RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1176
(232 letters)
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex,
box H/ACA, snoRNP, pseudouridine synthase, RNA
modification; 1.95A {Methanocaldococcus jannaschii}
SCOP: b.122.1.1 d.265.1.2
Length = 357
Score = 235 bits (602), Expect = 3e-77
Identities = 72/221 (32%), Positives = 112/221 (50%), Gaps = 20/221 (9%)
Query: 1 NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEK 60
+ ++L V+ T +G +P +R I++ I+ G V +DKP P+SHEV W+K+IL +K
Sbjct: 35 DKEELIVKEEVETNWDYGCNPYERKIEDLIKYGVVVVDKPRGPTSHEVSTWVKKILNLDK 94
Query: 61 TGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAV--ENVAKASKK-KM 117
GH GTLDPK +G L V ++RAT+ + KEY+ + LH E++ + K+
Sbjct: 95 AGHGGTLDPKVTGVLPVALERATKTIPMWHIPPKEYVCLMHLHRDASEEDILRVFKEFTG 154
Query: 118 MIKQGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGT 177
I Q P A ++ + + + L+ D + +KCQ+GT
Sbjct: 155 RIYQ------------RPPLKAA-VKRRLRIRKIH-ELELLDKD--GKDVLFRVKCQSGT 198
Query: 178 YVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQ 218
Y+R C +G LG A M ELRR +SG E+D V +
Sbjct: 199 YIRKLCEDIGEALGTSAHMQELRRTKSGCFEEKD-AVYLQD 238
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase,
pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces
cerevisiae} PDB: 3uai_A
Length = 400
Score = 231 bits (592), Expect = 3e-75
Identities = 120/232 (51%), Positives = 145/232 (62%), Gaps = 38/232 (16%)
Query: 1 NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEK 60
NFDKL VR+ HYTP+P G SPL+R ++ YI +G +NLDKPSNPSSHEVVAWIKRILRCEK
Sbjct: 28 NFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGVINLDKPSNPSSHEVVAWIKRILRCEK 87
Query: 61 TGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIK 120
TGHSGTLDPK +GCLIVCIDRATRLVKSQQ AGKEY+ I +LH A+++ +
Sbjct: 88 TGHSGTLDPKVTGCLIVCIDRATRLVKSQQGAGKEYVCIVRLHDALKDEKD-------LG 140
Query: 121 QGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKS--------------NLISSDVTLST 166
+ L + L P + S NLI D +
Sbjct: 141 RSL------------ENLTGALFQRPP-----LISAVKRQLRVRTIYESNLIEFDNKRNL 183
Query: 167 GIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQ 218
G+ W C+AGTY+RT CVH+G++LGVG M ELRR RSG SE D +VT
Sbjct: 184 GVFWASCEAGTYMRTLCVHLGMLLGVGGHMQELRRVRSGALSENDNMVTLHD 235
Score = 50.6 bits (121), Expect = 1e-07
Identities = 16/31 (51%), Positives = 19/31 (61%)
Query: 111 KASKKKMMIKQGLLDKHGKPNENTPASYLAE 141
A KKK M G LDK+G+ NENTP + E
Sbjct: 355 VAQKKKQMKADGKLDKYGRVNENTPEQWKKE 385
>2aus_C Pseudouridine synthase; isomerase, structural protein,
isomerase-structural protein; 2.10A {Pyrococcus abyssi}
PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A*
2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A
Length = 334
Score = 227 bits (581), Expect = 3e-74
Identities = 83/229 (36%), Positives = 121/229 (52%), Gaps = 38/229 (16%)
Query: 3 DKLNVRTNHY-TPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKT 61
++ V+ + T +G P +R I+ +I+ G +NLDKP P+SHEVVAWIKRIL EK
Sbjct: 16 REVIVKDDKAETNPKWGFPPDKRPIELHIQYGVINLDKPPGPTSHEVVAWIKRILNLEKA 75
Query: 62 GHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQ 121
GH GTLDPK SG L V ++RATR+V++ AGKEY+++ LH V + I+
Sbjct: 76 GHGGTLDPKVSGVLPVALERATRVVQALLPAGKEYVALMHLHGDVP--------EDKIRA 127
Query: 122 GLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNL--------ISS----DVTLSTGII 169
+ + E+ P P ++S + + ++ +
Sbjct: 128 VM------------KEFEGEIIQRP---P--LRSAVKRRLRTRKVYYIEILEIDGRDVLF 170
Query: 170 WLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQ 218
+ +AGTY+R+ H+GL LGVGA M ELRR RSG E++ LVT
Sbjct: 171 RVGVEAGTYIRSLIHHIGLALGVGAHMAELRRTRSGPFKEDETLVTLHD 219
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation,
lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima}
SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A
Length = 309
Score = 91.9 bits (229), Expect = 3e-22
Identities = 25/70 (35%), Positives = 41/70 (58%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G + KP P+SH+VV +++ L+ K GH GTLDP G LI+ +++ TR+++ +
Sbjct: 4 GILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDL 63
Query: 93 GKEYISIFKL 102
K Y +L
Sbjct: 64 KKVYWVKMRL 73
Score = 50.3 bits (121), Expect = 1e-07
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 172 KCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEED 211
+ GTY+R+ C+ +G LG GA +EL R G + E+
Sbjct: 164 EVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEE 203
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification,
structural genomics, PSI, structure initiative; 1.90A
{Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2
Length = 316
Score = 91.1 bits (227), Expect = 4e-22
Identities = 28/70 (40%), Positives = 45/70 (64%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G V +DKP+ +SH+VV +RI + GH+GTLDP +G L++ I+RAT+++ +A
Sbjct: 7 GIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAA 66
Query: 93 GKEYISIFKL 102
K Y + +L
Sbjct: 67 PKSYAATIRL 76
Score = 50.3 bits (121), Expect = 1e-07
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 173 CQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSG 205
C +GTY+R +G LGVG + LRR R G
Sbjct: 173 CSSGTYIRALARDLGDALGVGGHVTALRRTRVG 205
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop,
lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli}
SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A
Length = 327
Score = 89.6 bits (223), Expect = 2e-21
Identities = 25/70 (35%), Positives = 39/70 (55%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G + LDKP SS++ + +KRI + GH+G LDP +G L +C+ AT+ + +
Sbjct: 26 GVLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDS 85
Query: 93 GKEYISIFKL 102
K Y I +L
Sbjct: 86 DKRYRVIARL 95
Score = 49.5 bits (119), Expect = 2e-07
Identities = 16/40 (40%), Positives = 19/40 (47%)
Query: 172 KCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEED 211
C GTY+RT +G LG GA +I LRR E
Sbjct: 186 HCSKGTYIRTIIDDLGEKLGCGAHVIYLRRLAVSKYPVER 225
>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10,
RNA modification, thump domai; HET: EPE; 2.0A {Homo
sapiens}
Length = 530
Score = 54.5 bits (130), Expect = 6e-09
Identities = 26/158 (16%), Positives = 62/158 (39%), Gaps = 21/158 (13%)
Query: 51 WIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVA 110
+ I ++ ++ + + +V + + + ++ K Y ++ + A++
Sbjct: 370 TSQEIKELQQKINNSSNKIQVRDLQLVTREAIGHMKEGEEEKTKTYSALIWTNKAIQ--- 426
Query: 111 KASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAPNKKPTY-MKSNLISSDVTLSTGII 169
K I+ K K ++ TP L A + + M++ + +
Sbjct: 427 -----KKDIEFLNDIKDLKIDQKTPLRVLHRRPLAVRARVIHFMETQYVDEHH----FRL 477
Query: 170 WLKCQAGTYVRTYC--------VHMGLVLGVGAQMIEL 199
LK QAGTY++ + ++G ++ V A ++EL
Sbjct: 478 HLKTQAGTYIKEFVHGDFGRTKPNIGSLMNVTADILEL 515
>3zv0_C H/ACA ribonucleoprotein complex subunit 4; cell cycle, RNP
assembly, X-linked dyskeratosis congenita; 2.80A
{Saccharomyces cerevisiae}
Length = 195
Score = 50.8 bits (121), Expect = 4e-08
Identities = 44/173 (25%), Positives = 66/173 (38%), Gaps = 44/173 (25%)
Query: 1 NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAG----------YVNLDKPSNPS-SHEVV 49
NFDKL VR+ HYTP+P G SPL+R ++ YI +G + + + + +
Sbjct: 34 NFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGPLETLLVGYKRIVVKDSAVNAVCYGAK 93
Query: 50 AWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENV 109
I +LR E+ IV I + + +S L S V
Sbjct: 94 LMIPGLLRYEEGIELYD--------EIVLITTKGEAI----AVAIAQMSTVDLASCDHGV 141
Query: 110 AKASKKKMM---------------------IKQGLLDKHGKPNENTPASYLAE 141
+ K+ +M G LDK+G+ NENTP + E
Sbjct: 142 VASVKRCIMERDLYPRRWGLGPVAQKKKQMKADGKLDKYGRVNENTPEQWKKE 194
>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 = 37.0 bits (85), Expect = 0.004
Identities = 41/280 (14%), Positives = 78/280 (27%), Gaps = 99/280 (35%)
Query: 2 FDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDK----PSNPSSH-----EVVAWI 52
F++L Y L + + I+ L + + ++ W+
Sbjct: 170 FEELRDLYQTYHVL----------VGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWL 219
Query: 53 KR----------------------------ILRCEKTG-HSGTLDPKTSGCLIVCIDRAT 83
+ ++ + G G L G T
Sbjct: 220 ENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVT 279
Query: 84 RLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELE 143
+ ++ + + + +V KA ++ G+ PN + P S L +
Sbjct: 280 AVAIAETDSWESFF---------VSVRKAIT--VLFFIGVRCYEAYPNTSLPPSILEDSL 328
Query: 144 AAPNKKPTYMKSNLISSDVTLS-TGIIWLKCQAGTYVRTYC--------VHMGLVLG--- 191
P+ M LS + + + Q YV V + LV G
Sbjct: 329 ENNEGVPSPM----------LSISNL--TQEQVQDYVNKTNSHLPAGKQVEISLVNGAKN 376
Query: 192 -V--G------AQMIELRRNR--SGI-QSEEDGLVTFRQE 219
V G + LR+ + SG+ QS + F +
Sbjct: 377 LVVSGPPQSLYGLNLTLRKAKAPSGLDQSR----IPFSER 412
>3tia_A Neuraminidase; 6-bladed beta-propeller, calcium binding,
glycosylation, ANT hydrolase-hydrolase inhibitor
complex; HET: NAG BMA MAN LNV; 1.80A {Influenza a virus}
PDB: 3tib_A* 3tic_A* 2bat_A* 1ivd_A* 1inh_A* 1inw_A*
1inx_A* 1ivc_A* 1ing_A* 1ive_A* 1ivf_A* 1ivg_A* 1nn2_A*
2aep_A* 2aeq_A*
Length = 469
Score = 28.9 bits (64), Expect = 1.4
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 3/61 (4%)
Query: 22 LQRTIQEYIRAGYVNLDKP---SNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVC 78
+ RTI + R+GY S P+S V + +G+SG + C+ C
Sbjct: 362 MGRTISKESRSGYETFKVIGGWSTPNSKSQVNRQVIVDNNNWSGYSGIFSVEGKSCINRC 421
Query: 79 I 79
Sbjct: 422 F 422
>1nsc_A Neuraminidase; hydrolase(O-glycosyl); HET: NAG SIA; 1.70A
{Influenza b virus} SCOP: b.68.1.1 PDB: 1a4g_A* 1nsb_A*
1a4q_A* 1nsd_A* 3k37_A* 3k36_A* 3k38_A* 3k39_A* 3k3a_A*
1b9v_A* 1b9s_A* 1b9t_A* 1inv_A* 1ivb_A* 1inf_A* 1vcj_A*
Length = 390
Score = 28.9 bits (64), Expect = 1.6
Identities = 11/61 (18%), Positives = 19/61 (31%), Gaps = 3/61 (4%)
Query: 22 LQRTIQEYIRAGYVNLDKP---SNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVC 78
RT+ + R G + S + + E +S + K C + C
Sbjct: 289 YSRTMSKTERMGMELYVRYDGDPWTDSDALAHSGVMVSMKEPGWYSFGFEIKDKKCDVPC 348
Query: 79 I 79
I
Sbjct: 349 I 349
>3cjh_B Mitochondrial import inner membrane translocase S TIM8; cyclic
heterohexamer, chaperone, M binding, mitochondrion,
protein transport; 2.60A {Saccharomyces cerevisiae}
Length = 64
Score = 26.4 bits (58), Expect = 1.7
Identities = 6/25 (24%), Positives = 13/25 (52%)
Query: 57 RCEKTGHSGTLDPKTSGCLIVCIDR 81
+C ++ + L + CL C++R
Sbjct: 24 KCVESVNDSNLSSQEEQCLSNCVNR 48
>3vbh_A EV71, genome polyprotein, capsid protein VP1; hand-foot-and-mouth
disease, enterovirus uncoating, P factor,
adaptor-sensor; HET: SPH; 2.30A {Human enterovirus 71}
PDB: 3vbf_A* 3vbo_A 3vbs_A* 4aed_A* 3vbr_A 3vbu_A
Length = 297
Score = 27.9 bits (61), Expect = 2.7
Identities = 12/87 (13%), Positives = 27/87 (31%), Gaps = 9/87 (10%)
Query: 20 SPLQRTIQEYIRAGYVNLD-KPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVC 78
S + ++ + + + SSH + L+ + G S ++
Sbjct: 10 SSIGDSVSRALTHALPAPTGQNTQVSSHRLDTGKVPALQAAEIGASSNASDESM------ 63
Query: 79 IDRATRLVKSQQSAGKEYISIFKLHSA 105
TR V + S + + F +
Sbjct: 64 --IETRCVLNSHSTAETTLDSFFSRAG 88
>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 = 27.6 bits (60), Expect = 2.7
Identities = 5/27 (18%), Positives = 10/27 (37%), Gaps = 6/27 (22%)
Query: 4 KLNVRTNHYTPLPFGKSP---LQRTIQ 27
KL Y +P ++ T++
Sbjct: 24 KLQASLKLYAD---DSAPALAIKATME 47
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
0.318 0.132 0.395
Gapped
Lambda K H
0.267 0.0556 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,433,566
Number of extensions: 192270
Number of successful extensions: 385
Number of sequences better than 10.0: 1
Number of HSP's gapped: 382
Number of HSP's successfully gapped: 23
Length of query: 232
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 142
Effective length of database: 4,188,903
Effective search space: 594824226
Effective search space used: 594824226
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 (21.7 bits)
S2: 56 (25.7 bits)