RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1723
(246 letters)
>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL
conjugation pathway, DNA damage, nucleus,
phosphoprotein; HET: 1PE; 2.40A {Saccharomyces
cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A
Length = 968
Score = 164 bits (417), Expect = 1e-46
Identities = 71/239 (29%), Positives = 112/239 (46%), Gaps = 13/239 (5%)
Query: 19 ESYRKSDSGFLQHIGMMARFDNILGNETIHTLEYLTSEIRSIFCHSTMVDRIAAMLNYFL 78
E K L A+ L ++++ E + +I + F +V R+A+MLNY L
Sbjct: 724 EEEDKELQTRLASASRQAKSSCGLADKSMKLFEIYSKDIPAAFVTPEIVYRLASMLNYNL 783
Query: 79 FHLVGPKMRNFKTSRRSPGKQEGVGSIPAERKLKLNISTSPYYYFSL-----SLPPSLLY 133
LVGPK K + A + +N+S + ++ S +L
Sbjct: 784 ESLVGPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSEQSEFISAVAKDERSFNRNLFV 843
Query: 134 LAR--------IGGASLIPDLRRVAVLVEKLGAQLQSDEALLAGAPDEYLDPIMNTIMLE 185
A + I L A E+ + ++ PDE+LDP+M TIM +
Sbjct: 844 RAVDILGRKTGLASPEFIEKLLNFANKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKD 903
Query: 186 PVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTMEQVIPNTQLQTQIQDWIRQCRQKS 244
PV LP+S+ +D+STI HLLSD TDPFNR PL +E V PN +L+ +I + +Q ++++
Sbjct: 904 PVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILCFKKQKKEEA 962
>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: g.44.1.2
Length = 98
Score = 115 bits (290), Expect = 2e-33
Identities = 54/84 (64%), Positives = 70/84 (83%)
Query: 161 QSDEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTM 220
Q +E A A DE+LDPIM+T+M +PV LPSSR T+D+STIARHLLSDQTDPFNRSPLTM
Sbjct: 10 QQEEETYADACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM 69
Query: 221 EQVIPNTQLQTQIQDWIRQCRQKS 244
+Q+ PNT+L+ +IQ W+ + +Q+S
Sbjct: 70 DQIRPNTELKEKIQRWLAERKQQS 93
>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin
ligase, E4 polyubiquitin chain EL factor,
phosphoprotein, UBL conjugation pathway; NMR {Homo
sapiens} PDB: 3l1x_A 3l1z_B
Length = 100
Score = 113 bits (285), Expect = 1e-32
Identities = 41/97 (42%), Positives = 60/97 (61%), Gaps = 1/97 (1%)
Query: 147 RRVAVLVEKLGAQLQSDEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLL 206
+ A VE++ A+ E + APDE+ DP+M+T+M +PV LPS +D+S I RHLL
Sbjct: 3 HKFAEKVEEIVAKNARAEIDYSDAPDEFRDPLMDTLMTDPVRLPSG-TIMDRSIILRHLL 61
Query: 207 SDQTDPFNRSPLTMEQVIPNTQLQTQIQDWIRQCRQK 243
+ TDPFNR LT + P +L+ QIQ W+R+ +
Sbjct: 62 NSPTDPFNRQTLTESMLEPVPELKEQIQAWMREKQNS 98
>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase,
UBL conjugation pathway; NMR {Mus musculus}
Length = 85
Score = 108 bits (271), Expect = 1e-30
Identities = 38/82 (46%), Positives = 53/82 (64%), Gaps = 1/82 (1%)
Query: 162 SDEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTME 221
S E + APDE+ DP+M+T+M +PV LPS +D+S I RHLL+ TDPFNR LT
Sbjct: 3 SAEIDYSDAPDEFRDPLMDTLMTDPVRLPSG-TVMDRSIILRHLLNSPTDPFNRQMLTES 61
Query: 222 QVIPNTQLQTQIQDWIRQCRQK 243
+ P +L+ QIQ W+R+ +
Sbjct: 62 MLEPVPELKEQIQAWMREKQSS 83
>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A
{Danio rerio} PDB: 2c2v_S 2oxq_C
Length = 179
Score = 88.5 bits (219), Expect = 5e-22
Identities = 28/101 (27%), Positives = 46/101 (45%), Gaps = 3/101 (2%)
Query: 140 ASLIPDLRRVAVLVEKLGAQLQSDEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKS 199
+ + + + +++L +Q+ PD I +M EP PS T D+
Sbjct: 74 SKMKSKHDKYLMDMDELFSQVDEKRKKRE-IPDYLCGKISFELMREPCITPSG-ITYDRK 131
Query: 200 TIARHLLSD-QTDPFNRSPLTMEQVIPNTQLQTQIQDWIRQ 239
I HL DP RSPLT +Q+IPN ++ I +I++
Sbjct: 132 DIEEHLQRVGHFDPVTRSPLTQDQLIPNLAMKEVIDAFIQE 172
>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin
ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana}
SCOP: g.44.1.2
Length = 78
Score = 63.4 bits (155), Expect = 1e-13
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 171 PDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHL-LSDQTDPFNRSPLTMEQVIPNTQL 229
P+ + PI +M +PV + + QT ++S+I + L +T P ++ L + PN L
Sbjct: 6 PEYFRCPISLELMKDPVIVSTG-QTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNYVL 64
Query: 230 QTQIQDWIRQ 239
++ I W
Sbjct: 65 KSLIALWCES 74
>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3
ligase, ubiquitinylation, TPR, heat-shock protein
complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2
Length = 281
Score = 62.2 bits (151), Expect = 1e-11
Identities = 26/70 (37%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 171 PDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSD-QTDPFNRSPLTMEQVIPNTQL 229
PD I +M EP PS T D+ I HL +P RSPLT EQ+IPN +
Sbjct: 206 PDYLCGKISFELMREPCITPSG-ITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAM 264
Query: 230 QTQIQDWIRQ 239
+ I +I +
Sbjct: 265 KEVIDAFISE 274
>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase;
1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB:
1n87_A
Length = 61
Score = 55.1 bits (133), Expect = 8e-11
Identities = 13/49 (26%), Positives = 24/49 (48%)
Query: 177 PIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTMEQVIP 225
I + PV P SR +KS + +++ DP PL++E+++
Sbjct: 7 AISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVE 55
>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 94
Score = 50.7 bits (121), Expect = 8e-09
Identities = 14/86 (16%), Positives = 30/86 (34%), Gaps = 9/86 (10%)
Query: 168 AGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPFN---------RSPL 218
+ + PI M +PV T ++ I R + S Q + +
Sbjct: 2 SSGSSGFTCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDI 61
Query: 219 TMEQVIPNTQLQTQIQDWIRQCRQKS 244
+I + L+ I++ ++ + S
Sbjct: 62 RKSDLIQDEALRRAIENHNKKRHRHS 87
>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring,
ATP-binding, chromosomal protein, coiled coil, DNA
damage; 2.31A {Saccharomyces cerevisiae}
Length = 267
Score = 39.9 bits (92), Expect = 3e-04
Identities = 12/86 (13%), Positives = 27/86 (31%), Gaps = 4/86 (4%)
Query: 163 DEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTD----PFNRSPL 218
D+ + G E PI P+ D+ I +L T +
Sbjct: 171 DDLQIEGGKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVV 230
Query: 219 TMEQVIPNTQLQTQIQDWIRQCRQKS 244
+M + + ++ + + + Q+
Sbjct: 231 SMRDFVRDPIMELRCKIAKMKESQEQ 256
>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 = 39.3 bits (91), Expect = 0.001
Identities = 41/260 (15%), Positives = 83/260 (31%), Gaps = 67/260 (25%)
Query: 16 VGHESYRKSDSGFLQHI-----GMMARF---DNILGNETIHTLEYLTSEIRSIFCHS-TM 66
+KS+S + + ++A F GN T +Y E+R ++ +
Sbjct: 133 AKRPFDKKSNSALFRAVGEGNAQLVAIFGGQ----GN----TDDYF-EELRDLYQTYHVL 183
Query: 67 VDRIAAMLNYFLFHLVGPKMRNFKTSRRSPGKQEGVGSIPAERKLKLNISTSPYYYFS-- 124
V L + + K G + L+ +T Y
Sbjct: 184 VGD--------LIKFSAETLSELIRTTLDAEKVFTQG-LNILEWLENPSNTPDKDYLLSI 234
Query: 125 -LSLPPSLL-----YL--ARIGGASLIP-DLRR-------------VAVLVEKLGAQLQS 162
+S P + Y+ A++ G + P +LR AV + A+ S
Sbjct: 235 PISCPLIGVIQLAHYVVTAKLLGFT--PGELRSYLKGATGHSQGLVTAVAI----AETDS 288
Query: 163 DEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTMEQ 222
E+ + + ++ I + + +++ +L D + P M
Sbjct: 289 WESFFVSV-RKAIT-VLFFIGVR------CYEAYPNTSLPPSILEDSLENNEGVPSPMLS 340
Query: 223 VIPNTQLQTQIQDWIRQCRQ 242
+ TQ Q+QD++ +
Sbjct: 341 ISNLTQ--EQVQDYVNKTNS 358
Score = 37.0 bits (85), Expect = 0.005
Identities = 34/234 (14%), Positives = 61/234 (26%), Gaps = 82/234 (35%)
Query: 13 EF--HVGHESYRKSDSGF---LQHIGMMARFD-NILGNETIHTLEYLTSEIRSIFCHSTM 66
+F +V F L + F+ L IH L +++ + T
Sbjct: 63 KFLGYVSSLVEPSKVGQFDQVLNLC--LTEFENCYLEGNDIHA---LAAKLLQE--NDTT 115
Query: 67 VDRIAAML-NYFLFHLVGPKMRNFKTSRRSPGKQEGVGSIPAERKLKLNISTSPYYYFSL 125
+ + ++ NY ++R K+
Sbjct: 116 LVKTKELIKNYI---------TARIMAKRPFDKKS------------------------- 141
Query: 126 SLPPSLLYLARIGGASLIPDLRRVAVLVEKLGAQLQSDEALLAGAPDEYLDPIMNTIMLE 185
+L G A L+ A+ G Q G D+Y + E
Sbjct: 142 --NSALFRAVGEGNAQLV------AI----FGGQ---------GNTDDYFE--------E 172
Query: 186 PVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTMEQVIPNTQLQTQIQDWIRQ 239
L + L I ++ R+ L E+V I +W+
Sbjct: 173 LRDLYQTYHVLVGDLIKFS--AETLSELIRTTLDAEKVFTQG---LNILEWLEN 221
Score = 28.5 bits (63), Expect = 2.6
Identities = 19/131 (14%), Positives = 39/131 (29%), Gaps = 39/131 (29%)
Query: 123 FSLSLPPSLLYLARIGGASLIPDLRR--VAVLVEKLGAQLQSDEA-----LLAGAPDEYL 175
L +P + ++A L+ +L E DE L+ ++L
Sbjct: 18 HVLLVPTASFFIAS--------QLQEQFNKILPEPTEGFAADDEPTTPAELVG----KFL 65
Query: 176 DPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTMEQV--------IPNT 227
+ + + EP + Q L L++ F L + N
Sbjct: 66 GYVSSLV--EPSKVGQFDQVL------NLCLTE----FENCYLEGNDIHALAAKLLQEND 113
Query: 228 QLQTQIQDWIR 238
+ ++ I+
Sbjct: 114 TTLVKTKELIK 124
>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing,
mRNA splicing; NMR {Homo sapiens}
Length = 92
Score = 35.1 bits (81), Expect = 0.003
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 7/79 (8%)
Query: 171 PDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPF-----NRSPLTMEQVIP 225
PDE L I IM + V +P + I L ++D +++ ++ + +I
Sbjct: 11 PDELLCLICKDIMTDAVVIPCCGNSYCDECIRTAL--LESDEHTCPTCHQNDVSPDALIA 68
Query: 226 NTQLQTQIQDWIRQCRQKS 244
N L+ + ++ +
Sbjct: 69 NKFLRQAVNNFKNETGYTK 87
>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding,
translesion synthesis, UB conjugation pathway; 1.80A
{Homo sapiens}
Length = 99
Score = 29.0 bits (65), Expect = 0.44
Identities = 12/88 (13%), Positives = 24/88 (27%), Gaps = 1/88 (1%)
Query: 158 AQLQSDEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPFNRSP 217
++ A++ D I + +P I + L P
Sbjct: 7 SRWPPGLAVMKTIDDLLRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVT 66
Query: 218 LTMEQVIPNTQLQTQIQDWIRQCRQKSL 245
+T + N L ++ + R L
Sbjct: 67 VTEPDLKNNRILD-ELVKSLNFARNHLL 93
>3h2z_A Mannitol-1-phosphate 5-dehydrogenase; PSI- protein structure
initiative, structural genomics, midwest for structural
genomics (MCSG); 1.90A {Shigella flexneri 2a str}
Length = 382
Score = 28.1 bits (63), Expect = 3.1
Identities = 10/58 (17%), Positives = 25/58 (43%), Gaps = 9/58 (15%)
Query: 22 RKSDSGFLQHIGMMARFDNILGNETI---HTLEYLTSEIRS-----IFCHSTMVDRIA 71
++ + G + ++A +N++ T H + L + ++ + + VDRI
Sbjct: 105 KRKEQGNESPLNIIA-CENMVRGTTQLKGHVMNALPEDAKAWVEEHVGFVDSAVDRIV 161
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 0.136 0.393
Gapped
Lambda K H
0.267 0.0659 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,652,415
Number of extensions: 208870
Number of successful extensions: 454
Number of sequences better than 10.0: 1
Number of HSP's gapped: 445
Number of HSP's successfully gapped: 29
Length of query: 246
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 155
Effective length of database: 4,160,982
Effective search space: 644952210
Effective search space used: 644952210
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: 56 (25.5 bits)