQKAFESGRGSV----RV 154
Query: 90 TVVLAILMQEVEGRRKILRGRKTITRT 116
VV GR + K + +
Sbjct: 155 LVVSDH------GREMAV-DMKVVHGS 174
>3kvc_A Retinoid isomerohydrolase; 7-bladed beta-propeller, monotopic
membrane protein, sensory transduction, vision,
isomerase, non-heme iron protein; 1.90A {Bos taurus}
PDB: 3fsn_A
Length = 533
Score = 28.5 bits (63), Expect = 2.1
Identities = 10/36 (27%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 43 EDD-VVVAFVYNQLEAEKVSTIFEFDLAKKV-PVCK 76
EDD VV++ V + +K + + + AK + V +
Sbjct: 481 EDDGVVLSVVVSPGAGQKPAYLLILN-AKDLSEVAR 515
>1x4q_A U4/U6 small nuclear ribonucleoprotein PRP3; PWI domain,
structural genomics, NPPSFA, national project on
protein structural and functional analyses; NMR {Homo
sapiens}
Length = 92
Score = 26.7 bits (58), Expect = 2.8
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 18 VDMTKVKLDILKPWITQKITQLLGMEDDVVVAF----VYNQLEAEKVSTIFEFDLAKKVP 73
+ ++K +LD LKPWI + + ++LG + VV V ++ +K + + L
Sbjct: 8 MALSKRELDELKPWIEKTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTL 67
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 0.133 0.378
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,327,590
Number of extensions: 187636
Number of successful extensions: 382
Number of sequences better than 10.0: 1
Number of HSP's gapped: 380
Number of HSP's successfully gapped: 17
Length of query: 228
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 138
Effective length of database: 4,188,903
Effective search space: 578068614
Effective search space used: 578068614
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: 55 (25.1 bits)