RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8359
(279 letters)
>2hye_C Cullin-4A, CUL-4A; beta propeller, ring finger, zinc finger,
propeller cluster, helical repeats, cullin repeats,
protein binding; HET: DNA; 3.10A {Homo sapiens} SCOP:
a.4.5.34 a.118.17.1 e.40.1.1 PDB: 4a0k_A* 4a0c_C 4a0l_E*
Length = 759
Score = 168 bits (425), Expect = 1e-47
Identities = 109/141 (77%), Positives = 123/141 (87%)
Query: 139 LTDADLRRTLQSLACGKTRVLKKTPASRDIEDCDRFRFNNDFTFKLFRIKINQIQMKETN 198
+ D++LRRTLQSLACGK RVL K+P +++ED D+F FN +F KLFRIKINQIQMKET
Sbjct: 619 IEDSELRRTLQSLACGKARVLIKSPKGKEVEDGDKFIFNGEFKHKLFRIKINQIQMKETV 678
Query: 199 EEQKATEERVFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIES 258
EEQ +T ERVFQDRQYQIDAAIVRIMKMRKTL HNLL+SEL+NQLKFPVKP DLKKRIES
Sbjct: 679 EEQVSTTERVFQDRQYQIDAAIVRIMKMRKTLGHNLLVSELYNQLKFPVKPGDLKKRIES 738
Query: 259 LIDRDYMERDKDKANSYNYMA 279
LIDRDYMERDKD N Y+Y+A
Sbjct: 739 LIDRDYMERDKDNPNQYHYVA 759
Score = 77.6 bits (190), Expect = 3e-16
Identities = 53/66 (80%), Positives = 55/66 (83%)
Query: 62 KVDLAKRLLVGKSASVDAEKSMLSKLKQECGGGFTSKLEGMFKDMELSKDINVAFKQYMG 121
K DLAKRLLVGKSASVDAEKSMLSKLK ECG FTSKLEGMFKDMELSKDI V FKQ+M
Sbjct: 454 KKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMVHFKQHMQ 513
Query: 122 NLKEDK 127
N +
Sbjct: 514 NQSDSG 519
>1ldj_A Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc ring finger,
ligase, ubiquitin, ubiquitination, SCF; 3.00A {Homo
sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 1u6g_A
1ldk_A 1ldk_B 3rtr_A
Length = 760
Score = 165 bits (418), Expect = 1e-46
Identities = 52/161 (32%), Positives = 81/161 (50%), Gaps = 5/161 (3%)
Query: 124 KEDKESTSNNALGIDLTDADLRRTLQSLACGKTRVLKKTPASRD---IEDCDRFRFNNDF 180
ED + + L + LQ L K VL+ A+ D ++ + +
Sbjct: 600 TEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLYLGY 659
Query: 181 TFKLFRIKINQIQMKETNEEQKATEERVFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELF 240
K R+ IN E +EQ+ T + + +DR+ I AAIVRIMKMRK L H LL E+
Sbjct: 660 KNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVL 719
Query: 241 NQLK--FPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279
QL F + +KK I+ LI+++Y+ER + ++Y+Y+A
Sbjct: 720 TQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA 760
Score = 78.7 bits (193), Expect = 1e-16
Identities = 34/66 (51%), Positives = 46/66 (69%)
Query: 62 KVDLAKRLLVGKSASVDAEKSMLSKLKQECGGGFTSKLEGMFKDMELSKDINVAFKQYMG 121
LAKRL+ SAS DAE SM+SKLKQ CG +TSKL+ MF+D+ +SKD+N FK+++
Sbjct: 451 AKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLT 510
Query: 122 NLKEDK 127
N +
Sbjct: 511 NSEPLD 516
>3dpl_C Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus interaction,
receptor, UBL conjugation, UBL conjugation pathway,
acetylation, cytoplasm; 2.60A {Homo sapiens} PDB: 3dqv_C
Length = 382
Score = 133 bits (336), Expect = 8e-37
Identities = 58/171 (33%), Positives = 85/171 (49%), Gaps = 15/171 (8%)
Query: 124 KEDKESTSNNALGIDLTDADLRRTLQSLACG---KTRVLKKTP---ASRDIEDCDRFRFN 177
+K S N L +L DA+LRRTL SL K +VL P + +D + F N
Sbjct: 212 PREKISFENLKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDFTEGTLFSVN 271
Query: 178 NDFT-----FKLFRIKINQIQMK--ETNEEQKATEERVFQDRQYQIDAAIVRIMKMRKTL 230
+F+ R KIN I T ++ E + Q R + AI++IMKMRK +
Sbjct: 272 QEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEAIIQIMKMRKKI 331
Query: 231 SHNLLLSELFNQLK--FPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279
S+ L +EL LK F + +K++IE LI+ Y+ RD+ N++ YMA
Sbjct: 332 SNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA 382
Score = 72.9 bits (178), Expect = 8e-15
Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 62 KVDLAKRLLVGKSASVDAEKSMLSKLKQ-ECGGGFTSKLEGMFKDMELSKDINVAFKQYM 120
K L +RL++ SA + E++M+ L++ + +KL MF+D+++S+D+N AFK+
Sbjct: 57 KAHLTRRLILDISADSEIEENMVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMH 116
Query: 121 GNLKEDKESTSNNAL 135
N K + S N
Sbjct: 117 KNNKLALPADSVNIK 131
>2do7_A Cullin-4B, CUL-4B; helix-turn-helix motif, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 125 bits (314), Expect = 1e-36
Identities = 76/90 (84%), Positives = 83/90 (92%)
Query: 190 NQIQMKETNEEQKATEERVFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKP 249
+ IQMKET EEQ +T ERVFQDRQYQIDAAIVRIMKMRKTLSHNLL+SE++NQLKFPVKP
Sbjct: 6 SGIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVSEVYNQLKFPVKP 65
Query: 250 ADLKKRIESLIDRDYMERDKDKANSYNYMA 279
ADLKKRIESLIDRDYMERDK+ N YNY+A
Sbjct: 66 ADLKKRIESLIDRDYMERDKENPNQYNYIA 95
>1iuy_A Cullin-3 homologue; winged helix, structural genomics, riken
structural genomics/proteomics initiative, RSGI, unknown
function; NMR {Mus musculus} SCOP: a.4.5.34
Length = 92
Score = 114 bits (287), Expect = 1e-32
Identities = 40/90 (44%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 192 IQMKETNEEQKATEERVFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLK--FPVKP 249
+ E++ E+K T ++V DR+++I+AAIVRIMK RK + HN+L++E+ QLK F P
Sbjct: 3 AKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPSP 62
Query: 250 ADLKKRIESLIDRDYMERDKDKANSYNYMA 279
+KKRIE LI+R+Y+ R + Y Y+A
Sbjct: 63 VVIKKRIEGLIEREYLARTPEDRKVYTYVA 92
>3o2p_E Cell division control protein 53; ligase, cell cycle; 2.23A
{Saccharomyces cerevisiae} PDB: 3o6b_B
Length = 88
Score = 104 bits (261), Expect = 6e-29
Identities = 30/87 (34%), Positives = 49/87 (56%), Gaps = 3/87 (3%)
Query: 195 KETNEEQKATEERVFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLK--FPVKPADL 252
+ E + E+ + +RQ ++A IVRIMK ++ L H L++E Q F K + +
Sbjct: 3 NKRLTEDERIEKELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMV 62
Query: 253 KKRIESLIDRDYMERDKDKANSYNYMA 279
K+ I+SLI + Y++R D SY Y+A
Sbjct: 63 KRAIDSLIQKGYLQRGDDG-ESYAYLA 88
>3tdu_C Cullin-1, CUL-1; E2:E3, ligase-protein binding complex; 1.50A {Homo
sapiens} PDB: 3tdz_C
Length = 77
Score = 102 bits (256), Expect = 3e-28
Identities = 33/75 (44%), Positives = 49/75 (65%), Gaps = 2/75 (2%)
Query: 207 RVFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLK--FPVKPADLKKRIESLIDRDY 264
+ +DR+ I AAIVRIMKMRK L H LL E+ QL F + +KK I+ LI+++Y
Sbjct: 3 NIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEY 62
Query: 265 MERDKDKANSYNYMA 279
+ER + ++Y+Y+A
Sbjct: 63 LERVDGEKDTYSYLA 77
>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 = 50.2 bits (119), Expect = 4e-07
Identities = 54/360 (15%), Positives = 97/360 (26%), Gaps = 143/360 (39%)
Query: 20 SKTRAWNRDTCSSLFPPRKQALSTHEK--SPIQISIKVNVSSVEKVDLAKRLL------- 70
S + R + + ++ + Q+ K NVS ++ ++ L
Sbjct: 96 SPIKTEQRQPS----MMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAK 151
Query: 71 ---------VGKS---ASVDAEKSMLSKLKQECGGGFTSKLEGMF--------KDMELSK 110
GK+ V K +C F +F + +
Sbjct: 152 NVLIDGVLGSGKTWVALDV------CLSYKVQCKMDF-----KIFWLNLKNCNSPETVLE 200
Query: 111 DINVAFKQYMGNLKEDKESTSNNALGIDLTDADLRRTLQS-------------------- 150
+ Q N + +SN L I A+LRR L+S
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWN 260
Query: 151 ---LACGKTRVLKKTPASRDIEDCDRFR---------------FNNDFTFKLFRIKINQI 192
L+C ++L T R + D D L ++
Sbjct: 261 AFNLSC---KILLTT---RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314
Query: 193 ------QMKETN-----------EEQKATEERVFQDRQYQIDAAIVRIMKMRKTLSHNLL 235
++ TN + AT + + D + I++ S N+L
Sbjct: 315 PQDLPREVLTTNPRRLSIIAESIRDGLATWDNW---KHVNCD-KLTTIIES----SLNVL 366
Query: 236 ----LSELFNQLK-FP--VK-PAD--------------------LKKRIESLIDRDYMER 267
++F++L FP P L K SL+++ E
Sbjct: 367 EPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY--SLVEKQPKES 424
Score = 31.0 bits (69), Expect = 0.49
Identities = 28/141 (19%), Positives = 49/141 (34%), Gaps = 19/141 (13%)
Query: 105 DMELS------KDINVAFKQYMGNLKEDKE--STSNNALGIDLTDADLRRTLQSL-ACGK 155
D E KDI F+ ++ + + I L+ ++ + S A
Sbjct: 8 DFETGEHQYQYKDILSVFED---AFVDNFDCKDVQDMPKSI-LSKEEIDHIIMSKDAVSG 63
Query: 156 TRVLKKTPASRDIEDCDRF---RFNNDFTFKLFRIKINQIQMKETNEEQKATEERVFQDR 212
T L T S+ E +F ++ F + IK Q Q +R++ D
Sbjct: 64 TLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN 123
Query: 213 QYQIDAAIVR---IMKMRKTL 230
Q + R +K+R+ L
Sbjct: 124 QVFAKYNVSRLQPYLKLRQAL 144
>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets,
alpha helices, AMY amyloidosis, blood coagulation,
disease mutation, glycoprot phosphoprotein; HET: NAG NDG
BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A*
2a45_G*
Length = 562
Score = 30.2 bits (67), Expect = 0.77
Identities = 32/164 (19%), Positives = 70/164 (42%), Gaps = 24/164 (14%)
Query: 81 KSMLSKLKQECGGGFTSKLEG----MFKDMELSKDINVAFKQYMGNLKEDKESTSNNALG 136
K ++ ++ Q+ FT+++ +F+ + +KD + M L+ D S +N
Sbjct: 52 KGLIDEVNQD----FTNRINKLKNSLFEYQKNNKDSHSLTTNIMEILRGDFSSANNRDNT 107
Query: 137 IDLTDADLRRTLQSLACGKTRVLKKTPASRDIED------CDRFRFNNDFTFKLF----- 185
+ DLR ++ L K +V++K + ++ D R D K+
Sbjct: 108 YNRVSEDLRSRIEVL---KRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGS 164
Query: 186 --RIKINQIQMKETNEEQKATEERVFQDRQYQIDAAIVRIMKMR 227
R ++ +K+ ++QK E+ + +D D + ++KM+
Sbjct: 165 CSRALAREVDLKDYEDQQKQLEQVIAKDLLPSRDRQHLPLIKMK 208
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.4 bits (65), Expect = 0.84
Identities = 7/70 (10%), Positives = 24/70 (34%), Gaps = 12/70 (17%)
Query: 191 QIQMKETNEEQKATEERVFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPA 250
++Q + + E R + ++ + + ++ K +N + + F
Sbjct: 97 RLQELDAASKVMEQEWRE-KAKKDLEEWNQRQSEQVEKNKINNRIADKAF---------- 145
Query: 251 DLKKRIESLI 260
++ +I
Sbjct: 146 -YQQPDADII 154
>3fbk_A RGS3, RGP3, regulator of G-protein signaling 3; all beta-sheet
fold, structural genomics, PSI-2, protein structure
initiative; 2.00A {Homo sapiens}
Length = 153
Score = 27.3 bits (61), Expect = 3.6
Identities = 9/33 (27%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 240 FNQ-LKFPVKPADLKKRIE-SLIDRDYMERDKD 270
F++ FPV+ D +KR+ ++ +R R
Sbjct: 78 FHEHFFFPVQEEDDQKRLLVTVWNRASQSRQSG 110
>1aj0_A DHPS, dihydropteroate synthase; antibiotic, resistance,
transferase, folate, biosynthesis; HET: PH2 SAN; 2.00A
{Escherichia coli} SCOP: c.1.21.1 PDB: 1aj2_A* 1ajz_A
3tyz_A* 3tyu_A* 3tzf_A* 3tzn_A
Length = 282
Score = 26.7 bits (60), Expect = 7.8
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 228 KTLSHNL-LLSEL--FNQLKFPV 247
K LSHN LL+ L F+ P+
Sbjct: 192 KNLSHNYSLLARLAEFHHFNLPL 214
>3tr9_A Dihydropteroate synthase; biosynthesis of cofactors, prosthetic
groups, and carriers, transferase; HET: PT1; 1.90A
{Coxiella burnetii}
Length = 314
Score = 26.8 bits (60), Expect = 8.7
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 228 KTLSHNL-LLSEL--FNQLKFPV 247
K +S N LL++L F + PV
Sbjct: 209 KNVSENFYLLNKLPEFVAMGLPV 231
>3mcm_A 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine
pyrophosphokinase/dihydropteroate...; folate, TIM
barrel, synthase, HPPK, DHPS; 2.20A {Francisella
tularensis subsp} PDB: 3mcn_A* 3mco_A*
Length = 442
Score = 27.0 bits (60), Expect = 8.9
Identities = 4/24 (16%), Positives = 7/24 (29%), Gaps = 4/24 (16%)
Query: 228 KTLSHNLLL----SELFNQLKFPV 247
K L E+ +L+
Sbjct: 373 KKSDTARYLLENIIEIKRRLELKA 396
>1tx2_A DHPS, dihydropteroate synthase; folate biosynthesis, pterine, MA
transferase; HET: 680; 1.83A {Bacillus anthracis} SCOP:
c.1.21.1 PDB: 1tww_A* 1twz_A* 1tx0_A* 1tws_A* 3h21_A*
3h22_A* 3h23_A* 3h24_A* 3h26_A* 3h2a_A* 3h2c_A* 3h2e_A*
3h2f_A* 3h2m_A* 3h2n_A* 3h2o_A* 3tya_A* 3tyb_A* 3tyc_A*
3tyd_A* ...
Length = 297
Score = 26.7 bits (60), Expect = 9.7
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 12/49 (24%)
Query: 228 KTLSHNL-LLSEL--FNQLKFPVKPADL----KKR-IESLIDRDYMERD 268
KT NL + L N L +PV L +K I ++D ER
Sbjct: 211 KTPEQNLEAMRNLEQLNVLGYPV----LLGTSRKSFIGHVLDLPVEERL 255
>2b69_A UDP-glucuronate decarboxylase 1; UDP-glucoronic acid decarboxylase,
structural genomics, STRU genomics consortium, SGC,
lyase; HET: MSE NAD UDP; 1.21A {Homo sapiens} SCOP:
c.2.1.2 PDB: 4ef7_A*
Length = 343
Score = 26.6 bits (59), Expect = 9.7
Identities = 6/26 (23%), Positives = 11/26 (42%), Gaps = 2/26 (7%)
Query: 200 EQKATEERVFQD--RQYQIDAAIVRI 223
E K E + +Q ++ + RI
Sbjct: 172 EGKRVAETMCYAYMKQEGVEVRVARI 197
>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex,
single-stranded DNA, isomerase/DNA complex; HET: DNA;
2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A*
2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A*
Length = 659
Score = 26.8 bits (60), Expect = 9.8
Identities = 4/14 (28%), Positives = 7/14 (50%)
Query: 256 IESLIDRDYMERDK 269
IE L R ++ +
Sbjct: 532 IELLFKRGFLTKKG 545
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 0.130 0.353
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,870,076
Number of extensions: 218151
Number of successful extensions: 659
Number of sequences better than 10.0: 1
Number of HSP's gapped: 643
Number of HSP's successfully gapped: 32
Length of query: 279
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 187
Effective length of database: 4,133,061
Effective search space: 772882407
Effective search space used: 772882407
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: 57 (25.8 bits)