RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16424
(295 letters)
>2cxh_A Probable BRIX-domain ribosomal biogenesis protein; 18S rRNA, IMP4,
U3 snoRNP, ribosomal biogenesis binding, structural
genomics, NPPSFA; 1.80A {Aeropyrum pernix} SCOP:
c.51.1.2
Length = 217
Score = 215 bits (549), Expect = 3e-70
Identities = 42/197 (21%), Positives = 73/197 (37%), Gaps = 20/197 (10%)
Query: 83 DDEYRWAGIEDPKIMITTSRDPSSRLKMFVKELRLIFPNSQRMNRGNYEMKQLIHACRAN 142
+ R +G+ +I++TTSR PS R++ FVK+L P + R RG+Y M++L
Sbjct: 23 GGKGRPSGVGGYRILVTTSRRPSPRIRSFVKDLSATIPGAFRFTRGHYSMEELAREAIIR 82
Query: 143 DVTDFIVVHEHRGIPDTLVICHLPYGPTAYFTMSDVIM---------RHDIPDL--GTMS 191
+VV E RG P ++ + GP + I+ R +P L G +
Sbjct: 83 GADRIVVVGERRGNP-GIIRVYAVEGPERPDNIVSFIVKGVSLSRERRWGLPSLRGGEVL 141
Query: 192 EQYPHLVFHNFKTQLGQRVMSILKYLFPVPKEDSK---RIVTFANHDDYISFRHHNYKRD 248
P + + + P+ I + ++FR+
Sbjct: 142 VARP--LDSGVAVEFADAFVIAFHARLKPPEAAGYVEAVIESLDARTVAVTFRYGGAP-- 197
Query: 249 GKDIELKEVGPRFQLKL 265
L+ P +K
Sbjct: 198 -VGPMLRLGKPAEMVKR 213
>1w94_A MIL, probable BRIX-domain ribosomal biogenesis protein; archaeal
IMP4-BRIX domain, IMP4 domain; 2.0A {Methanothermobacter
thermautotrophicusorganism_taxid} SCOP: c.51.1.2
Length = 156
Score = 130 bits (327), Expect = 9e-38
Identities = 30/168 (17%), Positives = 60/168 (35%), Gaps = 15/168 (8%)
Query: 96 IMITTSRDPSSRLKMFVKELRLIFPNSQRMNRGNYEMKQLIHACRANDVTDFIVVHEHRG 155
+++TTSR PS R + F + L I + +NRG ++ ++ R VV E G
Sbjct: 2 MLLTTSRKPSQRTRSFSQRLSRIM-GWRYINRGKMSLRDVLIEAR----GPVAVVSERHG 56
Query: 156 IPDTLVICHLPYGPTAYFTMSDVIMRHDIPDLGTMSEQYPHLVFHNFKTQLGQRVMSILK 215
P + G + + + P+L V + + + +++
Sbjct: 57 NPARITF-LDERGGERGYILFNPSFEMKKPEL------ADKAVRVSSCPPGSEGLCNLM- 108
Query: 216 YLFPVPKEDSKRIVTFANHDDYISFRHHNYKRDGKDIELKEVGPRFQL 263
V + S+ + ++Y R G K + F++
Sbjct: 109 -GLEVDESSSRDAWSIRTDEEYAWVMELMDAR-GTPAGFKLLIRDFRV 154
>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 = 46.4 bits (109), Expect = 8e-06
Identities = 46/308 (14%), Positives = 97/308 (31%), Gaps = 79/308 (25%)
Query: 11 EYLYRKSLEEKQRAIQEKKDRLRKSLDGNKKIPTD--------LKNQALSLQRKLDWEDE 62
+Y Y+ L + A + D + D K I + K+ R
Sbjct: 15 QYQYKDILSVFEDAFVDNFD-CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73
Query: 63 GPELAVSIGTETSGGGLTHQDDEYRWAGIEDPKIMITTSRDPSSRLKMFVKELRLIFPNS 122
E V E + + Y++ + P + T R PS +M++++ ++ ++
Sbjct: 74 KQEEMVQKFVEEV-----LRIN-YKF--LMSP--IKTEQRQPSMMTRMYIEQRDRLYNDN 123
Query: 123 QRMNRGNYEMKQLIHACRAN----DVTDFIVVHEHRGIP-------------DTLVICHL 165
Q + N Q R +++ G+ V C +
Sbjct: 124 QVFAKYNVSRLQPYLKLRQALLELRPAKNVLID---GVLGSGKTWVALDVCLSYKVQCKM 180
Query: 166 PYGPTAYFTMSDVIMRHDIPDLGTMSEQYPHLVFHNFKTQLGQRVMSILKYLFPVPKEDS 225
+ + + + + + M ++ + + N+ ++
Sbjct: 181 DFK-IFWLNLKN---CNSPETVLEMLQKLLYQIDPNWTSR-------------------- 216
Query: 226 KRIVTFANHDDYISFRHHNYKRDGKDIELKEVGPRFQLKLYEIKLGTLDTVEAADTEWAL 285
++H I R H+ + EL+ + + K YE L L V+ A W
Sbjct: 217 ------SDHSSNIKLRIHSIQA-----ELRRL---LKSKPYENCLLVLLNVQNAKA-WNA 261
Query: 286 FRMG-RIL 292
F + +IL
Sbjct: 262 FNLSCKIL 269
Score = 36.8 bits (84), Expect = 0.007
Identities = 50/301 (16%), Positives = 81/301 (26%), Gaps = 99/301 (32%)
Query: 14 YRKSLEEKQRAI--QEKKDRLRKSLDGNKKIPTDLKNQALSLQRKLDWEDEGPELAVS-I 70
SL+ + E K L K LD P DL + L+ P +S I
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLD---CRPQDLPREVLTT---------NP-RRLSII 333
Query: 71 GTETSGGGLTHQDDEYRWAGIEDPKIMITTS---RDPSSRLKMFVKELRLIFPNS----- 122
G T D ++ + +I +S +P+ KMF L +FP S
Sbjct: 334 AESIRDGLATW--DNWKHVNCDKLTTIIESSLNVLEPAEYRKMF-DRL-SVFPPSAHIPT 389
Query: 123 ---------------QRM----------NRGNYEMKQLIHA------CRANDVTDFIVVH 151
+ + E I + + +
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL---- 445
Query: 152 EHRGIPDTLVICHLPYGPTAYFTMSDVIMRHDIPDLGTMSEQY--PHLVFHNFKTQLGQR 209
HR I D Y F D+I + +QY H+ H + +R
Sbjct: 446 -HRSIVDH-------YNIPKTFDSDDLIPPYL--------DQYFYSHIGHHLKNIEHPER 489
Query: 210 VMSILKYLF-----------------PVPKEDSKRIVTFANHDDYISFRHHNYKRDGKDI 252
M++ + +F + + YI Y+R I
Sbjct: 490 -MTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAI 548
Query: 253 E 253
Sbjct: 549 L 549
Score = 36.0 bits (82), Expect = 0.015
Identities = 28/173 (16%), Positives = 57/173 (32%), Gaps = 33/173 (19%)
Query: 13 LYRKSLEEKQRA-----IQEKKDRLRKSLDGNKKIPTDLKNQALSLQRKLDWEDEGPELA 67
L++ SL EKQ I L+ L+ + + + ++ + D +D P
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH-YNIPKTFDSDDLIPPYL 469
Query: 68 VS-----IGTETSGGGLTHQDDE-------YRWAGIEDPKI-MITTSRDPSSRLKMFVKE 114
IG + +R+ +E KI +T+ + S + +++
Sbjct: 470 DQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRF--LEQ-KIRHDSTAWNASGSILNTLQQ 526
Query: 115 LRL----IFPNSQRMNRGNYEMKQLIHACRAN-------DVTDFIVVHEHRGI 156
L+ I N + R + + N D+ ++ E I
Sbjct: 527 LKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAI 579
>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 = 36.9 bits (84), Expect = 0.002
Identities = 14/54 (25%), Positives = 18/54 (33%), Gaps = 24/54 (44%)
Query: 20 EKQRAIQEKKDRLRKSLDGNKKIPTDLKNQALSLQRKLDWEDEGPELAVSIGTE 73
EKQ +L KK+ LK A +D P LA+ E
Sbjct: 18 EKQ------------AL---KKLQASLKLYA---------DDSAPALAIKATME 47
Score = 28.8 bits (63), Expect = 1.6
Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 13/33 (39%)
Query: 253 ELKEVGPRFQLKLYEIKLGTLDTVEAADTEWAL 285
LK++ LKLY A D+ AL
Sbjct: 21 ALKKLQAS--LKLY-----------ADDSAPAL 40
>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 = 0.007
Identities = 46/258 (17%), Positives = 78/258 (30%), Gaps = 89/258 (34%)
Query: 32 LRKSLDG----NKKIPTDLKNQALSLQRKLDWED------EGPELAVSIGTE-------T 74
LR L G ++ + T A+++ WE + + IG T
Sbjct: 263 LRSYLKGATGHSQGLVT-----AVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNT 317
Query: 75 SGGGLTHQDDEYRWAGIEDPKIMITTSRDPSSRLKMFVKELRLIFPNSQRMNRGNYEMKQ 134
S +D G+ P M++ S +++ +V + P ++
Sbjct: 318 SLPPSILEDSLENNEGVPSP--MLSISNLTQEQVQDYVNKTNSHLPAGKQ---------- 365
Query: 135 LIHACRANDVTDFIVVHEHRGIPDTL--VICHL-----PYGPTAYFTMSDVIMRHDIPDL 187
+ N + +V G P +L + L P G D + IP
Sbjct: 366 -VEISLVNGAKNLVVS----GPPQSLYGLNLTLRKAKAPSG-------LD---QSRIP-- 408
Query: 188 GTMSEQYPHLV---------FHNFKTQLGQRVMSILKYLFP----VPKEDSKRIVTFANH 234
SE+ FH S L P + K+ K V+F
Sbjct: 409 --FSERKLKFSNRFLPVASPFH-----------S--HLLVPASDLINKDLVKNNVSFNAK 453
Query: 235 DDYISFRHHNYKRDGKDI 252
D I + + DG D+
Sbjct: 454 DIQIPV-YDTF--DGSDL 468
Score = 33.5 bits (76), Expect = 0.11
Identities = 54/303 (17%), Positives = 81/303 (26%), Gaps = 142/303 (46%)
Query: 16 KSLEEKQRAIQEKKDRLRKSLDGNKKIPTDLKNQALSLQRKLDWEDEGPELAVSIGTETS 75
+L ++Q +Q+ ++ L K++ L N G + V S
Sbjct: 342 SNLTQEQ--VQDYVNKTNSHLPAGKQVEISLVN--------------GAKNLV-----VS 380
Query: 76 GGGLTHQDDEYRWAGIEDPKIMITTSRDPSSRLKMFVKELRLIF----------PNSQRM 125
G P P S L LR P S+R
Sbjct: 381 G-----------------P---------PQS-LYGLNLTLRKAKAPSGLDQSRIPFSER- 412
Query: 126 NRGNYEMKQLIHACRANDVTDFIVVHEHRGIPDTLVICHLPY-GPTAYFTMSDVIMRHDI 184
K F+ V P H P + D+ +++++
Sbjct: 413 -------KLKFSNR-------FLPV----ASP-----FHSHLLVPASDLINKDL-VKNNV 448
Query: 185 P----DLGTMSEQYPHLVFHNFKTQLGQ--RVM--SILKYLF------PV--PKEDSKRI 228
D+ Q P V+ T G RV+ SI + + PV +
Sbjct: 449 SFNAKDI-----QIP--VYD---TFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFK- 497
Query: 229 VTFANHDDYISF-----------RHHNYKRDGKDIELKEVGPRFQLKLYEIKLGTLDTVE 277
A H + F H N +DG G R I GTLD
Sbjct: 498 ---ATH--ILDFGPGGASGLGVLTHRN--KDGT-------GVR------VIVAGTLDINP 537
Query: 278 AAD 280
D
Sbjct: 538 DDD 540
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.7 bits (66), Expect = 0.69
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 7 RLRREYLYRKSLEEKQRAIQEKKDRLR----KSLD 37
R RE RK L+E A + + R K L+
Sbjct: 88 RKWRE-EQRKRLQELDAASKVMEQEWREKAKKDLE 121
>3eff_K Voltage-gated potassium channel; FULL length KCSA, bulge helix,
cell membrane, ION transport, ionic channel, membrane,
transmembrane; 3.80A {Streptomyces lividans}
Length = 139
Score = 29.5 bits (66), Expect = 0.77
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 3 RRQARLRREYLYRKSLEEKQRAIQEKKDRLRKSLDGNKK 41
R E ++ RA+ E+ DRL + LD N++
Sbjct: 101 RGHFVRHSEKAAEEAYTRTTRALHERFDRLERMLDDNRR 139
>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain,
chromatin regulator, coiled coil, nucleus, repressor,
transcription; 2.20A {Saccharomyces cerevisiae} PDB:
3hgq_A
Length = 328
Score = 29.1 bits (65), Expect = 1.5
Identities = 15/94 (15%), Positives = 30/94 (31%), Gaps = 15/94 (15%)
Query: 177 DVIMRHDIPDLGTMSEQYPHLVFHNFKTQLGQRVMSILKYLFPVPKEDSKRIVTFANH-- 234
+++ H +P + HL ++ K S+L+ L + +E
Sbjct: 84 YLLIDHYMPKSLITRDVPAHLAENSGK-------FSVLRDLINLVQEYETETAIVCRPGR 136
Query: 235 -----DDYISFRHHNYKR-DGKDIELKEVGPRFQ 262
+ + + KR DG I+ F
Sbjct: 137 TMDLLEALLLGNKVHIKRYDGHSIKSAAAANDFS 170
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin
subfragment 2, heavy meromyosin, essential light chain,
motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP:
i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 29.4 bits (66), Expect = 1.9
Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 2/59 (3%)
Query: 2 LRRQARLRREYLYRKS--LEEKQRAIQEKKDRLRKSLDGNKKIPTDLKNQALSLQRKLD 58
L +A R L K LEE ++ + + + + ++ Q L L+ +L+
Sbjct: 907 LYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLE 965
Score = 28.3 bits (63), Expect = 3.9
Identities = 9/53 (16%), Positives = 27/53 (50%)
Query: 5 QARLRREYLYRKSLEEKQRAIQEKKDRLRKSLDGNKKIPTDLKNQALSLQRKL 57
+AR+ E + L+ +++ +Q++ L + L+ + L+ + ++ K+
Sbjct: 933 EARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKI 985
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 29.1 bits (65), Expect = 2.0
Identities = 49/228 (21%), Positives = 73/228 (32%), Gaps = 85/228 (37%)
Query: 69 SIGTETSGGGLTHQDDEYRWAGIEDPKIMITTSRDPSSRLKMFVKEL---------RLI- 118
SIG E G L G K+++TTSR + + + LI
Sbjct: 488 SIGAEVLQGLLQ--------GG---AKVVVTTSRFSKQVTDYY-QSIYAKYGAKGSTLIV 535
Query: 119 FPNSQRMNRGNYEMKQLIHACRANDVTDFIVVHEHRGIPDTLVICHLPYGPTAYF---TM 175
P N+G+ DV I E I DT L + A +
Sbjct: 536 VP----FNQGSK-----------QDVEALI---EF--IYDTEKNGGLGWDLDAIIPFAAI 575
Query: 176 SDVIMRHDIPDLGTMSEQYPHLVFHNFKTQLGQRVM--SILKYLFPVPKEDSKR-IVTFA 232
+ ++ + + SE R+M +IL+ + V K+ S R I T
Sbjct: 576 PEQ--GIELEHIDSKSE-------------FAHRIMLTNILRMMGCVKKQKSARGIETRP 620
Query: 233 NHDDYI---SFRHHNYKRDGKDIELKEVGPRFQLKLY-EIKLGTLDTV 276
I S H + DG +Y E KL L+T+
Sbjct: 621 AQ--VILPMSPNHGTFGGDG---------------MYSESKLS-LETL 650
>3pjs_K KCSA, voltage-gated potassium channel; ION channel, conducts K+
IONS, cell membrane, transport PROT; 3.80A {Streptomyces
lividans} PDB: 1f6g_A
Length = 166
Score = 27.9 bits (62), Expect = 2.3
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 3 RRQARLRREYLYRKSLEEKQRAIQEKKDRLRKSLDGNKK 41
++Q E ++ RA+ E+ DRL + LD N++
Sbjct: 128 QQQFVRHSEKAAEEAYTRTTRALHERFDRLERMLDDNRR 166
>3q3y_A HEVB EV93 3C protease; cysteine trypsin-like protease, 3C cysteine
protease (picorn antiviral compound 1 (AG7404); HET:
XNV; 1.32A {Human enterovirus B} PDB: 3q3x_A* 3ruo_A*
2ztx_A 2vb0_A 2zty_A 2ztz_A 2zu3_A* 2zu1_A
Length = 191
Score = 27.2 bits (60), Expect = 4.9
Identities = 12/67 (17%), Positives = 20/67 (29%), Gaps = 6/67 (8%)
Query: 143 DVTDFIVVHEHRGIPDTLVICHLPYGPTAYFTMSDVIMRHDIPDLGTMSEQYPHLVFH-N 201
D+ F+ E L I + Y + V + + + N
Sbjct: 87 DIRGFLAREEVEVNEAVLAINTSKFPNM-YIPVGQVTDYGFL----NLGGTPTKRMLVYN 141
Query: 202 FKTQLGQ 208
F T+ GQ
Sbjct: 142 FPTRAGQ 148
>1cqq_A Type 2 rhinovirus 3C protease; viral protein, hydrolase; HET: AG7;
1.85A {Human rhinovirus 2} SCOP: b.47.1.4 PDB: 2xya_A*
Length = 180
Score = 26.8 bits (59), Expect = 7.4
Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 4/66 (6%)
Query: 143 DVTDFIVVHEHRGIPDTLVICHLPYGPTAYFTMSDVIMRHDIPDLGTMSEQYPHLVFHNF 202
D+ +I +E L + PT + DV+ +I G Q ++ +++
Sbjct: 85 DIRRYIPNNEDDYPNCNLALLANQPEPT-IINVGDVVSYGNILLSGN---QTARMLKYSY 140
Query: 203 KTQLGQ 208
T+ G
Sbjct: 141 PTKSGY 146
>1oy0_A Ketopantoate hydroxymethyltransferase; domain swapping, structural
genomics, PSI, protein structure initiative; 2.80A
{Mycobacterium tuberculosis} SCOP: c.1.12.8
Length = 281
Score = 26.8 bits (60), Expect = 9.2
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 10/37 (27%)
Query: 132 MKQLIHACRANDVTDFIVVHEHRGIPDTLVICHLPYG 168
+ +LI R VV RG P LV+ LP+G
Sbjct: 79 IDELIPLVRG-------VV---RGAPHALVVADLPFG 105
>3qzr_A 3C protein; chymotrypsin-fold, beta-ribbon, hydrolysis, nucleus,
hydrola hydrolase inhibitor complex; HET: AG7; 1.04A
{Human enterovirus 71} PDB: 3osy_A 3qzq_A* 3r0f_A*
3sjo_A* 3sjk_A 3sji_A* 3sj8_A* 3sj9_A
Length = 187
Score = 26.4 bits (58), Expect = 9.7
Identities = 15/66 (22%), Positives = 21/66 (31%), Gaps = 4/66 (6%)
Query: 143 DVTDFIVVHEHRGIPDTLVICHLPYGPTAYFTMSDVIMRHDIPDLGTMSEQYPHLVFHNF 202
D+T FI + TLVI V L + + +NF
Sbjct: 89 DITKFIPENISTASDATLVINTEHMPS----MFVPVGDVVQYGFLNLSGKPTHRTMMYNF 144
Query: 203 KTQLGQ 208
T+ GQ
Sbjct: 145 PTKAGQ 150
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
0.321 0.138 0.409
Gapped
Lambda K H
0.267 0.0625 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,722,691
Number of extensions: 289101
Number of successful extensions: 752
Number of sequences better than 10.0: 1
Number of HSP's gapped: 735
Number of HSP's successfully gapped: 43
Length of query: 295
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 202
Effective length of database: 4,105,140
Effective search space: 829238280
Effective search space used: 829238280
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: 57 (26.0 bits)