RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9121
(203 letters)
>2i7x_A Protein CFT2; polyadenylation, metallo-B-lactamase, PRE-mRNA
processing, artemis, V(D)J recombination, double-strand
break repair; 2.50A {Saccharomyces cerevisiae} SCOP:
d.157.1.10
Length = 717
Score = 54.8 bits (131), Expect = 4e-09
Identities = 22/204 (10%), Positives = 52/204 (25%), Gaps = 76/204 (37%)
Query: 4 YSLSSHPNKACYILRFKEMTIMLDCGLCALPLMHFLPLPIIPTAKFNNLPSWIPRECTEA 63
++RF +T+++D G +
Sbjct: 7 CCDDGSGTTVGSVVRFDNVTLLIDPG------WNP------------------------- 35
Query: 64 QLEGELKECCGKVFVDSAPEFQPPLSQLVDFSEVNMILISNY----LSMLALPFITEGT- 118
KV + ++ E+++I++S L +L + +
Sbjct: 36 ----------SKVSYEQCIKYWEK-----VIPEIDVIILSQPTIECLGAHSLLYYNFTSH 80
Query: 119 -GFEGVVYATEPTLQIGKFYLEELVQYIEKTPKLTSASHWKDISHLISPFSEDIKPRSWR 177
VYAT P + +G+ + S +
Sbjct: 81 FISRIQVYATLPVINLGRVSTIDSYA------------------------SAGVIGPYDT 116
Query: 178 QLYNLQSVYASLARVQMVGYDEKL 201
+L+ + S + + Y + +
Sbjct: 117 NKLDLEDIEISFDHIVPLKYSQLV 140
>2i7t_A Cleavage and polyadenylation specificity factor 73 kDa subunit;
metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J
recombination; 2.10A {Homo sapiens} SCOP: d.157.1.10
PDB: 2i7v_A
Length = 459
Score = 41.8 bits (99), Expect = 7e-05
Identities = 36/190 (18%), Positives = 61/190 (32%), Gaps = 78/190 (41%)
Query: 14 CYILRFKEMTIMLDCGLCALPLMHFLPLPIIPTAKFNNLPSWIPRECTEAQLEGELKECC 73
C IL FK IMLDCG +H
Sbjct: 27 CIILEFKGRKIMLDCG------IHP----------------------------------- 45
Query: 74 GKVFVDSAPEFQPPLSQLVDFSEVNMILISNYLSML----ALPFITEGTGFEGVVYATEP 129
G +D+ P D +E++++LIS+ L ALP+ + T F+G + T
Sbjct: 46 GLEGMDALPYIDLI-----DPAEIDLLLISH--FHLDHCGALPWFLQKTSFKGRTFMTHA 98
Query: 130 TLQIGKFYLEELVQYIEKTPKLTSASHWKDISHLISPFSEDIKPRSWRQLYNLQSVYASL 189
T I ++ L + V+ + LY + S+
Sbjct: 99 TKAIYRWLLSDYVKVSNISAD--------------------------DMLYTETDLEESM 132
Query: 190 ARVQMVGYDE 199
+++ + + E
Sbjct: 133 DKIETINFHE 142
>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp
family, KH domain, ribonuclease, ME beta-lactamase
superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB:
3af6_A*
Length = 651
Score = 41.2 bits (97), Expect = 1e-04
Identities = 24/195 (12%), Positives = 53/195 (27%), Gaps = 78/195 (40%)
Query: 14 CYILRFKEMTIMLDCGLCALPLMHFLPLPIIPTAKFNNLPSWIPRECTEAQLEGELKECC 73
+++ E +++D G ++ + ++
Sbjct: 204 ALLVQTDESFVLVDFG------VN-------VAMLNDPYKAF------------------ 232
Query: 74 GKVFVDSAPEF-QPPLSQLVDFSEVNMILISNYLSMLA-------LPFITEGTGFEGVVY 125
P F P ++ ++ I+I++ A LP++ F+G +Y
Sbjct: 233 --------PHFDAPEFQYVLREGLLDAIIITH-----AHLDHCGMLPYLFRYNLFDGPIY 279
Query: 126 ATEPTLQIGKFYLEELVQYIEKTPKLTSASHWKDISHLISPFSEDIKPRSWRQLYNLQSV 185
T PT + + D + S P LY + +
Sbjct: 280 TTPPTRDLMVLLQK-------------------DFIEIQQ--SNGQDP-----LYRPRDI 313
Query: 186 YASLARVQMVGYDEK 200
+ + Y E
Sbjct: 314 KEVIKHTITLDYGEV 328
>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor;
hydrolase, KH, metallo-beta-lactamase; 3.10A
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 636
Score = 36.9 bits (86), Expect = 0.003
Identities = 27/193 (13%), Positives = 51/193 (26%), Gaps = 82/193 (42%)
Query: 14 CYILRFKEMTIMLDCGLCALPLMHFLPLPIIPTAKFNNLPSWIPRECTEAQLEGELKECC 73
C L+ ++LDCG ++ +
Sbjct: 195 CLYLQTPNSRVLLDCG------VNV----------------------------AGGDD-- 218
Query: 74 GKVFVDSAPEFQPPLSQLVDFSEVNMILISNYLSMLA-------LPFITEGTGFEGVVYA 126
+S P P ++ ++I++ A LP++ G++G VY
Sbjct: 219 ----KNSYPYLNVP---EFTLDSLDAVIITH-----AHLDHSGFLPYLYH-YGYDGPVYC 265
Query: 127 TEPTLQIGKFYLEELVQYIEKTPKLTSASHWKDISHLISPFSEDIKPRSWRQLYNLQSVY 186
T PT + D + E +N++ V
Sbjct: 266 TAPTRDLMTLLQL-------------------DHIDIAHREDE-------PLPFNVKHVK 299
Query: 187 ASLARVQMVGYDE 199
S+ + Y E
Sbjct: 300 KSVKHTITLDYGE 312
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit;
hydrolase, metallo-beta-lactamase, beta-CAsp, RNA
processing; 2.59A {Methanosarcina mazei}
Length = 640
Score = 36.5 bits (85), Expect = 0.005
Identities = 26/195 (13%), Positives = 55/195 (28%), Gaps = 83/195 (42%)
Query: 14 CYILRFKEMTIMLDCGLCALPLMHFLPLPIIPTAKFNNLPSWIPRECTEAQLEGELKECC 73
C++L E I++DCG ++ E
Sbjct: 199 CFLLSTPESRILIDCG------VN--------------------------VGSDE----- 221
Query: 74 GKVFVDSAPEFQPPLSQLVDFSEVNMILISNYLSMLA-------LPFITEGTGFEGVVYA 126
+ P P + ++++ +++++ A +P + + G+EG VY
Sbjct: 222 -----NMTPYLYVPE--VFPLNQIDAVIVTH-----AHLDHQGLVPLLFK-YGYEGPVYC 268
Query: 127 TEPTLQIGKFYLEELVQYIEKTPKLTSASHWKDISHLISPFSEDIKPRSWRQLYNLQSVY 186
T PT + D + + + + Y V
Sbjct: 269 TPPTRDLMVLLQL-------------------DYIDVAAKEGK-------KIPYESGMVA 302
Query: 187 ASLARVQMVGYDEKL 201
+L + Y+E
Sbjct: 303 KTLKHTIPLDYEEVT 317
>3iek_A Ribonuclease TTHA0252; metallo beta lactamase fold, endonuclease,
hydrolase, metal- nuclease, RNA-binding, rRNA
processing; HET: FLC; 2.05A {Thermus thermophilus} PDB:
2dkf_A* 3iel_A* 3iem_A* 2zdf_A* 3idz_A* 2zdd_A* 3ie0_A*
2zde_A* 3ie1_A* 2zdw_A* 3a4y_A* 2yvd_A* 3ie2_A*
Length = 431
Score = 33.2 bits (77), Expect = 0.041
Identities = 8/40 (20%), Positives = 12/40 (30%), Gaps = 14/40 (35%)
Query: 14 CYILRFKEMTIMLDCGLCALPLMH--------FLPLPIIP 45
++L ++LDCG M P P
Sbjct: 16 AHLLLAGGRRVLLDCG------MFQGKEEARNHAPFGFDP 49
Score = 30.9 bits (71), Expect = 0.23
Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 110 ALPFITEGTGFEGVVYATEPTLQI 133
LP + G+ G VYAT T+ +
Sbjct: 67 RLPKLFR-EGYRGPVYATRATVLL 89
>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 = 30.7 bits (68), Expect = 0.20
Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 10/26 (38%)
Query: 62 EAQ----LEGELKECCGKVFV-DSAP 82
E Q L+ LK ++ DSAP
Sbjct: 18 EKQALKKLQASLK-----LYADDSAP 38
>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 = 31.4 bits (70), Expect = 0.22
Identities = 26/134 (19%), Positives = 45/134 (33%), Gaps = 24/134 (17%)
Query: 4 YS-LSSHPNKACYILRFKEMT-IMLDCGLCALPLMHFLPLPIIPTAKFNNLPSWIPRECT 61
YS + H + R + LD FL I + N I
Sbjct: 474 YSHIGHHLKNIEHPERMTLFRMVFLD--------FRFLEQKIRHDSTAWNASGSI----- 520
Query: 62 EAQLEGELKECCGKVFVDSAPEFQPPLSQLVDFS---EVNMILISNYLSMLALPFITEGT 118
+LK D+ P+++ ++ ++DF E N+I S Y +L + + E
Sbjct: 521 -LNTLQQLKFY-KPYICDNDPKYERLVNAILDFLPKIEENLI-CSKYTDLLRIALMAED- 576
Query: 119 GFEGVVYATEPTLQ 132
E + +Q
Sbjct: 577 --EAIFEEAHKQVQ 588
Score = 28.3 bits (62), Expect = 2.3
Identities = 21/121 (17%), Positives = 41/121 (33%), Gaps = 30/121 (24%)
Query: 77 FVDSAPEFQPPLSQLVD-FSEVNMI-LISNYLSMLA--LPFITEGTGFEGVVYATEPTL- 131
F+ +A L + + L+ YL LP E V T P
Sbjct: 280 FLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP--RE-------VLTTNPRRL 330
Query: 132 -QIGKFYLEELVQYIEKTPKLTSASHWKDI-----SHLISPFSEDIKPRSWRQLYNLQSV 185
I + + L + +WK + + +I ++P +R++++ SV
Sbjct: 331 SIIAESIRDGLATW----------DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380
Query: 186 Y 186
+
Sbjct: 381 F 381
>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 = 27.7 bits (61), Expect = 3.0
Identities = 28/135 (20%), Positives = 44/135 (32%), Gaps = 52/135 (38%)
Query: 36 MHFLPL--P------------IIPTAKFNNLPSW------IPRECTE-----AQLEGELK 70
FLP+ P I NN+ S+ IP T L G +
Sbjct: 418 NRFLPVASPFHSHLLVPASDLINKDLVKNNV-SFNAKDIQIPVYDTFDGSDLRVLSGSIS 476
Query: 71 E------CCGKVFVDSAPEFQPPLSQLVDF-----SEVNMILISNYLSMLALPFITEGTG 119
E V ++ +F+ + ++DF S + ++ N +GTG
Sbjct: 477 ERIVDCIIRLPVKWETTTQFKA--THILDFGPGGASGLGVLTHRN----------KDGTG 524
Query: 120 FEGVVYATEPTLQIG 134
V+ A TL I
Sbjct: 525 VR-VIVAG--TLDIN 536
Score = 26.6 bits (58), Expect = 9.0
Identities = 27/141 (19%), Positives = 46/141 (32%), Gaps = 57/141 (40%)
Query: 101 LISNYLSMLAL---PFITEGTG--FEGV------VYATEPTLQIGKF--------YLEEL 141
LI NY++ + PF + F V + A F Y EEL
Sbjct: 122 LIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAI--------FGGQGNTDDYFEEL 173
Query: 142 VQYIEKTPK------LTSASHWKDISHLISP-------FSEDIKPRSWRQLYN------- 181
+ + +T + ++ + +S LI F++ + W L N
Sbjct: 174 -RDLYQTYHVLVGDLIKFSA--ETLSELIRTTLDAEKVFTQGLNILEW--LENPSNTPDK 228
Query: 182 --LQSVYASL---ARVQMVGY 197
L S+ S +Q+ Y
Sbjct: 229 DYLLSIPISCPLIGVIQLAHY 249
>1vq8_O 50S ribosomal protein L18E; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: c.12.1.1 PDB: 1vq4_O*
1vq5_O* 1vq6_O* 1vq7_O* 1s72_O* 1vq9_O* 1vqk_O* 1vql_O*
1vqm_O* 1vqn_O* 1vqo_O* 1vqp_O* 1yhq_O* 1yi2_O* 1yij_O*
1yit_O* 1yj9_O* 1yjn_O* 1yjw_O* 2otj_O* ...
Length = 116
Score = 26.6 bits (59), Expect = 3.5
Identities = 9/46 (19%), Positives = 18/46 (39%), Gaps = 6/46 (13%)
Query: 137 YLEELVQYIEKTPKLTSASHWKDISHLISPFSEDIKPRSWRQLYNL 182
L L+ ++ + + + W D++ + KPR NL
Sbjct: 7 RLSSLIADLKSAARSSGGAVWGDVAERLE------KPRRTHAEVNL 46
>1zkp_A Hypothetical protein BA1088; zinc binding protein, structural
genomics, PSI, protein STRU initiative; 1.50A {Bacillus
anthracis str} SCOP: d.157.1.9
Length = 268
Score = 26.9 bits (60), Expect = 5.0
Identities = 10/52 (19%), Positives = 19/52 (36%), Gaps = 9/52 (17%)
Query: 1 MKVYSL---SSHPNK----ACYILRFKEMTIMLDCGLCALPLM--HFLPLPI 43
MK+ + P + Y+ +++DCG L + + P I
Sbjct: 25 MKMTVVGFWGGFPEAGEATSGYLFEHDGFRLLVDCGSGVLAQLQKYITPSDI 76
>1mn8_A Core protein P15; helical bundle, viral protein; 1.00A {Moloney
murine leukemia virus} SCOP: a.61.1.6
Length = 100
Score = 25.8 bits (56), Expect = 5.2
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 148 TPKLTSASHWKDISHLISPFSEDIKPRSWRQLYN 181
TP + HWKD+ + S D+K R W +
Sbjct: 8 TPLSLTLGHWKDVERIAHNQSVDVKKRRWVTFCS 41
>1uhu_A Product of riken cDNA 3110009E22; structural genomics, riken
structural genomics/proteomics initiative, RSGI, unknown
function; NMR {Mus musculus} SCOP: a.61.1.6
Length = 105
Score = 25.8 bits (56), Expect = 5.8
Identities = 10/34 (29%), Positives = 13/34 (38%)
Query: 148 TPKLTSASHWKDISHLISPFSEDIKPRSWRQLYN 181
TP + HW +I S +IK WR
Sbjct: 8 TPLSLTLDHWSEIRSRAHNLSVEIKKGPWRTFCA 41
>2qyb_A Membrane protein, putative; GAF domain, domain of putative membrane
protein, PSI-2, MCSG structural genomics; 2.40A
{Geobacter sulfurreducens pca}
Length = 181
Score = 25.8 bits (57), Expect = 7.9
Identities = 7/54 (12%), Positives = 18/54 (33%)
Query: 73 CGKVFVDSAPEFQPPLSQLVDFSEVNMILISNYLSMLALPFITEGTGFEGVVYA 126
G+ F+ + +F + ++ S +P +G G++
Sbjct: 75 IGEAFLSNRLQFVNDTQYMTKPLTRELMQKEGIKSFAHIPISRKGEPPFGILSV 128
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
0.322 0.138 0.424
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,080,462
Number of extensions: 169427
Number of successful extensions: 289
Number of sequences better than 10.0: 1
Number of HSP's gapped: 286
Number of HSP's successfully gapped: 25
Length of query: 203
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 114
Effective length of database: 4,216,824
Effective search space: 480717936
Effective search space used: 480717936
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 (21.9 bits)
S2: 55 (24.9 bits)