RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11807
(88 letters)
>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 = 35.4 bits (81), Expect = 8e-04
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 18/54 (33%)
Query: 51 EKPHVFYGQLLDWLRWL----------------VAWQPVILALIQGVNYMLDLK 88
+ Q L+ L WL ++ P+I +IQ +Y++ K
Sbjct: 203 LDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISC-PLI-GVIQLAHYVVTAK 254
>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 69
Score = 33.0 bits (75), Expect = 0.001
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 1 MDNDIMTCKTYCIFIFHEFCIRGWCIVGKKQICPYCKEKVDLK 43
+ N + T C +F C+R + CP C++K++ K
Sbjct: 29 VQNGRLIVSTECGHVFCSQCLRDS--LKNANTCPTCRKKINHK 69
>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase,
ubiquitylation, sumoylation, zinc-FI metal binding
protein; 1.80A {Rattus norvegicus}
Length = 71
Score = 31.0 bits (70), Expect = 0.008
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 1 MDNDIMTCKTYCIFIFHEFCIRGWCIVGKKQICPYCKEKVDLK 43
+ N + T C +F C+R CP C++K++ K
Sbjct: 24 VQNGRLIVSTECGHVFCSQCLRDSL--KNANTCPTCRKKINHK 64
>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin
ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB:
2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A
2ldr_A*
Length = 389
Score = 32.4 bits (73), Expect = 0.009
Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 1 MDNDIMTCKTYCIFIFHEFCIRGWCIVGKKQICPYCKEKVD 41
+ND C + C+ W + Q CP+C+ ++
Sbjct: 339 AENDKDVKIEPCGHLMCTSCLTSWQ-ESEGQGCPFCRCEIK 378
>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 74
Score = 30.3 bits (68), Expect = 0.017
Identities = 8/33 (24%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 7 TCKTYCIFIFHEFCIRGWCIVGKKQICPYCKEK 39
+C+T C H C+ + + CP+C +
Sbjct: 30 SCET-CGIRMHLPCVAKYFQSNAEPRCPHCNDY 61
>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch
signaling, structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: g.44.1.1
Length = 114
Score = 30.6 bits (68), Expect = 0.026
Identities = 11/38 (28%), Positives = 14/38 (36%), Gaps = 3/38 (7%)
Query: 4 DIMTCKTYCIFIFHEFCIRGWCIVGKKQ---ICPYCKE 38
++ T C FH C+ G K CP CK
Sbjct: 53 MVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKT 90
>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding;
HET: SUC; 1.50A {Homo sapiens}
Length = 64
Score = 29.4 bits (66), Expect = 0.034
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 1 MDNDIMTCKTYCIFIFHEFCIRGWCIVGKKQICPYCKEKVDLK 43
+ N + T C +F C+R CP C++K++ K
Sbjct: 17 VQNGRLIVSTECGHVFCSQCLRDSL--KNANTCPTCRKKINHK 57
>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 71
Score = 29.4 bits (66), Expect = 0.044
Identities = 8/31 (25%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 10 TYCIFIFHEFCIRGWCIVGKKQICPYCKEKV 40
C +F C++G +GK+ C C++++
Sbjct: 31 LPCKHVFCYLCVKGASWLGKR--CALCRQEI 59
>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium, NESG; HET: MSE; 2.29A {Homo
sapiens}
Length = 100
Score = 29.1 bits (65), Expect = 0.071
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 10 TYCIFIFHEFCIRGWCIVGKKQICPYCKEKVDLKLMFVNLW 50
+C + CIR W + Q CP+C+ + L+ + W
Sbjct: 39 PHCSKLCCFSCIRRWLTEQRAQ-CPHCRAPLQLRELVNCRW 78
>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 70
Score = 28.5 bits (64), Expect = 0.090
Identities = 7/27 (25%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 15 IFHEFCIRGWCIVGKKQICPYCKEKVD 41
F + CI W + + CP C+ ++
Sbjct: 35 SFCQKCIDKWS--DRHRNCPICRLQMT 59
>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila
melanogaster}
Length = 381
Score = 29.4 bits (65), Expect = 0.10
Identities = 9/42 (21%), Positives = 14/42 (33%), Gaps = 9/42 (21%)
Query: 12 CIFIFHEFCIRGW---------CIVGKKQICPYCKEKVDLKL 44
C+ H C+ W + CP+CK K+
Sbjct: 334 CVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSF 375
>3nw0_A Non-structural maintenance of chromosomes element homolog; E3
ligase, Zn, metal binding protein; 2.92A {Homo sapiens}
Length = 238
Score = 29.3 bits (65), Expect = 0.11
Identities = 8/33 (24%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 6 MTCKTYCIFIFHEFCIRGWCIVGKKQICPYCKE 38
+C+T C H C+ + + CP+C +
Sbjct: 194 QSCET-CGIRMHLPCVAKYFQSNAEPRCPHCND 225
>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid
herpesvirus 1} SCOP: g.44.1.1
Length = 68
Score = 27.8 bits (62), Expect = 0.15
Identities = 9/27 (33%), Positives = 11/27 (40%), Gaps = 2/27 (7%)
Query: 15 IFHEFCIRGWCIVGKKQICPYCKEKVD 41
F CI W + CP CK V+
Sbjct: 27 AFCYVCITRWI--RQNPTCPLCKVPVE 51
>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 26.0 bits (57), Expect = 0.86
Identities = 6/28 (21%), Positives = 13/28 (46%)
Query: 16 FHEFCIRGWCIVGKKQICPYCKEKVDLK 43
H+ C++ W + C CK + ++
Sbjct: 44 VHQACLQQWIKSSDTRCCELCKYEFIME 71
>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 81
Score = 26.0 bits (57), Expect = 0.95
Identities = 7/32 (21%), Positives = 8/32 (25%), Gaps = 2/32 (6%)
Query: 10 TYCIFIFHEFCIRGWCIVGKKQICPYCKEKVD 41
T C F E C C C +
Sbjct: 31 TKCRHYFCESCALEHFR--ATPRCYICDQPTG 60
>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing,
mRNA splicing; NMR {Homo sapiens}
Length = 92
Score = 25.9 bits (57), Expect = 1.2
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 5/31 (16%)
Query: 9 KTYCIFIFHEFCIRGWCIVGKKQICPYCKEK 39
+YC + CIR + + CP C +
Sbjct: 34 NSYC-----DECIRTALLESDEHTCPTCHQN 59
>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace
motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3
Length = 60
Score = 24.3 bits (53), Expect = 2.4
Identities = 5/27 (18%), Positives = 10/27 (37%)
Query: 17 HEFCIRGWCIVGKKQICPYCKEKVDLK 43
H C+ W + + C C + +
Sbjct: 34 HRSCLSTWLTISRNTACQICGVVYNTR 60
>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS),
leukemia, transcription regulation; NMR {Homo sapiens}
SCOP: g.44.1.1
Length = 56
Score = 24.2 bits (53), Expect = 2.4
Identities = 7/27 (25%), Positives = 9/27 (33%), Gaps = 2/27 (7%)
Query: 16 FHEFCIRGWCIVGKKQICPYCKEKVDL 42
H C C+ CP C+ L
Sbjct: 25 LHTLCSG--CLEASGMQCPICQAPWPL 49
>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 72
Score = 24.7 bits (54), Expect = 2.7
Identities = 9/31 (29%), Positives = 11/31 (35%), Gaps = 2/31 (6%)
Query: 10 TYCIFIFHEFCIRGWCIVGKKQICPYCKEKV 40
T C+ F + CI CP C V
Sbjct: 32 TECLHTFCKSCIVRH--FYYSNRCPKCNIVV 60
>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein
of testis, proliferation potential-related protein,
protein P2P-R; NMR {Homo sapiens}
Length = 74
Score = 24.3 bits (53), Expect = 2.9
Identities = 8/35 (22%), Positives = 13/35 (37%), Gaps = 5/35 (14%)
Query: 9 KTYCIFIFHEFCIRGWCIVGKKQICPYCKEKVDLK 43
+YC + CIR + + CP C +
Sbjct: 36 NSYC-----DECIRTALLESDEHTCPTCHQNDVSP 65
>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA
polymer binding protein, RNA binding protein; 2.10A
{Saccharomyces cerevisiae}
Length = 157
Score = 25.1 bits (54), Expect = 3.1
Identities = 8/30 (26%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 36 CKEKVDLKLMFVNLWEKPHVFYGQLLDWLR 65
KEK+ L +++W++ +F L+ +R
Sbjct: 116 HKEKI-RML--LDIWDRSGLFQKSYLNAIR 142
>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 = 25.2 bits (54), Expect = 3.6
Identities = 16/99 (16%), Positives = 26/99 (26%), Gaps = 32/99 (32%)
Query: 5 IMTCKTY---CIFIFHEFCIRGWCIVGKKQICPYCKEKVDLKLMFVNLWEKPHVFYGQLL 61
+ C +Y C F F W + C + M L + +
Sbjct: 168 LDVCLSYKVQCKMDFKIF----WLNLKN------CNSPETVLEMLQKLLYQIDPNWTSRS 217
Query: 62 D--------------WLRWLVAWQPVILALIQGVNYMLD 86
D LR L+ +P L+ +L
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLL-----VLL 251
>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb,
E3-ligase, nuclear protein, chromosomal protein,
transcription regulation; 2.0A {Mus musculus} PDB:
3rpg_B 2h0d_A
Length = 108
Score = 24.4 bits (53), Expect = 3.8
Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 2/34 (5%)
Query: 16 FHEFCIRGWCIVGKKQICPYCKEKVDLKLMFVNL 49
F + CI + K CP C +V +N+
Sbjct: 38 FCKTCIVRYLETSKY--CPICDVQVHKTRPLLNI 69
>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 81
Score = 24.1 bits (52), Expect = 4.3
Identities = 9/42 (21%), Positives = 16/42 (38%), Gaps = 2/42 (4%)
Query: 2 DNDIMTCKTYCIFIFHEFCIRGWCIVGKKQICPYCKEKVDLK 43
D + C FH C+ W + CP C++ ++
Sbjct: 38 QEDCVVVWGECNHSFHNCCMSLWVK--QNNRCPLCQQDWVVQ 77
>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex,
chimera; 2.21A {Rattus norvegicus}
Length = 133
Score = 24.4 bits (52), Expect = 5.1
Identities = 9/34 (26%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 8 CKTYCIFIFHEFCIRGWCIVGKKQICPYCKEKVD 41
T C +F C+R + CP C++K++
Sbjct: 93 VSTECGHVFCSQCLRDS--LKNANTCPTCRKKIN 124
>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase,
protein binding complex; 4.80A {Homo sapiens}
Length = 149
Score = 24.2 bits (52), Expect = 5.4
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 5/27 (18%)
Query: 17 HEF---CIRGWCIVGKKQICPYCKEKV 40
H F CI W +K CP C++ +
Sbjct: 84 HSFCSYCINEWM--KRKIECPICRKDI 108
>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA
damage, chromatin regulator, chromosomal protein, DNA
repair, metal-binding; 2.12A {Homo sapiens}
Length = 115
Score = 24.1 bits (52), Expect = 5.5
Identities = 7/41 (17%), Positives = 11/41 (26%), Gaps = 6/41 (14%)
Query: 17 HEFCIRGWCIVG----KKQICPYCKEKVDLKLMFVNLWEKP 53
H C C CP+C+ +V +
Sbjct: 35 HTLCKP--CFQSTVEKASLCCPFCRRRVSSWTRYHTRRNSL 73
>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha,
coiled coil, cytoplasm, metal- binding, UBL
conjugation, UBL conjugation pathway; 2.20A {Homo
sapiens}
Length = 170
Score = 24.3 bits (52), Expect = 5.8
Identities = 10/40 (25%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 10 TYCIFIFHEFCIRGWCIVGKKQICPYCKEKVDLKLMFVNL 49
T C F + CI I CP E + +F +
Sbjct: 34 TPCGHRFCKACIIKS-IRDAGHKCPVDNEILLENQLFPDN 72
>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 74
Score = 23.6 bits (51), Expect = 6.9
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 12 CIFIFHEFCIRGWCIVGKKQICPYCKEKV 40
C FH C+ W + +++CP C V
Sbjct: 36 CKHAFHRKCLIKW--LEVRKVCPLCNMPV 62
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 24.2 bits (52), Expect = 7.0
Identities = 4/9 (44%), Positives = 4/9 (44%)
Query: 30 KQICPYCKE 38
CP CK
Sbjct: 21 VLTCPECKV 29
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
0.334 0.148 0.547
Gapped
Lambda K H
0.267 0.0544 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,452,866
Number of extensions: 69667
Number of successful extensions: 405
Number of sequences better than 10.0: 1
Number of HSP's gapped: 391
Number of HSP's successfully gapped: 55
Length of query: 88
Length of database: 6,701,793
Length adjustment: 56
Effective length of query: 32
Effective length of database: 5,138,217
Effective search space: 164422944
Effective search space used: 164422944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.5 bits)
S2: 51 (23.8 bits)