RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14580
(149 letters)
>2dmj_A Poly (ADP-ribose) polymerase family, member 1; zinc finger, PARP-1,
ADPRT, NAD(+) ADP-ribosyltransferase 1, poly(ADP-ribose)
synthetase 1; NMR {Homo sapiens}
Length = 106
Score = 96.5 bits (240), Expect = 5e-27
Identities = 29/102 (28%), Positives = 49/102 (48%), Gaps = 6/102 (5%)
Query: 2 SDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHID 61
S DK + V+ AK+GR+ CKKC + I ++R+A M +P GK+ W+H
Sbjct: 3 SGSSGMAESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFS 62
Query: 62 CILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPE 103
C +V R +++ G+ +L +DQ++V
Sbjct: 63 CFWKVGHSIRHPDVEVD------GFSELRWDDQQKVKKTAEA 98
>3od8_A Poly [ADP-ribose] polymerase 1; protein-DNA complex, PARP zinc
finger, DNA binding protein-D complex; 2.40A {Homo
sapiens} PDB: 3oda_A
Length = 116
Score = 96.6 bits (240), Expect = 6e-27
Identities = 28/93 (30%), Positives = 48/93 (51%), Gaps = 6/93 (6%)
Query: 9 PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFK 68
DK + V+ AK+GR+ CKKC + I ++R+A M +P GK+ W+H C +V
Sbjct: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGH 82
Query: 69 KQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRF 101
R +++ G+ +L +DQ++V
Sbjct: 83 SIRHPDVEVD------GFSELRWDDQQKVKKTA 109
>1uw0_A DNA ligase III; DNA repair, zinc finger, PARP-like finger, cell
division, DNA replication, nuclear protein; HET: DNA;
NMR {Homo sapiens} SCOP: g.39.1.12
Length = 117
Score = 95.9 bits (238), Expect = 1e-26
Identities = 43/123 (34%), Positives = 66/123 (53%), Gaps = 13/123 (10%)
Query: 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKK 69
++ F VD AK G +GCKKCK+KI G RI K+ NPF G MK+W+HI C+ E ++
Sbjct: 3 EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 62
Query: 70 QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKT 129
R TT KIE + ++ GW++L ++E++ + K + +KK+
Sbjct: 63 ARATTKKIEDLTELEGWEELEDNEKEQITQHIADL-----------SSKAAGTPKKKAVV 111
Query: 130 PKK 132
K
Sbjct: 112 QAK 114
>1v9x_A Poly (ADP-ribose) polymerase; PARP, DNA repair, inflammation, cell
death, structural genomics; NMR {Arabidopsis thaliana}
Length = 114
Score = 95.4 bits (237), Expect = 1e-26
Identities = 32/121 (26%), Positives = 49/121 (40%), Gaps = 11/121 (9%)
Query: 8 NPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVF 67
K + + AK+ RS CK CK I+ R+ K+ + G M W+H CIL+
Sbjct: 4 GSSGHKPWRAEYAKSSRSSCKTCKSVINKENFRLGKLVQSTHFDGIMPMWNHASCILK-- 61
Query: 68 KKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKS 127
T +I+ VDD+ G + L EDQ+++ +SS S
Sbjct: 62 -----KTKQIKSVDDVEGIESLRWEDQQKIRKYVE----SGAGSNTSTSTGTSTSSSGPS 112
Query: 128 K 128
Sbjct: 113 S 113
>3odc_A Poly [ADP-ribose] polymerase 1; protein-DNA complex, PARP zinc
finger, DNA binding protein-D complex; 2.80A {Homo
sapiens} PDB: 3ode_A 2l31_A
Length = 111
Score = 93.1 bits (231), Expect = 1e-25
Identities = 26/106 (24%), Positives = 48/106 (45%), Gaps = 4/106 (3%)
Query: 10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVF 67
+ +F + AK+ RS CK C +KI+ G VR++K +P G + +W+H C ++
Sbjct: 5 KTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFVK-- 62
Query: 68 KKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRD 113
++ + G+ L ED+E + + P E +
Sbjct: 63 NREELGFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEGLEHHH 108
>2cs2_A Poly [ADP-ribose] polymerase-1; DNA BIND, DNA repair, necrosis,
apoptosis, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 134
Score = 92.5 bits (229), Expect = 4e-25
Identities = 32/133 (24%), Positives = 54/133 (40%), Gaps = 6/133 (4%)
Query: 2 SDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHH 59
S + +F + AK+ RS CK C +KI+ G VR++K +P G + +W+H
Sbjct: 5 SSGGSKAEKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYH 64
Query: 60 IDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKI 119
C ++ ++ + G+ L ED+E + + P E + D E
Sbjct: 65 PGCFVK--NREELGFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEGKRKGD--EVDG 120
Query: 120 PSSSEKKSKTPKK 132
KK P
Sbjct: 121 VDEVAKKKSGPSS 133
>4av1_A Poly [ADP-ribose] polymerase 1; transferase, PARP1, DNA-binding
domain, DBD, DNA repair, CAN poly- ADP(ribosyl)ation;
3.10A {Homo sapiens} PDB: 2l30_A
Length = 223
Score = 92.2 bits (228), Expect = 5e-24
Identities = 29/124 (23%), Positives = 55/124 (44%), Gaps = 6/124 (4%)
Query: 10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKK 69
DK + V+ AK+GR+ CKKC + I ++R+A M +P GK+ W+H C +V
Sbjct: 25 HSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHS 84
Query: 70 QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKT 129
R +++ G+ +L +DQ++V + + + + ++
Sbjct: 85 IRHPDVEVD------GFSELRWDDQQKVKKTAEAGGVTGKGQDGIGSKAEKTLGDFAAEY 138
Query: 130 PKKK 133
K
Sbjct: 139 AKSN 142
Score = 81.0 bits (199), Expect = 8e-20
Identities = 25/103 (24%), Positives = 46/103 (44%), Gaps = 4/103 (3%)
Query: 3 DKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHI 60
+ +F + AK+ RS CK C +KI+ G VR++K +P G + +W+H
Sbjct: 122 GIGSKAEKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHP 181
Query: 61 DCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPE 103
C ++ ++ + G+ L ED+E + + P
Sbjct: 182 GCFVK--NREELGFRPEYSASQLKGFSLLATEDKEALKKQLPG 222
>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 = 36.0 bits (82), Expect = 0.003
Identities = 27/173 (15%), Positives = 49/173 (28%), Gaps = 47/173 (27%)
Query: 1 MSDKEEP------NP----------EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKM 44
++ P NP D W D K C K I +
Sbjct: 313 CRPQDLPREVLTTNPRRLSIIAESIRDGLATW-DNWK--HVNCDKLTTII--------ES 361
Query: 45 GYNPFGSGKMKQWHHIDCILEVFKKQRQTTAK-IEVVDDMGGWDDLTPEDQEEVLSRFPE 103
N + ++ L VF + ++ W D+ D V+++
Sbjct: 362 SLNVLEPAEYRK-MFDR--LSVFPPSAHIPTILLSLI-----WFDVIKSDVMVVVNKL-- 411
Query: 104 SLRESNKDRDVPERK--IPS-SSEKKSKTPK-----KKAVAYFCLIRPLCFQN 148
+ S ++ E IPS E K K + V ++ + + +
Sbjct: 412 -HKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDD 463
Score = 33.3 bits (75), Expect = 0.028
Identities = 13/83 (15%), Positives = 26/83 (31%), Gaps = 29/83 (34%)
Query: 54 MKQWHHIDC-----------ILEVFKKQRQ---TTAKIEVVDDMGG-----------WDD 88
+K + +C F + TT +V D +
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT 297
Query: 89 LTPEDQEEVLSRF----PESLRE 107
LTP++ + +L ++ P+ L
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPR 320
Score = 26.0 bits (56), Expect = 7.2
Identities = 20/105 (19%), Positives = 38/105 (36%), Gaps = 29/105 (27%)
Query: 49 FGSGKMKQWHHIDCILEVFKKQ--------------RQTTAKIEVVDDMGGWDDLTP--- 91
F +G+ Q+ + D IL VF+ + +K E+ + D ++
Sbjct: 9 FETGEH-QYQYKD-ILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR 66
Query: 92 ------EDQEEVLSRFPESLRESN----KDRDVPERKIPSSSEKK 126
QEE++ +F E + N E++ PS +
Sbjct: 67 LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRM 111
>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 = 30.4 bits (68), Expect = 0.25
Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 7/36 (19%)
Query: 97 VLSRFPESL-------RESNKDRDVPERKIPSSSEK 125
V+S P+SL R++ + + +IP S K
Sbjct: 378 VVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERK 413
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 28.2 bits (62), Expect = 0.88
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 10/53 (18%)
Query: 88 DLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKTPKKK---AVAY 137
+ + E +E S+ +K + P +I S E K K +AY
Sbjct: 123 NYSSEVKEN-------SVDSDDKAKVPPLIRIVSGLELSDTKQKGKKFLVIAY 168
>1kbl_A PPDK, pyruvate phosphate dikinase; transferase, phosphotransferase;
1.94A {Clostridium symbiosum} SCOP: c.1.12.2 c.8.1.1
d.142.1.5 PDB: 1kc7_A* 1dik_A 1ggo_A 1jde_A 2dik_A
2r82_A 2fm4_A
Length = 873
Score = 27.8 bits (62), Expect = 1.4
Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 58 HHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPE 116
H + I++ K+++ V D DLT +D +E+ +F +E+ + P+
Sbjct: 149 SHFEKIIDAMKEEK------GVHFDT----DLTADDLKELAEKFKAVYKEAMNGEEFPQ 197
>2gvk_A Heme peroxidase; PC04261D, structural genomics, joint center for
structural G JCSG, protein structure initiative, PSI;
HET: MSE; 1.60A {Bacteroides thetaiotaomicron} SCOP:
d.58.4.14
Length = 317
Score = 27.2 bits (60), Expect = 2.0
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 82 DMGGWDDLTPEDQEEVLSR 100
DM W+ L E QE+V+ R
Sbjct: 196 DMVAWNALPVEQQEKVIGR 214
>1x61_A Thyroid receptor interacting protein 6; LIM domain,
OPA-interacting protein 1, zyxin related protein 1
(ZRP-1), structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 72
Score = 25.5 bits (56), Expect = 2.5
Identities = 7/43 (16%), Positives = 15/43 (34%), Gaps = 10/43 (23%)
Query: 20 AKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDC 62
+G SGC C + + + + + + H+ C
Sbjct: 1 GSSGSSGCGGCGEDVVGDGAGVVALD---------RVF-HVGC 33
>2hpg_A ABC transporter, periplasmic substrate-binding protein; periplasmic
binding protein, thermophilic proteins, trap- transport;
HET: MSE; 1.90A {Thermotoga maritima}
Length = 327
Score = 26.5 bits (59), Expect = 3.7
Identities = 8/49 (16%), Positives = 19/49 (38%), Gaps = 7/49 (14%)
Query: 86 WDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKTPKKKA 134
++ L E Q+ + E + ++ + KI E++ K +
Sbjct: 238 FNSLPKEYQKIIE----EEMDKAGIEV---SLKIMKELEEEYKQKCIEK 279
>3mca_A HBS1, elongation factor 1 alpha-like protein; protein protein
complex, translation regulation; 2.74A
{Schizosaccharomyces pombe}
Length = 592
Score = 26.2 bits (58), Expect = 5.2
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 81 DDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKTPKKKAVAY 137
D+ G ++LT E +EE S +RE+ + E++I + +K+V Y
Sbjct: 18 DEEPGEEELTEEQEEEFRSAVAT-VRETLLGVPISEKEIADTV-WYYYFDVEKSVNY 72
>2iiz_A Melanin biosynthesis protein TYRA, putative; NP_716371.1, putative
melanin biosynthesis protein TYRA, STR genomics, PSI-2;
HET: MSE HEM; 2.30A {Shewanella oneidensis} SCOP:
d.58.4.14 PDB: 2hag_A*
Length = 312
Score = 26.0 bits (57), Expect = 5.7
Identities = 4/16 (25%), Positives = 9/16 (56%)
Query: 82 DMGGWDDLTPEDQEEV 97
++ W L + QE++
Sbjct: 189 NLSKWHRLPLKKQEDI 204
>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha;
transferase, protein biosynthesis, protein synthesis
transferase complex; HET: TPO ANP; 2.50A {Saccharomyces
cerevisiae} PDB: 2a1a_A* 1q46_A
Length = 175
Score = 25.5 bits (56), Expect = 6.8
Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 5/66 (7%)
Query: 57 WHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDL-----TPEDQEEVLSRFPESLRESNKD 111
I I ++ + + A + VD G+ DL + ED + ++ +S +
Sbjct: 52 RRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSIL 111
Query: 112 RDVPER 117
R E+
Sbjct: 112 RYCAEK 117
>4f8a_A Potassium voltage-gated channel subfamily H membe; probable
regulatory domain of potassium channel, membrane PR
transport protein; 2.20A {Mus musculus}
Length = 160
Score = 25.3 bits (56), Expect = 7.3
Identities = 5/16 (31%), Positives = 8/16 (50%)
Query: 92 EDQEEVLSRFPESLRE 107
E+VL P+ +R
Sbjct: 3 HMTEKVLQICPKDMRA 18
>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical
domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5
Length = 182
Score = 25.2 bits (55), Expect = 8.8
Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 5/66 (7%)
Query: 57 WHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDL-----TPEDQEEVLSRFPESLRESNKD 111
I I ++ + R + VD G+ DL +PE+ + +F +S +
Sbjct: 52 RRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSIL 111
Query: 112 RDVPER 117
R V E
Sbjct: 112 RHVAEV 117
>2xwv_A Sialic acid-binding periplasmic protein SIAP; transport protein,
trap, sugar transport; HET: SLB; 1.05A {Haemophilus
influenzae} PDB: 2xxk_A* 2xa5_A* 2wyp_A* 2wx9_A* 2xwo_A*
2xwk_A* 2v4c_A* 2wyk_A* 2xwi_A* 3b50_A* 2cey_A 2cex_A
Length = 312
Score = 25.3 bits (56), Expect = 9.3
Identities = 9/49 (18%), Positives = 18/49 (36%), Gaps = 8/49 (16%)
Query: 86 WDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKTPKKKA 134
+ +L + Q+ V ++ + K K+ EK T +K
Sbjct: 223 YKELPEDLQKVVK----DAAENAAKY----HTKLFVDGEKDLVTFFEKQ 263
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
0.315 0.133 0.406
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,344,503
Number of extensions: 130633
Number of successful extensions: 299
Number of sequences better than 10.0: 1
Number of HSP's gapped: 286
Number of HSP's successfully gapped: 37
Length of query: 149
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 64
Effective length of database: 4,328,508
Effective search space: 277024512
Effective search space used: 277024512
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: 42 (22.0 bits)
S2: 53 (24.2 bits)