RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4278
(197 letters)
>3uek_A Poly(ADP-ribose) glycohydrolase; mammalian PArg, macrodomain; 1.95A
{Rattus norvegicus} PDB: 3uel_A*
Length = 588
Score = 166 bits (422), Expect = 4e-49
Identities = 84/166 (50%), Positives = 115/166 (69%), Gaps = 4/166 (2%)
Query: 20 QELDQLETDIFFKQLLPKIISLALRLPNVLQCGIPLLKAHSNHSITLSQLQIASLLANAF 79
+ L++ E ++ +LP ++ +AL LPN+ IPLLK NHS+T+SQ QIASLLANAF
Sbjct: 191 KVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLKQKMNHSVTMSQEQIASLLANAF 250
Query: 80 LCTYPRRNSNQPESQYANFPCINFSRLFQAQSSCVSEKLKCLINYFVRVTTKDPTGLVTY 139
CT+PRRN+ + +S+Y+++P INF+RLF+ +SS EKLK L YF RVT K PTGLVT+
Sbjct: 251 FCTFPRRNA-KMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTF 309
Query: 140 SRRYLPHSQLPHWGDSRRKLPDLFISSEGMIE-NQRGLLQVDFANK 184
+R+ L P W + L L ++ EG IE N RG+LQVDFAN+
Sbjct: 310 TRQSL--EDFPEWERCDKPLTRLHVTYEGTIEGNGRGMLQVDFANR 353
>4fc2_A Poly(ADP-ribose) glycohydrolase; mouse, PArg; 1.91A {Mus musculus}
Length = 521
Score = 163 bits (412), Expect = 4e-48
Identities = 84/166 (50%), Positives = 115/166 (69%), Gaps = 4/166 (2%)
Query: 20 QELDQLETDIFFKQLLPKIISLALRLPNVLQCGIPLLKAHSNHSITLSQLQIASLLANAF 79
+ L++ E ++ +LP ++ +AL LPN+ IPLLK NHS+T+SQ QIASLLANAF
Sbjct: 134 KVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLKQKMNHSVTMSQEQIASLLANAF 193
Query: 80 LCTYPRRNSNQPESQYANFPCINFSRLFQAQSSCVSEKLKCLINYFVRVTTKDPTGLVTY 139
CT+PRRN+ + +S+Y+++P INF+RLF+ +SS EKLK L YF RVT K PTGLVT+
Sbjct: 194 FCTFPRRNA-KMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTF 252
Query: 140 SRRYLPHSQLPHWGDSRRKLPDLFISSEGMIE-NQRGLLQVDFANK 184
+R+ L P W + L L ++ EG IE N RG+LQVDFAN+
Sbjct: 253 TRQSL--EDFPEWERCEKPLTRLHVTYEGTIEGNGRGMLQVDFANR 296
>4epp_A Poly(ADP-ribose) glycohydrolase; marco domain, PAR; HET: APR; 1.95A
{Tetrahymena thermophila} PDB: 4epq_A*
Length = 477
Score = 142 bits (358), Expect = 2e-40
Identities = 45/172 (26%), Positives = 78/172 (45%), Gaps = 11/172 (6%)
Query: 19 FQELDQLETDIFFKQLLPKIISLALRLPNVLQCGIPLLKAHSNHSITLSQLQIASLLANA 78
F++LD+ E F +Q +PKI L L++ Q + K + S+ +I+ ++
Sbjct: 95 FEQLDKEEQTYFLEQFIPKICQLVLKIKK-KQLKNQIPKESKIYEAAFSREEISYYVSCM 153
Query: 79 FLCTYPRRNSNQPESQYANFPCINFSRLFQAQSSCVSEKLKCLINYFVRV---TTKDPTG 135
FLC ++ Y +F I L Q + EK+KC Y + + K+
Sbjct: 154 FLCILKDQDR----KIYKDFRLIYLKDLVQQINIRRQEKIKCFYEYLKQALDFSEKESKE 209
Query: 136 LVTYSRRYLPH-SQLPHWGDSRR--KLPDLFISSEGMIENQRGLLQVDFANK 184
+V + R +W D + KL ++ ++ + +IE+ G LQVDFAN
Sbjct: 210 VVIFQRINCGQLEDYENWVDKLKAIKLKNVQLTDDKLIEDFPGTLQVDFANC 261
>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 = 37.3 bits (86), Expect = 0.002
Identities = 15/95 (15%), Positives = 29/95 (30%), Gaps = 25/95 (26%)
Query: 56 LKAHSNHSITLSQLQI-------------ASLLANAFLCTYPRR-----NSNQPESQ--- 94
+ A+S +TLS + AS L F P ++P +
Sbjct: 1 MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAEL 60
Query: 95 YANFPCINF--SRLFQAQSSCVSEKLKCLINYFVR 127
F + + S + ++ + L + F
Sbjct: 61 VGKF--LGYVSSLVEPSKVGQFDQVLNLCLTEFEN 93
Score = 30.8 bits (69), Expect = 0.31
Identities = 24/128 (18%), Positives = 37/128 (28%), Gaps = 43/128 (33%)
Query: 27 TDIFFKQLLPKIISLALRLPNVLQCGIPLLKAHSNHSITLSQLQIASLLANAFLCTYPRR 86
+++ +Q+ + LP Q I L+ N ++ SL L R+
Sbjct: 342 SNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPP---QSLYG---LNLTLRK 395
Query: 87 NSNQPESQYANFPCINFSRLFQAQSSCVSEKLKCLINYFVRVTTKDPTGLVTYSRRYLP- 145
+ P FS KLK +S R+LP
Sbjct: 396 AKAPSGLDQSRIP---FSE----------RKLK-------------------FSNRFLPV 423
Query: 146 ----HSQL 149
HS L
Sbjct: 424 ASPFHSHL 431
>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 = 34.1 bits (77), Expect = 0.028
Identities = 27/159 (16%), Positives = 53/159 (33%), Gaps = 31/159 (19%)
Query: 32 KQLLPKIISLAL-RLPNVLQCGIPLLKAHSNHSITLSQLQIASLLANAFLCT---YPRRN 87
K LL K + LP + P +++ IA + + L T + N
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNPRR-------LSI----IAESIRD-GLATWDNWKHVN 351
Query: 88 SNQP----ESQYANFPCINFSRLFQA-----QSSCVSEKLKCLINYFVRVTTKDPTGLVT 138
++ ES + ++F S+ + L L + V D +V
Sbjct: 352 CDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL--IWFDVIKSDVMVVVN 409
Query: 139 YSRRYLPHSQLPHWGDSRR-KLPDLFISSEGMIENQRGL 176
+Y S + +P +++ + +EN+ L
Sbjct: 410 KLHKY---SLVEKQPKESTISIPSIYLELKVKLENEYAL 445
>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 = 26.8 bits (58), Expect = 3.9
Identities = 10/41 (24%), Positives = 13/41 (31%), Gaps = 18/41 (43%)
Query: 20 QELDQLETDIFFKQLLPKIISLALRLPNVLQCGIPLL--KA 58
Q L +L+ SL L + P L KA
Sbjct: 20 QALKKLQA------------SLKLYADD----SAPALAIKA 44
>1q5n_A 3-carboxy-CIS,CIS-muconate cycloisomerase; CMLE, aromatic
degradation; 2.30A {Acinetobacter calcoaceticus} SCOP:
a.127.1.1
Length = 454
Score = 27.3 bits (61), Expect = 4.1
Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 151 HWGDSRRKLPDLFISSEGMIENQRGL---LQVDFANKSHHLEI 190
W LP++F + G +E + ++V+ N ++E
Sbjct: 323 AWHAEWLSLPEIFQLTAGALERTLDVLKGMEVNAENMHQNIEC 365
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 3cw1_A
Length = 231
Score = 26.1 bits (57), Expect = 6.8
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 115 SEKLKCLINYFVRVTTKD 132
S K+ I+Y +R +D
Sbjct: 6 SSKMLQHIDYRMRCILQD 23
>1re5_A 3-carboxy-CIS,CIS-muconate cycloisomerase; homotetramer, fumarase
class II cycloisomerase, molecular EV isomerase; HET:
CIT; 2.60A {Pseudomonas putida} SCOP: a.127.1.1
Length = 450
Score = 26.5 bits (59), Expect = 7.4
Identities = 9/43 (20%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 151 HWGDSRRKLPDLFISSEGMIENQRGL---LQVDFANKSHHLEI 190
W LPD+ G + + + ++VD A +L++
Sbjct: 319 LWHAEWETLPDICCLVSGALRQAQVIAEGMEVDAARMRRNLDL 361
>3c8t_A Fumarate lyase; structural genomics, PSI-2, protein structure
initiat YORK SGX research center for structural
genomics, nysgxrc; 2.20A {Mesorhizobium SP}
Length = 451
Score = 26.1 bits (58), Expect = 8.7
Identities = 8/43 (18%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 151 HWGDSRRKLPDLFISSEGMIENQRGL---LQVDFANKSHHLEI 190
W +P+ F + G++ + LQV +L+
Sbjct: 317 PWHLEWSAVPEGFAVASGILYQAEFMLGGLQVFPDRMRENLDH 359
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
0.323 0.137 0.413
Gapped
Lambda K H
0.267 0.0489 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,824,415
Number of extensions: 147214
Number of successful extensions: 205
Number of sequences better than 10.0: 1
Number of HSP's gapped: 196
Number of HSP's successfully gapped: 14
Length of query: 197
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 108
Effective length of database: 4,216,824
Effective search space: 455416992
Effective search space used: 455416992
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 (22.0 bits)
S2: 55 (25.5 bits)