RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4844
(254 letters)
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding,
exonucle binding, mitochondrion, rRNA processing; 3.00A
{Saccharomyces cerevisiae}
Length = 977
Score = 264 bits (676), Expect = 3e-82
Identities = 84/247 (34%), Positives = 136/247 (55%), Gaps = 13/247 (5%)
Query: 13 VMKIVREHYLRDDLSCGSELCLACDTKEAILDKIPTSSKAILDKIPTSSSKKYMEPHYLL 72
KIVREHYLR D+ C S C C + ++ + + HY++
Sbjct: 8 ATKIVREHYLRSDIPCLSRSCTKC--PQIVVPDAQNELPKFILSDSPLELSAPIGKHYVV 65
Query: 73 LDTNIILEQIDILEEP-TLCNVILVQTILQEVKHRSSSVYKRLKDLI--SNPSRKFYVFV 129
LDTN++L+ ID+LE P +VI+ Q +L EV+++S VY RL+ L S+ ++F VF
Sbjct: 66 LDTNVVLQAIDLLENPNCFFDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDHKRFIVFH 125
Query: 130 NEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHL-ESAVRVILLSEDVRNRDLA---T 185
NE T+VE+ P E++NDRNDRA+R+ WY EHL + V+L++ D NR+ A
Sbjct: 126 NEFSEHTFVERLPNETINDRNDRAIRKTCQWYSEHLKPYDINVVLVTNDRLNREAATKEV 185
Query: 186 QSGLLTSSIEGYISTLSNGEPLLDKLSKKEAVVETSVKDS----LYPLHATPSEIHAGIK 241
+S ++T S+ YI L N + + D + + ++ + +D+ +P + + + + G+K
Sbjct: 186 ESNIITKSLVQYIELLPNADDIRDSIPQMDSFDKDLERDTFSDFTFPEYYSTARVMGGLK 245
Query: 242 NQSLLQG 248
N L QG
Sbjct: 246 NGVLYQG 252
>2dok_A Telomerase-binding protein EST1A; telomerase-associated protein,
unknown function; 1.80A {Homo sapiens} PDB: 2hww_A
2hwx_A
Length = 186
Score = 45.5 bits (107), Expect = 3e-06
Identities = 23/175 (13%), Positives = 50/175 (28%), Gaps = 38/175 (21%)
Query: 68 PHYLLLDTNIILEQIDILE---EPTLCNVILVQTILQEV-----KHRSSSVYKRLKDLIS 119
P +L+ DTN ++ + L E +++ ++ E+ + ++
Sbjct: 12 PLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGGYARVVQ 71
Query: 120 NPSRKFYVFVNEHH-----------------YETYVEQEPGESVNDRNDRALRRVATWYE 162
+RK F+ + E ND + Y
Sbjct: 72 EKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYC 131
Query: 163 EH-------------LESAVRVILLSEDVRNRDLATQSGLLTSSIEGYISTLSNG 204
+ + V+LL++D R A + I +++ G
Sbjct: 132 KDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQVG 186
>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 = 43.3 bits (101), Expect = 5e-05
Identities = 48/287 (16%), Positives = 87/287 (30%), Gaps = 78/287 (27%)
Query: 11 WLVMKIVREHYLRDDLSCGSELCLACDTKEAILDKIPTSSKAILDKIPTSSSKKYMEPHY 70
WL +K L +L D ++ K + I + Y
Sbjct: 186 WLNLKNCNSP--ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPY 243
Query: 71 ----LLLDTNI----ILEQIDILEEPTLCNVILVQTILQEVKHRSSSVYKRLKDLISNPS 122
L+L N+ ++ C IL+ T R V D +S +
Sbjct: 244 ENCLLVLL-NVQNAKAWNAFNLS-----CK-ILLTT-------RFKQVT----DFLSAAT 285
Query: 123 RKFYVFVNEHHYETYVEQE------------------------P------GESVNDRNDR 152
+HH T E P ES+ D
Sbjct: 286 TT--HISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT 343
Query: 153 A--LRRVATW-YEEHLESAVRVILLSEDVRNR--DLAT--QSGLLTSSIEGYISTL---- 201
+ V +ES++ V L + R L+ S + + + +S +
Sbjct: 344 WDNWKHVNCDKLTTIIESSLNV-LEPAEYRKMFDRLSVFPPSAHIPTIL---LSLIWFDV 399
Query: 202 --SNGEPLLDKLSKKEAVVETSVKDSLYPLHATPSEIHAGIKNQSLL 246
S+ +++KL K ++VE K+S + + E+ ++N+ L
Sbjct: 400 IKSDVMVVVNKLHKY-SLVEKQPKESTISIPSIYLELKVKLENEYAL 445
Score = 38.3 bits (88), Expect = 0.002
Identities = 32/220 (14%), Positives = 65/220 (29%), Gaps = 63/220 (28%)
Query: 28 CG-SELCLACDTKEAILDKIPTSSKAILDKIPTS----SSKKYMEPHYLLLDTNIILEQI 82
G + +A D S + K+ + K P +L +L QI
Sbjct: 161 SGKT--WVALDV---------CLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209
Query: 83 DILEEPTLCNVILVQTILQEVKHRSSSVYKRLKDLISNPSRKFYVFVNEHHYETYVEQEP 142
D N +K R S+ L+ L+ + + + V
Sbjct: 210 D-------PNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV------------- 249
Query: 143 GESVNDRNDRALRRVATWYEEHLES---AVRVILLSEDVRNRDLATQSGLLTSSIEGYIS 199
L V + + + +++L + + D + + S++ +
Sbjct: 250 -----------LLNV--QNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSM 296
Query: 200 TLSNGEPLLDKLSKKEAVVETSVKDSLYPLHATPSEIHAG 239
TL+ E + L K ++ +D P E+
Sbjct: 297 TLTPDE-VKSLLLK---YLDCRPQDL-------PREVLTT 325
Score = 37.9 bits (87), Expect = 0.003
Identities = 27/202 (13%), Positives = 52/202 (25%), Gaps = 69/202 (34%)
Query: 69 HYLLLDTNII-LEQIDILE--EPTL-----CNVIL-----------VQTILQEVKHRSSS 109
H++ +T + DIL E C + + I+ K S
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMS-KDAVSG 63
Query: 110 VYKRLKDLISNPSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHLESAV 169
+ L+S FV E Y +
Sbjct: 64 TLRLFWTLLSKQEEMVQKFVEEVLRINY---------------------KF--------- 93
Query: 170 RVILLSEDVRNRDLATQSGLLTSSIEGYISTLSNGEPLLDKL--SKKEAVVETSVKDSLY 227
L ++ Q ++T L N + K S+ + ++ ++ +L
Sbjct: 94 ----LMSPIKTEQR--QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLK--LRQALL 145
Query: 228 PLHATPSEIHAGIKNQSLLQGM 249
L + L+ G+
Sbjct: 146 EL-----RPAKNV----LIDGV 158
Score = 28.7 bits (63), Expect = 2.5
Identities = 36/213 (16%), Positives = 74/213 (34%), Gaps = 62/213 (29%)
Query: 6 VQSSVWL------VMKIVREHYLRDDLSCGSELCLACDTKEAI-------------LDKI 46
+ S +W VM +V + + KE+ L+
Sbjct: 391 LLSLIWFDVIKSDVMVVVNK--------LHKYSLVEKQPKESTISIPSIYLELKVKLENE 442
Query: 47 PTSSKAILDKIPTSSSKKYMEPHYLLLDT------NII---LEQIDILEEPTLCNVILV- 96
++I+D + K + + L+ + I L+ I+ E TL ++ +
Sbjct: 443 YALHRSIVDHY--NIPKTF-DSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLD 499
Query: 97 -QTILQEVKH------RSSSVYKRLKDLISNPSRKF--YVFVNEHHYETYVE------QE 141
+ + Q+++H S S+ L+ L + + Y+ N+ YE V +
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTLQQL-----KFYKPYICDNDPKYERLVNAILDFLPK 554
Query: 142 PGESVNDRNDRALRRVATWYEEH--LESAVRVI 172
E++ L R+A E+ E A + +
Sbjct: 555 IEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587
>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA
degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A
{Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5
b.40.4.5 b.40.4.16
Length = 760
Score = 32.3 bits (74), Expect = 0.17
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 223 KDSLYPLHATPSEIHAGIKNQSLLQGM 249
D +P + + + + G+KN L QG
Sbjct: 10 SDFTFPEYYSTARVMGGLKNGVLYQGN 36
>2dg7_A Putative transcriptional regulator; helix-turn-helix motif, TETR
family, gene regulation; 2.30A {Streptomyces coelicolor}
Length = 195
Score = 29.6 bits (67), Expect = 0.65
Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 3/54 (5%)
Query: 139 EQEPGESVNDRNDRALRRVATWYEEHLESAV---RVILLSEDVRNRDLATQSGL 189
+PG + A+ +V +E A VI S +++ R+ + +
Sbjct: 72 AADPGAAPLTAVLDAMSQVGAQLVAQVEGAAQRRAVIDASPELQERERTKSAAI 125
>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+
protein; 2.10A {Human papillomavirus type 18} SCOP:
c.37.1.20
Length = 212
Score = 29.8 bits (67), Expect = 0.72
Identities = 9/63 (14%), Positives = 20/63 (31%)
Query: 28 CGSELCLACDTKEAILDKIPTSSKAILDKIPTSSSKKYMEPHYLLLDTNIILEQIDILEE 87
+++ + D T + LD P S +K+ L ++ I ++
Sbjct: 102 TDTKVAMLDDATTTCWTYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKD 161
Query: 88 PTL 90
Sbjct: 162 NRW 164
>3k8x_A Acetyl-COA carboxylase; transferase, carboxyltransferase, AC
tepraloxydim, ATP-binding, biotin, fatty acid
biosynthesis; HET: B89; 2.30A {Saccharomyces cerevisiae}
PDB: 1w2x_A* 3h0s_A* 3h0j_A* 3h0q_A* 1od2_A* 1od4_A*
3pgq_A* 3tvu_A* 3tv5_A* 3tvw_A* 3tz3_A* 1uyr_A* 1uys_A*
1uyt_A 1uyv_A
Length = 758
Score = 29.8 bits (67), Expect = 0.94
Identities = 25/116 (21%), Positives = 45/116 (38%), Gaps = 20/116 (17%)
Query: 108 SSVYKRLKDLISNPSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHLES 167
+ KRL + SR + SV+ +DR VATW EE+ ++
Sbjct: 658 EYLIKRLSHQVGEASRL--------EKIARIRSWYPASVDHEDDRQ---VATWIEENYKT 706
Query: 168 AVRVILLSEDVRNRDLATQ-SGLLTSSIEGYISTLSNGEPLLDKLS--KKEAVVET 220
+ + ++ A + + S + I LS ++ LS KE +++T
Sbjct: 707 LDDKL---KGLKLESFAQDLAKKIRSDHDNAIDGLSE---VIKMLSTDDKEKLLKT 756
>1gnw_A Glutathione S-transferase; herbicide detoxification; HET: GTX;
2.20A {Arabidopsis thaliana} SCOP: a.45.1.1 c.47.1.5
PDB: 1bx9_A*
Length = 211
Score = 29.1 bits (66), Expect = 1.1
Identities = 8/42 (19%), Positives = 15/42 (35%)
Query: 125 FYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHLE 166
E +++ E+V + L +V YE L+
Sbjct: 114 ASKLAFEQIFKSIYGLTTDEAVVAEEEAKLAKVLDVYEARLK 155
>2rae_A Transcriptional regulator, ACRR family protein; TETR/ACRR family
transcriptional regulator, structural genom 2, RHA08332,
MCSG; 2.20A {Rhodococcus SP}
Length = 207
Score = 28.9 bits (65), Expect = 1.3
Identities = 7/54 (12%), Positives = 15/54 (27%), Gaps = 3/54 (5%)
Query: 139 EQEPGESVNDRNDRALRRVATWYEEHLESAV---RVILLSEDVRNRDLATQSGL 189
Q + D AL + + + +IL ++ + G
Sbjct: 82 AQPDDIPIVDGLTAALLQFNAFPASEEINHRKRMGLILRVPALQAYSVVMYEGW 135
>2nra_C PI protein; protein-DNA complex, DNA replication, replication-DNA
comple; 3.10A {Escherichia coli} SCOP: a.4.5.10 a.4.5.10
Length = 276
Score = 28.2 bits (62), Expect = 2.9
Identities = 13/110 (11%), Positives = 29/110 (26%), Gaps = 2/110 (1%)
Query: 76 NIILEQIDILEEPTLCNV--ILVQTILQEVKHRSSSVYKRLKDLISNPSRKFYVFVNEHH 133
+ L ID E V I + + K S Y++LK+ +
Sbjct: 37 YMALALIDSKEPLERGRVFKIRAEDLAALAKITPSLAYRQLKEGGKLLGASKISLRGDDI 96
Query: 134 YETYVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDL 183
E + + ++ + W + + + +
Sbjct: 97 IALAKELNLLSTAKNSSEELDLNIIEWIAYSPDEGYLSLKFTRTIEPYIS 146
>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA
translocation, nucleotide-binding, DNA-binding; 3.00A
{Bovine papillomavirus type 1} PDB: 2gxa_A*
Length = 305
Score = 27.9 bits (62), Expect = 3.4
Identities = 11/54 (20%), Positives = 18/54 (33%)
Query: 37 DTKEAILDKIPTSSKAILDKIPTSSSKKYMEPHYLLLDTNIILEQIDILEEPTL 90
D A T + LD P S +K+ + ++ ID+ E
Sbjct: 179 DATHACWRYFDTYLRNALDGYPVSIDRKHKAAVQIKAPPLLVTSNIDVQAEDRY 232
>3zvr_A Dynamin-1; hydrolase, DRP1, DRP, endocytosis, mitochondrial
fission, GT stalk, PH, BSE, membrane fission; HET: 1PE;
3.10A {Rattus norvegicus} PDB: 3snh_A
Length = 772
Score = 27.5 bits (60), Expect = 5.3
Identities = 12/60 (20%), Positives = 24/60 (40%)
Query: 77 IILEQIDILEEPTLCNVILVQTILQEVKHRSSSVYKRLKDLISNPSRKFYVFVNEHHYET 136
+ +Q+ L+EP++ V +V + L + S ++ L R + E T
Sbjct: 432 TVKKQVQKLKEPSIKCVDMVVSELTSTIRKCSEKLQQYPRLREEMERIVTTHIREREGRT 491
>3dcf_A Transcriptional regulator of the TETR/ACRR family; YP_290855.1,
structural genomics, joint center for structural
genomics, JCSG; 2.50A {Thermobifida fusca YX}
Length = 218
Score = 26.9 bits (60), Expect = 5.8
Identities = 11/90 (12%), Positives = 29/90 (32%), Gaps = 8/90 (8%)
Query: 83 DILEEPTLCNVIL--VQTILQEVKHRSSSVYKRLKDLISNPSRKFYVFVNEHHYETYVEQ 140
D+L + N I+ + S +R+ L+ + + + +
Sbjct: 77 DVLFA--IVNSIVDEALERFHAIAAGPGSPGERIHALL----VEHTRTILRNLDANTLFY 130
Query: 141 EPGESVNDRNDRALRRVATWYEEHLESAVR 170
++ +R +R+ Y E ++
Sbjct: 131 NERGLLSPEREREMRKREREYTEIMQRLYA 160
>3ljb_A Interferon-induced GTP-binding protein MX1; four-helix-bundle,
antiviral protein; 2.40A {Homo sapiens}
Length = 271
Score = 26.5 bits (58), Expect = 8.1
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 76 NIILEQIDILEEPT---LCNVI-LVQTILQEVKHRSSSVYKRLKDLISNPSRKF 125
I+ +QI LEEP L V +V+ +V ++ + L +
Sbjct: 91 TIVKQQIKALEEPAVDMLHTVTDMVRLAFTDVSIKNFEEFFNLHRTAKSKIEDI 144
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
0.316 0.132 0.370
Gapped
Lambda K H
0.267 0.0472 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,705,416
Number of extensions: 207641
Number of successful extensions: 429
Number of sequences better than 10.0: 1
Number of HSP's gapped: 419
Number of HSP's successfully gapped: 22
Length of query: 254
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 163
Effective length of database: 4,160,982
Effective search space: 678240066
Effective search space used: 678240066
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: 56 (26.0 bits)