RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8191
(257 letters)
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding,
lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB:
2ist_A 1qyu_A 1prz_A
Length = 325
Score = 309 bits (794), Expect = e-106
Identities = 102/238 (42%), Positives = 142/238 (59%), Gaps = 23/238 (9%)
Query: 27 IKLDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKN 86
I LDI+YED +III+NK LVVHP GN GT+ + LL YP + +VPRAGIVHRLDK+
Sbjct: 81 IPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKD 140
Query: 87 SSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPKLNGMINAAIMRNPHNRIKMTV 146
++GLMVVAK++ + LV L+ + R+Y A+ G G ++ I R+P R M V
Sbjct: 141 TTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAV 200
Query: 147 SKNFNAKPALTYY---ERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNL 203
KPA+T+Y E + + +R L+TGRTHQIRVHM + H +VGD +
Sbjct: 201 HP--MGKPAVTHYRIMEHF-------RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 251
Query: 204 YG------KKYSKSLI-----FNRQALHAYKLGLIHPKNNLKLKWRINLPDDISKLIT 250
YG K S++ I F+RQALHA L L HP + ++++W +P D+ +LI
Sbjct: 252 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 309
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA
complex; HET: FOU; 2.05A {Escherichia coli}
Length = 217
Score = 273 bits (701), Expect = 1e-93
Identities = 64/217 (29%), Positives = 106/217 (48%), Gaps = 11/217 (5%)
Query: 27 IKLDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKN 86
L I+Y+D+ I+++NK +GL+ P + + P+A VHRLD
Sbjct: 10 PWLVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRI-----QRDYPQAESVHRLDMA 64
Query: 87 SSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPKLN-GMINAAIMRNPHNRIKMT 145
+SG++VVA + + L Q + +++Y+A VWG P G+++ ++ + NR K
Sbjct: 65 TSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQK 124
Query: 146 VSKNFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNLYG 205
V KPA T YE + + + + TGR+HQ+RVHM LGH I+GD Y
Sbjct: 125 VCYE-TGKPAQTEYEVVEYA---ADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYA 180
Query: 206 KKYSKSLIFNRQALHAYKLGLIHPKNNLKLKWRINLP 242
++++ R LHA L + HP + ++
Sbjct: 181 SPEARAM-APRLLLHAEMLTITHPAYGNSMTFKAPAD 216
>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine
syntase, RNA binding, lyase; 2.00A {Escherichia coli}
SCOP: d.265.1.3 PDB: 1xpi_A
Length = 228
Score = 270 bits (694), Expect = 2e-92
Identities = 71/232 (30%), Positives = 115/232 (49%), Gaps = 21/232 (9%)
Query: 29 LDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKNSS 88
I+YED+ I++LNK +G VH G G + + L + P +VHRLD+++S
Sbjct: 2 DVIMYEDDHILVLNKPSGTAVHGGSGLSFGVI-EGLRALRP---EARFLELVHRLDRDTS 57
Query: 89 GLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWG-IPKLNGMINAAIMRNPHNRIKMTVS 147
G+++VAK + L QL+ +Q+ YLA+V G + A +++N + V
Sbjct: 58 GVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVR 117
Query: 148 KNFNAKPALTYY---ERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNLY 204
+ KP+ T + ER +L+RC+ TGRTHQIRVH Q+ GH I D+ Y
Sbjct: 118 VSQEGKPSETRFKVEERY-------AFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRY 170
Query: 205 G-KKYSKSLI-----FNRQALHAYKLGLIHPKNNLKLKWRINLPDDISKLIT 250
G +++ + L NR LHA L HP ++ + + + + +
Sbjct: 171 GDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQ 222
>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 = 33.5 bits (76), Expect = 0.066
Identities = 35/198 (17%), Positives = 65/198 (32%), Gaps = 69/198 (34%)
Query: 71 LINVPRAGIVHRLDKNSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPKLNGMI 130
L+N + +VV+ +S L L RK A P +G+
Sbjct: 370 LVNGAKN-------------LVVSGPPQSLYGLNLTL------RKAKA-----P--SGLD 403
Query: 131 NAAIMRNPHNRIKMTVSKNF---NAKPALTYYERLATGIIN----KKHISLIRCNLKTGR 183
+ R P + K+ S F + P ++ A+ +IN K ++S +++
Sbjct: 404 QS---RIPFSERKLKFSNRFLPVAS-PFHSHLLVPASDLINKDLVKNNVSFNAKDIQ--- 456
Query: 184 THQIRVHMQWLGHGIVGDNLYGKKYSKSLIFN--RQALHAYKLGLIHPKNNLKLKWRINL 241
I V+ G +L + S S+ + L +KW
Sbjct: 457 ---IPVY-----DTFDGSDL--RVLSGSISERIVDCIIR------------LPVKWETTT 494
Query: 242 PDDISKLITF-----SGI 254
+ ++ F SG+
Sbjct: 495 QFKATHILDFGPGGASGL 512
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta
sheet, isomerase; 1.60A {Escherichia coli}
Length = 217
Score = 32.2 bits (74), Expect = 0.11
Identities = 28/137 (20%), Positives = 43/137 (31%), Gaps = 51/137 (37%)
Query: 11 IKPKKNFFLNKTEK-----KVIKLDIIYEDNEIIILNKSAGLVV-------HPAIGNLSG 58
+K F N K + + + +I+ NK ++
Sbjct: 9 NTMQKTSFRNHQVKRFSSQRSTRRKPENQPTRVILFNKPYDVLPQFTDEAGRK------- 61
Query: 59 TLFDNLLEIYPFLINVPR---AGIVHRLDKNSSGLMVVAKSIKSYIHLVN--QLKMHI-- 111
TL + I V AG RLD++S GL+V L N L+ +
Sbjct: 62 TLKE--------FIPVQGVYAAG---RLDRDSEGLLV----------LTNNGALQARLTQ 100
Query: 112 ----VQRKYLAMVWGIP 124
+ Y V GIP
Sbjct: 101 PGKRTGKIYYVQVEGIP 117
>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 = 32.5 bits (73), Expect = 0.15
Identities = 21/129 (16%), Positives = 43/129 (33%), Gaps = 38/129 (29%)
Query: 23 EKKVIKL-DIIYEDNEIIILNKSAGLVVHPAIGNLSG-------TLFDN-LLEIYPFLI- 72
+ +KL + E L + +++ +G SG + F I
Sbjct: 134 LQPYLKLRQALLE------LRPAKNVLIDGVLG--SGKTWVALDVCLSYKVQCKMDFKIF 185
Query: 73 -------NVPRAGI------VHRLDKNSSGLMVVAKSIKSYIH-LVNQLKMHIVQRKY-- 116
N P + ++++D N + + +IK IH + +L+ + + Y
Sbjct: 186 WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYEN 245
Query: 117 ----LAMVW 121
L V
Sbjct: 246 CLLVLLNVQ 254
Score = 31.7 bits (71), Expect = 0.26
Identities = 18/152 (11%), Positives = 46/152 (30%), Gaps = 48/152 (31%)
Query: 122 GIPKLNGMINAAIMRNPHNRIK-----------MTVSKNFNA-KPALT--YYERLATGI- 166
P+ +I A +R+ + + N +PA ++RL+ +
Sbjct: 325 TNPRRLSII-AESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS--VF 381
Query: 167 -----INKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNLYGKKYSKSLIFNRQALHA 221
I +SLI ++ + + SL+ +
Sbjct: 382 PPSAHIPTILLSLIWFDVIKSDVMVVVNKLH----------------KYSLVEKQPKEST 425
Query: 222 YKLGLIHPKNNLKLKWRINLPDDIS---KLIT 250
I ++ L+ ++ L ++ + ++
Sbjct: 426 IS---IP---SIYLELKVKLENEYALHRSIVD 451
Score = 30.6 bits (68), Expect = 0.58
Identities = 36/194 (18%), Positives = 72/194 (37%), Gaps = 47/194 (24%)
Query: 7 ELIIIKPKKNFFLNKTEKK-VIKLDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLL 65
+++ K K + K K+ I + IY + ++ + N+ A +H +++
Sbjct: 405 MVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA---LH-----------RSIV 450
Query: 66 EIYPFLINVPRAGIVHRLDKNSSGLMVVAKSIKSYI--HLVNQL---KMHIVQRKYLAMV 120
+ Y N+P+ D + + + S+I HL N +M + + +L
Sbjct: 451 DHY----NIPKT-----FDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFR 501
Query: 121 WGIPKLNGMINAAIMRNPHNRIKMTVSKNFNAKPALT----YYERL-----------ATG 165
+ K+ + + N I T+ + KP + YERL
Sbjct: 502 FLEQKI---RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEEN 558
Query: 166 IINKKHISLIRCNL 179
+I K+ L+R L
Sbjct: 559 LICSKYTDLLRIAL 572
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta
sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia
coli}
Length = 189
Score = 31.0 bits (71), Expect = 0.23
Identities = 24/109 (22%), Positives = 36/109 (33%), Gaps = 46/109 (42%)
Query: 34 EDNEIIILNKSAGLVV-------HPAIGNLSGTLFDNLLEIYPFLINVPR---AGIVHRL 83
+ +I+ NK ++ TL + I V AG RL
Sbjct: 9 QPTRVILFNKPYDVLPQFTDEAGRK-------TLKE--------FIPVQGVYAAG---RL 50
Query: 84 DKNSSGLMVVAKSIKSYIHLVN--QLKMHI------VQRKYLAMVWGIP 124
D++S GL+V L N L+ + + Y V GIP
Sbjct: 51 DRDSEGLLV----------LTNNGALQARLTQPGKRTGKIYYVQVEGIP 89
>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA
complex, S4 domain, alpha/beta protein, isomerase,
RNA-binding, rRNA processing; HET: FHU; 3.00A
{Escherichia coli}
Length = 290
Score = 27.2 bits (61), Expect = 5.0
Identities = 31/184 (16%), Positives = 58/184 (31%), Gaps = 71/184 (38%)
Query: 34 EDNEIIILNKSAGLV--VHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKNSSGLM 91
ED +I LNK G+V + ++ ++P + RLDK+S GL+
Sbjct: 65 EDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFP----------IGRLDKDSQGLI 114
Query: 92 VVAKSIKSYI-----HLVNQLKMH---IVQRKYLAMVWGIPKLNGMINAAIMRNPHNRIK 143
LVN++ + +++YL ++ I +
Sbjct: 115 ---------FLTNHGDLVNKI-LRAGNDHEKEYLV------TVDKPITEEFI-------- 150
Query: 144 MTVSKNFNAKPALTYYERLATGI-----------INKKHISLIRCNLKTGRTHQIRVHMQ 192
++ G+ + K+ + R L G QIR +
Sbjct: 151 ----------------RGMSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCE 194
Query: 193 WLGH 196
G+
Sbjct: 195 HFGY 198
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome,
RNA modifying enzyme, isomerase; 2.60A {Escherichia
coli}
Length = 237
Score = 27.3 bits (61), Expect = 5.3
Identities = 33/178 (18%), Positives = 59/178 (33%), Gaps = 57/178 (32%)
Query: 33 YEDNEIIILNKSAGLV------VHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKN 86
D +I LNK G+V I + ++ ++P + RLDK+
Sbjct: 11 GSDLVLIALNKPVGIVSTTEDGERDNIVDF----VNHSKRVFP----------IGRLDKD 56
Query: 87 SSGLMVVAKSIKSYI----HLVNQLKMH---IVQRKYLAMVWGIPKLNGMINAAIMRNPH 139
S GL+ + LVN++ + +++YL ++ I +R
Sbjct: 57 SQGLIF--------LTNHGDLVNKI-LRAGNDHEKEYLV------TVDKPITEEFIR--- 98
Query: 140 NRIKMTVS-KNFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGH 196
+ V K + K+ + R L G QIR + G+
Sbjct: 99 -GMSAGVPILGTVTKKC----------KVKKEAPFVFRITLVQGLNRQIRRMCEHFGY 145
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase;
2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB:
1ksl_A 1ksv_A*
Length = 234
Score = 26.7 bits (60), Expect = 6.5
Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 24/81 (29%)
Query: 22 TEKKVIKLD----IIYEDNEIIILNKSAGLV------VHPAIGNLSGTLFDNLLE-IYPF 70
+ + D +LNK G V HP + L + + ++
Sbjct: 45 LPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDHPTVLYF---LDEPVAWKLHA- 100
Query: 71 LINVPRAGIVHRLDKNSSGLM 91
RLD +++GL+
Sbjct: 101 ---------AGRLDIDTTGLV 112
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural
genomics, lyase; 1.59A {Haemophilus influenzae} SCOP:
d.265.1.3 d.66.1.5
Length = 243
Score = 26.7 bits (60), Expect = 8.0
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 33/85 (38%)
Query: 25 KVIKLDIIYEDNEII---------ILNKSAGLV------VHPAIGNLSGTLFDNLLEIYP 69
++ + D IY ++E++ +LNK G V +P T++
Sbjct: 42 QISQEDEIYFEDELLTWIEEGQYFMLNKPQGCVCSNDDGDYP-------TIYQ------- 87
Query: 70 FLINVPRAGIVH---RLDKNSSGLM 91
+ P AG +H RLD +++GL+
Sbjct: 88 -FFDYPLAGKLHSAGRLDVDTTGLV 111
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
0.324 0.141 0.419
Gapped
Lambda K H
0.267 0.0491 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,971,860
Number of extensions: 235069
Number of successful extensions: 386
Number of sequences better than 10.0: 1
Number of HSP's gapped: 374
Number of HSP's successfully gapped: 16
Length of query: 257
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 165
Effective length of database: 4,133,061
Effective search space: 681955065
Effective search space used: 681955065
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.9 bits)