RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3604
(496 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 = 81.7 bits (203), Expect = 9e-18
Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 18/76 (23%)
Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKY-----------------WFPQAGLDI 265
LN LP D+KVV V + AR D L+R Y+Y W + LD+
Sbjct: 79 LNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHPSPLLRHRALWVRRP-LDL 137
Query: 266 DAMHKAAQYLVGTHDF 281
+AM +A L+G H+F
Sbjct: 138 EAMEEALSLLLGRHNF 153
>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 = 81.0 bits (201), Expect = 2e-17
Identities = 27/76 (35%), Positives = 36/76 (47%), Gaps = 18/76 (23%)
Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKY-----------------WFPQAGLDI 265
+N NLP DI V VP+ + ARF R Y+Y F + LD
Sbjct: 81 VNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEP-LDA 139
Query: 266 DAMHKAAQYLVGTHDF 281
+ MH+AAQ L+G +DF
Sbjct: 140 ERMHRAAQCLLGENDF 155
>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 = 56.8 bits (136), Expect = 1e-08
Identities = 65/497 (13%), Positives = 145/497 (29%), Gaps = 123/497 (24%)
Query: 13 KSSVVALLAE----------------VGFDAADNAALETLVEICQACKYTCLTVTAKVLS 56
K+ V + + + LE L ++ + S
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLL-----YQIDPNWTSRS 217
Query: 57 SHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAVTSVIGLVIKEVGGLSH----DF- 111
H K RI + + + Y+ + LV+ V +
Sbjct: 218 DHSSNIK-LRIHSIQ------AELRRLLKSKPYENCL-----LVLLNVQNAKAWNAFNLS 265
Query: 112 CE-LANRQQPMLADVLLALIELGIPI-HGLDTYAKRPMRTVF-----------PPVAPST 158
C+ L + + D L A I + H T ++++ P +T
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT 325
Query: 159 QPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNEL- 217
P+ LSI+ ++ + ++ +T I S L + E
Sbjct: 326 NPRRLSIIAESIRD-GLATWDNWK--------HVNCDKLTTIIESSL----NVLEPAEYR 372
Query: 218 PYLKML-----NNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAA 272
L + ++P + + W V + Y ++
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL------VEKQ----PK 422
Query: 273 QYLVGTHD--FRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVVDSEPSF--- 327
+ + K+ N + +V H + + + +D+ + +
Sbjct: 423 ESTISIPSIYLELKVKLE--NEYALHRSIVDHYNIPKTFDS---DDLIPPYLDQYFYSHI 477
Query: 328 ----KKGQGNEKPEIIQQL-VD---IEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFL 379
K + E+ + + + +D +E+ +I+ W+++G+ +L+ L
Sbjct: 478 GHHLKNIEHPERMTLFRMVFLDFRFLEQ--KIRHDSTAWNASGS-----------ILNTL 524
Query: 380 AWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESKCTMGDLDINHLIEGEF 439
+ Y+ + + L + +LP + E + + SK T D+ +
Sbjct: 525 QQLKFYKPYICDNDPKYERLVNAIL-DFLPKIEENL---IC-SKYT----DLLRIA---L 572
Query: 440 DSRPGRILSETGKLAPR 456
+ I E K R
Sbjct: 573 MAEDEAIFEEAHKQVQR 589
>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 = 40.4 bits (94), Expect = 0.002
Identities = 70/422 (16%), Positives = 119/422 (28%), Gaps = 148/422 (35%)
Query: 155 APSTQPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEE--S 212
A ST+P L++ ++ H +P + + + L P E +
Sbjct: 3 AYSTRP--LTLSHGSLE--HVLLVPTAS--------FFIASQLQEQFNKILPEPTEGFAA 50
Query: 213 DDN-----EL--PYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQA---G 262
DD EL +L +++ + P K L F G
Sbjct: 51 DDEPTTPAELVGKFLGYVSSLVE-----------PSKVGQFDQVLNLCLTE-FENCYLEG 98
Query: 263 LDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAG------VTSA-WQNVQFN 315
DI H A L+ +D + + + N+ A SA ++ V
Sbjct: 99 NDI---HALAAKLLQENDTTLVKTKEL---IKNYITARIMAKRPFDKKSNSALFRAVGEG 152
Query: 316 DIKEVVDSEPSFKKGQGNEKPEI-IQQLVDI-EKYPRI------KSAQFPWS-STGATTP 366
+ + V F GQGN + ++L D+ + Y + SA+
Sbjct: 153 NAQLVA----IFG-GQGN--TDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDA 205
Query: 367 NELFRRVFLLSFLAWVD--------QYRIRQTAHCNI------FTNLCTFYVPTYLPSLG 412
++F + + L W++ Y I L + V
Sbjct: 206 EKVFTQGL--NILEWLENPSNTPDKDY----LLSIPISCPLIGVIQLAHYVV-------- 251
Query: 413 EMIKDTVRESKCTMGDLDINHLIEG---------------------EFD---SRPGRILS 448
T + T G+L ++G F + +L
Sbjct: 252 -----TAKLLGFTPGEL--RSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLF 304
Query: 449 ETGKLAPRVFQHFSEHSLRLS----SDTMTEQCPRVRVPM--------------VTEVNK 490
G R ++ + SL S S E P PM V + N
Sbjct: 305 FIGV---RCYEAYPNTSLPPSILEDSLENNEGVPS---PMLSISNLTQEQVQDYVNKTNS 358
Query: 491 HL 492
HL
Sbjct: 359 HL 360
Score = 32.3 bits (73), Expect = 0.42
Identities = 66/460 (14%), Positives = 119/460 (25%), Gaps = 193/460 (41%)
Query: 7 TNRSLLKSSVVALLAEVGFDAA-----------DNAALETLVEICQACKYTCLTVTAKVL 55
R K S AL VG A + E L ++ Y T VL
Sbjct: 133 AKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDL-----YQ----TYHVL 183
Query: 56 SSHKEREKEDRIGESEGTCAE-VTSVEDC---YQR-----NWYKRAVTS----------- 95
D I S T +E + + D + + W + +
Sbjct: 184 -------VGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPI 236
Query: 96 ---VIGL-------VIKEVGGLSHDFCELANRQQPML---ADVLLALIELGIPIHGLDTY 142
+IG+ V ++ G + EL + + ++ A+ I D++
Sbjct: 237 SCPLIGVIQLAHYVVTAKLLGFTPG--ELRSYLKGATGHSQGLVTAVA-----IAETDSW 289
Query: 143 ------AKRPMRTVF----------PPVAPSTQPKPLSILQ----AGVKQPHPPHIPPYL 182
++ + +F P + P SIL+ P P
Sbjct: 290 ESFFVSVRKAITVLFFIGVRCYEAYPNTSL-----PPSILEDSLENNEGVPSP------- 337
Query: 183 PLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIK---------- 232
L I + + Y+ N++LP +
Sbjct: 338 ---------------MLSIS------NLTQEQVQ-DYVNKTNSHLPAGKQVEISLVNGAK 375
Query: 233 --VVAWSPVPEKYS-ARFDCLFRNYKYWFPQAGLD-------------------IDA--- 267
VV+ P P+ S + R K +GLD + +
Sbjct: 376 NLVVS-GP-PQ--SLYGLNLTLRKAK---APSGLDQSRIPFSERKLKFSNRFLPVASPFH 428
Query: 268 ---MHKAAQYLVG--------------------THDFRNLCKMNVGNGVVNFKRLVTHAG 304
+ A+ + T D +L ++ G+ +
Sbjct: 429 SHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLS-GSISERIVDCIIRLP 487
Query: 305 VTSAWQNVQFNDIKEVVDSEPSFKKGQGNEKPEIIQQLVD 344
V W+ ++D P G G + + D
Sbjct: 488 VK--WETTTQFKATHILDFGPGGASGLGV----LTHRNKD 521
Score = 29.2 bits (65), Expect = 3.8
Identities = 8/38 (21%), Positives = 14/38 (36%)
Query: 27 AADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKE 64
A D AL+T+ + K + + S E +
Sbjct: 1856 AGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEG 1893
Score = 28.5 bits (63), Expect = 6.4
Identities = 29/140 (20%), Positives = 37/140 (26%), Gaps = 58/140 (41%)
Query: 17 VALLA-EVGFDAADNAALETLVE--ICQACK---------YTCLTVTAKVLS-------- 56
AL E AA E L + A Y L A V+S
Sbjct: 1734 PALTLMEK-------AAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVV 1786
Query: 57 -----SHKEREKEDRIGESE--------GTCAEVTSVEDCYQRNWYKRAVTSVIGLVIKE 103
+ + D +G S G A S E A+ V+ V K
Sbjct: 1787 FYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQE----------ALQYVVERVGKR 1836
Query: 104 VGGLSHDFCELAN----RQQ 119
G E+ N QQ
Sbjct: 1837 TGW----LVEIVNYNVENQQ 1852
>1ur3_M Hypothetical oxidoreductase YDHF; NADP binding, aldo-keto
reductase; 2.57A {Escherichia coli} SCOP: c.1.7.1 PDB:
1og6_A*
Length = 319
Score = 33.0 bits (76), Expect = 0.20
Identities = 8/50 (16%), Positives = 17/50 (34%), Gaps = 7/50 (14%)
Query: 189 HAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSP 238
+ + + T ++ D L L+ L ++ +AWS
Sbjct: 190 QSRLPFTLATNQVEISPVHQPLL-LDGTLDQLQQLR------VRPMAWSC 232
>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 = 28.0 bits (61), Expect = 5.1
Identities = 6/17 (35%), Positives = 8/17 (47%), Gaps = 2/17 (11%)
Query: 403 YVPTYLPSLGEMIKDTV 419
Y P+L IK T+
Sbjct: 32 YADDSAPALA--IKATM 46
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
0.320 0.135 0.411
Gapped
Lambda K H
0.267 0.0482 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,553,209
Number of extensions: 458154
Number of successful extensions: 942
Number of sequences better than 10.0: 1
Number of HSP's gapped: 931
Number of HSP's successfully gapped: 13
Length of query: 496
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 399
Effective length of database: 3,993,456
Effective search space: 1593388944
Effective search space used: 1593388944
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: 59 (27.1 bits)