RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 009253
(539 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 = 77.1 bits (191), Expect = 4e-16
Identities = 38/135 (28%), Positives = 56/135 (41%), Gaps = 25/135 (18%)
Query: 78 KKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSS 137
+++ L Y GT + GLQ Q L T++GELE AL G +
Sbjct: 2 RRLLLLCEYDGTLFAGLQRQG--RGLRTVQGELERALPGIGA-LPKAVA---------AG 49
Query: 138 RTDKGVHSLATMIC---LKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSF 194
RTD GVH+LA M ++ IP + + +N LP ++KV F
Sbjct: 50 RTDAGVHALA-MPFHVDVESAIPVEKV---------PEALNRLLPEDLKVVGAREVAPDF 99
Query: 195 DPRRECNLRKYSYLL 209
R++ R Y Y +
Sbjct: 100 HARKDALWRAYRYRI 114
Score = 40.1 bits (95), Expect = 0.001
Identities = 20/83 (24%), Positives = 31/83 (37%), Gaps = 6/83 (7%)
Query: 360 SASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAV-KRKLLPRDIL 418
+ E V + G+SF+ Q+R MVGT + V K P +
Sbjct: 163 PGERELLEARLQVAEGEAG---LEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLK 219
Query: 419 TLSLAKHSRIVL-PLAPSEVLFL 440
+ L R + P AP+ L+
Sbjct: 220 AI-LKTADRRLAGPTAPAHGLYF 241
>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 = 76.4 bits (189), Expect = 9e-16
Identities = 35/135 (25%), Positives = 53/135 (39%), Gaps = 25/135 (18%)
Query: 78 KKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSS 137
K+AL + Y G+ Y G Q Q + +++ +LE AL + + I +
Sbjct: 4 YKIALGIEYDGSKYYGWQRQNEVR---SVQEKLEKALSQVAN---------EPITVFCAG 51
Query: 138 RTDKGVHSLATMIC---LKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSF 194
RTD GVH + AW G VNA+LP +I V + F
Sbjct: 52 RTDAGVHGTG-QVVHFETTALRKDAAW---TLG------VNANLPGDIAVRWVKTVPDDF 101
Query: 195 DPRRECNLRKYSYLL 209
R R+Y Y++
Sbjct: 102 HARFSATARRYRYII 116
Score = 44.0 bits (105), Expect = 6e-05
Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 8/83 (9%)
Query: 360 SASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAV-KRKLLPRDIL 418
S + +R + + + YV + I +F+ H +R +VG+ + V I
Sbjct: 165 SRTPWRNVMHINVTRHG-----PYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIA 219
Query: 419 TLSLAKHSRIVL-PLAPSEVLFL 440
L LA R + A +E L+L
Sbjct: 220 EL-LAAKDRTLAAATAKAEGLYL 241
>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 = 55.8 bits (134), Expect = 3e-08
Identities = 105/593 (17%), Positives = 186/593 (31%), Gaps = 184/593 (31%)
Query: 13 WSARSITSTLSTVGFSNKISAVNLLPLSCYRCPASSSSKSSPSVSHTLTRPTPNSSDDKW 72
+S R +T LS + V L+P + + +S + + L PT + D
Sbjct: 4 YSTRPLT--LS----HGSLEHVLLVPTASF--FIASQLQEQ--FNKILPEPTEGFAADD- 52
Query: 73 EPVRKKKVALR-VGYVGTDYRGLQMQRDEHSLSTIEGELETAL--FKAGGIRESNYGNLQ 129
EP ++ + +GYV + + + + L L F E+ Y L+
Sbjct: 53 EPTTPAELVGKFLGYVSS-------LVEPSKVGQFDQVLNLCLTEF------ENCY--LE 97
Query: 130 KIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVF--SI 187
+H+LA ++ ++ + K + IK + +
Sbjct: 98 ----------GNDIHALAA------KLLQ----ENDTTLVKTKEL-------IKNYITAR 130
Query: 188 LPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEG----EH 243
+ ++R FD + S L A E ++ + AI F G +
Sbjct: 131 IMAKRPFDKKSN------SALFRA----------VGEGNAQL--V-AI---FGGQGNTDD 168
Query: 244 PFHNYTE-RSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLG 302
F E R Y+ G + K + + + + + E F++ L
Sbjct: 169 YF---EELRDLYQTYHVLVGDLIKFS---AETLSELIRTTLDAEKVFTQG--------LN 214
Query: 303 IGGEISSDDEKANQNSMVS--------GVHQEDC----CNQHANGLKDQN---------- 340
I + + +++ ++S GV Q G
Sbjct: 215 ILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLL--GFTPGELRSYLKGATG 272
Query: 341 -SSSVIRAR-------WLYETDEADKLSASHFRKIFSCSCGKLE----KSLGFGYVEISI 388
S ++ A W + +F E SL +E S+
Sbjct: 273 HSQGLVTAVAIAETDSW----ESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSL 328
Query: 389 S-GE---SFMLHQIR----KMVGTAVAVKRKLLPRD-ILTLSL---AKHSRIVL--PLAP 434
E S ML I + V V LP + +SL AK+ +V+ P P
Sbjct: 329 ENNEGVPSPMLS-ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKN--LVVSGP--P 383
Query: 435 SE----VLFLRANSFSVRTRPGVTRPEMQTMVE-SEEILKMVDEFYTSVTLPEVSKFL-D 488
L LR + G+ Q+ + SE LK + F V P S L
Sbjct: 384 QSLYGLNLTLR----KAKAPSGLD----QSRIPFSERKLKFSNRFLP-VASPFHSHLLVP 434
Query: 489 ATKSPWTEWIENLEKFTS----IPNEQLDEVRNAWQLWKEKRFESKTIVESAI 537
A+ + ++N F + IP V + + + R S +I E +
Sbjct: 435 ASDLINKDLVKNNVSFNAKDIQIP------VYDTFD-GSDLRVLSGSISERIV 480
Score = 47.7 bits (113), Expect = 1e-05
Identities = 55/314 (17%), Positives = 96/314 (30%), Gaps = 109/314 (34%)
Query: 266 KRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQNSMVSGVHQ 325
K +KA++D V++R + + GFS + +I + N ++
Sbjct: 1637 KTSKAAQD-VWNRADNHFKDTYGFSIL-------------DIVIN----NPVNLTI---- 1674
Query: 326 EDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVE 385
H G K + IR + E KIF K +
Sbjct: 1675 ------HFGGEKGKR----IRENYSAMIFETIVDGKLKTEKIF--------KEINEHSTS 1716
Query: 386 ISISGESFMLH-----QIRKMVGTAVAV-----KRKLLPRDILTLSLAKHSRIVLPL--- 432
+ E +L Q + A + L+P D A HS L
Sbjct: 1717 YTFRSEKGLLSATQFTQPA-LTLMEKAAFEDLKSKGLIPADAT---FAGHS-----LGEY 1767
Query: 433 ----APSEVLFLRANSFS-----VRTRPGVTRPEMQTMVESEEILK----MVDEFYTSVT 479
+ ++V+ S V R G+T MQ V +E+ + M+ ++
Sbjct: 1768 AALASLADVM-----SIESLVEVVFYR-GMT---MQVAVPRDELGRSNYGMI-----AIN 1813
Query: 480 LPEVSKFLDATKSPWTEWIENLEKFTS---------IPNEQ---------LDEVRNAWQL 521
V+ +E + K T + N+Q LD V N
Sbjct: 1814 PGRVAASFSQEAL--QYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNF 1871
Query: 522 WKEKRFESKTIVES 535
K ++ + + +S
Sbjct: 1872 IKLQKIDIIELQKS 1885
Score = 45.8 bits (108), Expect = 4e-05
Identities = 71/433 (16%), Positives = 122/433 (28%), Gaps = 148/433 (34%)
Query: 30 KISAVNLLPLSCYRCPASSSSKSSPSVSHT------LTRPTPNSSDD--KWEPVRKKKVA 81
K SA L L ++ + + L P+ D P+ +
Sbjct: 189 KFSAETLSELI------RTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIG 242
Query: 82 LR--VGYVGT----DYRGLQMQRDEHSLSTIEGELETALFKAGGI-RESNYGNLQKI--- 131
+ YV T + +++ + L TA+ A ES + +++K
Sbjct: 243 VIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITV 302
Query: 132 -AWARSSRTDKGVHSLATMICLKMEIPPDAWKDD-------P------YGIDLA------ 171
+ GV +PP +D P +
Sbjct: 303 LFFI-------GVRCYEAYPNT--SLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYV 353
Query: 172 KRVNAHLPRNIKVF-SILPSQRSF---DPRRECNLRKYSYLLPAEVIGINSQLTAAEIDS 227
+ N+HLP +V S++ ++ P P + G+N L A+ S
Sbjct: 354 NKTNSHLPAGKQVEISLVNGAKNLVVSGP-------------PQSLYGLNLTLRKAKAPS 400
Query: 228 HISDFNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEE---SEG 284
+ D + I PF S+ RK + S R F V S
Sbjct: 401 GL-DQSRI--------PF------SE--RKL----KFSNR--------FLPVASPFHSHL 431
Query: 285 EEDGFSKVEESDGEEDLGIGGEISSDDEKANQNSMVSGVHQ----EDCCNQHAN---GLK 337
+ +DL ++ N + V+ D + +
Sbjct: 432 LVPASDLI-----NKDL------VKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIV 480
Query: 338 DQNSSSVIRAR--WLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFML 395
D +IR W + + A+H L FG SG +
Sbjct: 481 DC----IIRLPVKW----ETTTQFKATHI--------------LDFG--PGGASGLGVLT 516
Query: 396 HQIRKMVGTAVAV 408
H+ + GT V V
Sbjct: 517 HRNKD--GTGVRV 527
Score = 37.0 bits (85), Expect = 0.020
Identities = 42/256 (16%), Positives = 70/256 (27%), Gaps = 93/256 (36%)
Query: 167 GIDL------AKRV----NAHLPRNIKVFSIL------PSQRS--FDPRRECNLRK-YSY 207
G+DL A+ V + H ++ FSIL P + F + +R+ YS
Sbjct: 1632 GMDLYKTSKAAQDVWNRADNHF-KDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSA 1690
Query: 208 LLPAEVIGINSQLTA--AEIDSHISDFNAILNEFEGEHPFHNYTE--------------- 250
++ ++ + EI+ H + + F E + T+
Sbjct: 1691 MIFETIVDGKLKTEKIFKEINEHSTSYT-----FRSEKGLLSATQFTQPALTLMEKAAFE 1745
Query: 251 --RSKYRRKP------HKTG------------------R-VSKRAKASKDAVFSRVEESE 283
+SK H G V R + A V E
Sbjct: 1746 DLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVA----VPRDE 1801
Query: 284 GEEDGF-------SKVEESDGEEDL-GIGGEISSDD----EKANQNSM-----VSGVHQE 326
+ +V S +E L + + E N N +G
Sbjct: 1802 LGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAG-DLR 1860
Query: 327 --DCCNQHANGLKDQN 340
D N +K Q
Sbjct: 1861 ALDTVTNVLNFIKLQK 1876
>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 = 44.5 bits (104), Expect = 9e-05
Identities = 62/391 (15%), Positives = 123/391 (31%), Gaps = 85/391 (21%)
Query: 199 ECNLRKYSYLLPAEVIGINSQLTAAEID-SHISDF-NAILNEFEGEHPFHNYTERSKYRR 256
E +Y Y +++ + D + D +IL++ E +H + S R
Sbjct: 10 ETGEHQYQY---KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR 66
Query: 257 -------KPHKTGRVSKRAKASKDAVFSRVEESEGEEDGF--SKVEESDGEEDLGIGGEI 307
K ++ V VEE F S ++ + + I
Sbjct: 67 LFWTLLSKQ-------------EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI 113
Query: 308 SSDDEKANQNSMVS--GVHQEDCCNQHANGL-KDQNSSSVIRARWLY------------E 352
D N N + + V + + L + + + +V+ + +
Sbjct: 114 EQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL----IDGVLGSGKTWVALD 169
Query: 353 TDEADKLSASHFRKIF-----SCSCGK--LEKSLGFGYVEISISGESFMLHQIRKMVGTA 405
+ K+ KIF +C+ + LE +I + S H +
Sbjct: 170 VCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL-LYQIDPNWTSRSDHSSNIKLRI- 227
Query: 406 VAVKRKLLPRDILTLSLAKHSRIVL-PLAPSEVLFLRANSFSVR------TR-PGVTRPE 457
+++ +L R +L ++ +VL + ++ N+F++ TR VT
Sbjct: 228 HSIQAEL--RRLLKSKPYENCLLVLLNVQNAKAW----NAFNLSCKILLTTRFKQVTDFL 281
Query: 458 MQTMVESEEILKMVDEFYTSVTLPEVSKFLD--ATKSPWTEWIENLEKFTSIP------N 509
+ + K+LD P E T+ P
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP-------REVLTTNPRRLSIIA 334
Query: 510 EQLDEVRNAWQLWKEKRFES-KTIVESAISV 539
E + + W WK + TI+ES+++V
Sbjct: 335 ESIRDGLATWDNWKHVNCDKLTTIIESSLNV 365
>1v7w_A Chitobiose phosphorylase; beta-sandwich, (alpha/alpha)6 barrel,
transferase; HET: NDG NAG; 1.60A {Vibrio proteolyticus}
SCOP: a.102.1.4 b.30.5.3 PDB: 1v7v_A* 1v7x_A*
Length = 807
Score = 29.3 bits (65), Expect = 3.8
Identities = 17/81 (20%), Positives = 30/81 (37%), Gaps = 4/81 (4%)
Query: 442 ANSFSVRTRPGVTRPEMQTMVESEEILKMVDEFYTSVTLPEVSKFLDATKSPWTEWIENL 501
+ +PG + + + + E Y V + A K+ W E
Sbjct: 247 SLHKQFTLQPGEEIRFAYILGIGKGNGERLREHYQDVA--NIDAAFAAIKAHWDERCAKF 304
Query: 502 EKFTSIPNEQLDEVRNAWQLW 522
+ + PN+ LD + NAW L+
Sbjct: 305 QVKS--PNQGLDTMINAWTLY 323
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.8 bits (61), Expect = 6.6
Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 25/93 (26%)
Query: 453 VTRPEMQTMVESEEILKMVDEFYTSVTLPEVSKFLDA-TKSPWTEWIE----NLEKFTSI 507
+ + + + E E I K +E + + LDA +K EW E +LE++
Sbjct: 74 IAQAD-RLTQEPESIRKWREEQR-----KRLQE-LDAASKVMEQEWREKAKKDLEEWNQR 126
Query: 508 PNEQLD----EVRNAWQLWKEKRF----ESKTI 532
+EQ++ R A +K F ++ I
Sbjct: 127 QSEQVEKNKINNRIA-----DKAFYQQPDADII 154
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 27.8 bits (61), Expect = 7.6
Identities = 6/42 (14%), Positives = 12/42 (28%), Gaps = 5/42 (11%)
Query: 464 SEEILKMVDEFYTSVTLPEVSKFLDATKSPWTEWIENLEKFT 505
EIL + + + +D T W + +
Sbjct: 180 PNEILFSENND-----MDNNNDGVDELNKKCTFWDAISKLYY 216
>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus} PDB: 3lvh_A
Length = 624
Score = 28.4 bits (63), Expect = 7.8
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 7/72 (9%)
Query: 68 SDDKWEPVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRE----- 122
+DD + + A G + LQM R + S +E EL AL K + E
Sbjct: 80 ADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFI 139
Query: 123 --SNYGNLQKIA 132
N ++Q++
Sbjct: 140 NGPNNAHIQQVG 151
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
0.315 0.130 0.377
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,935,684
Number of extensions: 460119
Number of successful extensions: 892
Number of sequences better than 10.0: 1
Number of HSP's gapped: 879
Number of HSP's successfully gapped: 17
Length of query: 539
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 441
Effective length of database: 3,965,535
Effective search space: 1748800935
Effective search space used: 1748800935
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 (21.6 bits)
S2: 60 (27.4 bits)