RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13081
(335 letters)
>1vs3_A TRNA pseudouridine synthase A; TRUA, tRNA modification, structural
NPPSFA, national project on protein structural and
function analyses; 2.25A {Thermus thermophilus}
Length = 249
Score = 158 bits (401), Expect = 7e-47
Identities = 62/246 (25%), Positives = 89/246 (36%), Gaps = 42/246 (17%)
Query: 1 MRPIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGV 60
MR + L Y G + G Q Q T+ L +AL GRTD+GV
Sbjct: 1 MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIG-----ALPKAVAAGRTDAGV 55
Query: 61 SAFCQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCL 120
A + + S + P E+ + LN LP D+KVV V + AR D L
Sbjct: 56 HALAMPFHVDVESAI--PVEK-------VPEALNRLLPEDLKVVGAREVAPDFHARKDAL 106
Query: 121 FRNYKY-----------------WFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGV 163
+R Y+Y W + LD++AM +A L+G H+F K
Sbjct: 107 WRAYRYRILVRPHPSPLLRHRALWVRRP-LDLEAMEEALSLLLGRHNFLGFAK--EETRP 163
Query: 164 VNFRRLVTHAGVTSAWQNVQFNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKP 223
L V R + FL Q+R ++ L VG G P
Sbjct: 164 GERELLEARLQVAEGEAG--------LEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPP 215
Query: 224 EIIQQL 229
E ++ +
Sbjct: 216 ESLKAI 221
>1dj0_A Pseudouridine synthase I; alpha/beta fold, RNA-binding motif,
RNA-modifying enzyme, lyase; 1.50A {Escherichia coli}
SCOP: d.265.1.1 PDB: 2nqp_A 2nr0_A 2nre_A
Length = 264
Score = 154 bits (391), Expect = 3e-45
Identities = 70/246 (28%), Positives = 99/246 (40%), Gaps = 44/246 (17%)
Query: 1 MRPIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGV 60
+ IAL I Y G Y+G+Q Q ++ L KAL + E + C GRTD+GV
Sbjct: 3 VYKIALGIEYDGSKYYGWQRQNEV-RSVQEKLEKALSQVA----NEPITVFCAGRTDAGV 57
Query: 61 SAFCQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCL 120
QVV + + + +N NLP DI V VP+ + ARF
Sbjct: 58 HGTGQVVHFETTALR--KDAA-------WTLGVNANLPGDIAVRWVKTVPDDFHARFSAT 108
Query: 121 FRNYKY-----------------WFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGV 163
R Y+Y F + LD + MH+AAQ L+G +DF + V
Sbjct: 109 ARRYRYIIYNHRLRPAVLSKGVTHFYEP-LDAERMHRAAQCLLGENDFTSFR--AVQCQS 165
Query: 164 VNFRRLVTHAGVTSAWQNVQFNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKP 223
R V H VT H +I++ F+ H +R I+ L VG N+
Sbjct: 166 RTPWRNVMHINVT----------RHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPE 215
Query: 224 EIIQQL 229
I +L
Sbjct: 216 SWIAEL 221
>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 = 41.6 bits (97), Expect = 4e-04
Identities = 58/341 (17%), Positives = 94/341 (27%), Gaps = 139/341 (40%)
Query: 1 MRPIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGV 60
RP+ L HG ++ A + A Q L + F
Sbjct: 6 TRPLTLS--------HG-SLEHVLLVPTASFFI-ASQ---L-----QEQFN--------- 38
Query: 61 SAFCQVVTLKIRSKLTSPGEE--SDDN-----EL--PYLKMLNNNLPRDIKVVAWSPVPE 111
L P E +DD EL +L +++ + P
Sbjct: 39 ------------KILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVE-----------PS 75
Query: 112 KYSARFDCLFRNYKYWFPQA---GLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFRR 168
K L F G DI H A L+ +D + + + N+
Sbjct: 76 KVGQFDQVLNLCLTE-FENCYLEGNDI---HALAAKLLQENDTTLVKTKEL---IKNYIT 128
Query: 169 LVTHAGVTSAWQNVQFNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLV--GQGNEKPEII 226
A F+ +S L+ + + L + GQGN
Sbjct: 129 ARIMAKR-----------------PFDKKSNSALFRAVGEGNAQLVAIFGGQGN------ 165
Query: 227 QQLVDIEKYPRKPVYPMVRGEPLNLYHTEFDNLTWHYDEIEVSHVLRDLHEDW-----SL 281
+ Y ++E LRDL++ + L
Sbjct: 166 -----TDDY---------------------------FEE------LRDLYQTYHVLVGDL 187
Query: 282 LSIKATMLGEMIKDTVRESK-CTMGDLDINHLIEGEFSRPG 321
+ A L E+I+ T+ K T G L+I +E + P
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQG-LNILEWLENPSNTPD 227
>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 = 36.4 bits (83), Expect = 0.016
Identities = 57/409 (13%), Positives = 105/409 (25%), Gaps = 141/409 (34%)
Query: 14 NYHGFQIQTS----SDNTIAHHLLKALQKT--CL-IEDKEKSSFA--------------- 51
++H +T I A C ++D KS +
Sbjct: 3 HHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVS 62
Query: 52 --------CCGRTDSGVSAFCQVVTLKIRSKLTSP-GEESDDNELPYLKMLN--NNLPRD 100
+ + V F + V L SP E + + + L D
Sbjct: 63 GTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYND 122
Query: 101 IKVVAWSPVP--EKYSARFDCLFRNYKYWFPQAGLDIDAMH---K---AAQYLVGTHDFR 152
+V A V + Y L + P + ID + K A ++
Sbjct: 123 NQVFAKYNVSRLQPYLKLRQAL-LELR---PAKNVLIDGVLGSGKTWVALDVC---LSYK 175
Query: 153 NLCKMNVGNGV--VNFRRLVTHAGVTSAWQNVQFNDSHHNICEFNIRSQGFLWHQIRCIM 210
CKM+ + +N + + V Q L +QI
Sbjct: 176 VQCKMD--FKIFWLNLKNCNSPETVLEMLQK--------------------LLYQIDPN- 212
Query: 211 SVLFLVGQGNEKPEIIQQLVDIEKYPRK----PVYPMVRGEPL----NLYHTE----FDN 258
+ + I ++ I+ R+ Y L N+ + + F+
Sbjct: 213 ----WTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE----NCLLVLLNVQNAKAWNAFNL 264
Query: 259 -----LT------------WHYDEIEVSHVLRDLHEDWSL------LSIKA--------- 286
LT I + H L D L +
Sbjct: 265 SCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT 324
Query: 287 ------TMLGEMIKDTV----------RESKCTMGDLDINHLIEGEFSR 319
+++ E I+D + + T+ + +N L E+ +
Sbjct: 325 TNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK 373
Score = 31.7 bits (71), Expect = 0.42
Identities = 31/229 (13%), Positives = 64/229 (27%), Gaps = 56/229 (24%)
Query: 73 SKLTSPGEES----DDNEL-PYLKML-----NNNLPRDIKVVAWSPVPEKYSARFDCLFR 122
KLT+ E S + E L + ++P + + W V +
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLH 412
Query: 123 NYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFRRLVTHAGVTSAWQN- 181
Y ++ + + K+ + N R +V H + + +
Sbjct: 413 KYSL------VEKQ----PKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD 462
Query: 182 ---VQFNDS-------HH-----NICEFNIRSQGFL---WHQIRCIMSVLFLVGQGNEKP 223
+ D HH + + FL + + + G+
Sbjct: 463 DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGS--- 519
Query: 224 EIIQQLVDIEKY-----PRKPVYPMVRGEPL--------NLYHTEFDNL 259
I+ L ++ Y P Y + L NL +++ +L
Sbjct: 520 -ILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDL 567
>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 = 1.1
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 5/26 (19%)
Query: 265 EIEVSHVLRDLHEDWSL--LSIKATM 288
+++ S L+ L+ D S L+IKATM
Sbjct: 24 KLQAS--LK-LYADDSAPALAIKATM 46
>2clq_A Mitogen-activated protein kinase kinase kinase 5; transferase,
metal-binding, apoptosis; HET: STU; 2.3A {Homo sapiens}
Length = 295
Score = 28.4 bits (64), Expect = 2.8
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 203 WHQIRCIMSVLFLVGQGNEKPEI 225
++++ + +F VG PEI
Sbjct: 225 FYELGEPQAAMFKVGMFKVHPEI 247
>2nq5_A 5-methyltetrahydropteroyltriglutamate-- homocysteine
methyltransferase; structural genomics, target 6426D,
PSI; 1.90A {Streptococcus mutans} PDB: 3l7s_A 3l7r_A
3t0c_A
Length = 755
Score = 28.7 bits (64), Expect = 3.4
Identities = 16/74 (21%), Positives = 26/74 (35%), Gaps = 11/74 (14%)
Query: 272 LRDLHEDWSLLSIKATMLGEMIKDTVRESKCTMGDLDINHLIEGEFSR-----------P 320
+R W I + I+ + DLD++ L+ GEF R
Sbjct: 431 IRRTRLAWKRGDISDAEYKQFIQAEIERWIRIQEDLDLDVLVHGEFERVDMVEFFGQKLA 490
Query: 321 GRILSETGEVRSRN 334
G ++ G V+S
Sbjct: 491 GFTTTKFGWVQSYG 504
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 0.137 0.427
Gapped
Lambda K H
0.267 0.0582 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,213,048
Number of extensions: 301914
Number of successful extensions: 558
Number of sequences better than 10.0: 1
Number of HSP's gapped: 548
Number of HSP's successfully gapped: 12
Length of query: 335
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 241
Effective length of database: 4,077,219
Effective search space: 982609779
Effective search space used: 982609779
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: 57 (26.1 bits)