RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7630
(160 letters)
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO
enzyme, structural genomics, protein structure
initiative; NMR {Desulfitobacterium hafniense dcb-2}
PDB: 2kw4_A
Length = 147
Score = 39.6 bits (93), Expect = 7e-05
Identities = 17/76 (22%), Positives = 25/76 (32%), Gaps = 10/76 (13%)
Query: 44 LHIYTDGSLINPEDGAGAGIFC-----ELFSFYKRLGTFTT--NFDGEIAAIKIALLQIL 96
+YTDGS +N + + + T N GEIAA A+ +
Sbjct: 7 YDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKAS 66
Query: 97 NRTNQFERAVILSDSK 112
+ IL D
Sbjct: 67 QLG---VKIRILHDYA 79
>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif,
hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1
PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A
2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*
Length = 142
Score = 36.0 bits (83), Expect = 0.001
Identities = 23/97 (23%), Positives = 31/97 (31%), Gaps = 10/97 (10%)
Query: 42 DWLHIYTDG-SLINPEDGAGAGIFC----ELFSFYKRLGTFTTNFDGEIAAIKIALLQIL 96
W + D S NP G+ LF + + TN GE AI L +
Sbjct: 10 IWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFER-EPIPI-GTNNMGEFLAIVHGLRYLK 67
Query: 97 NRTNQFERAVILSDSKAAIHPMNSVHLNSCPALEASN 133
R R I S+S+ AI + S
Sbjct: 68 ER---NSRKPIYSNSQTAIKWVKDKKAKSTLVRNEET 101
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 34.5 bits (80), Expect = 0.005
Identities = 22/78 (28%), Positives = 32/78 (41%), Gaps = 10/78 (12%)
Query: 42 DWLHIYTDGS-LINPEDGAGAGIFCEL-----FSFYKRLGTFTTNFDGEI-AAIKIALLQ 94
D++ +YTDG N AGI + RL TN EI AA K A ++
Sbjct: 6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACK-A-IE 63
Query: 95 ILNRTNQFERAVILSDSK 112
N + V+ ++S
Sbjct: 64 QAKTQN-INKLVLYTNSM 80
>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV,
RNAse H, reverse transcriptase, transcription; 1.50A
{Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A
3v1r_A* 2hb5_A
Length = 165
Score = 32.5 bits (74), Expect = 0.026
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 8/70 (11%)
Query: 46 IYTDGS-LINP-EDGAGAGIFCEL-FSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQF 102
YTDGS + + AGA + E + + L T+ E+ A+ A L++
Sbjct: 26 WYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQA-LKMAEG---- 80
Query: 103 ERAVILSDSK 112
++ + +DS+
Sbjct: 81 KKLNVYTDSR 90
>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 = 33.1 bits (75), Expect = 0.031
Identities = 29/211 (13%), Positives = 52/211 (24%), Gaps = 86/211 (40%)
Query: 2 DSFEITHSLFLEETF----RKQDVAPLIAKT-----------------M----------- 29
+SF ++ + F R + P + M
Sbjct: 290 ESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQV 349
Query: 30 --ALETINTRYPSDDWLHIYTDGSLIN----------PED-----------GAGAG---- 62
+ N+ P+ + I SL+N P+ A +G
Sbjct: 350 QDYVNKTNSHLPAGKQVEI----SLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQS 405
Query: 63 -IFCELFSFYKRLGTFTTNFDGEIAA------IKIALLQILNRTNQFERAVILSDSKAAI 115
I FS +R F+ F +A+ + A I + V + I
Sbjct: 406 RI---PFS--ERKLKFSNRFL-PVASPFHSHLLVPASDLINKDLV--KNNVSFNAKDIQI 457
Query: 116 ---HPMNSVHLNSCPALEASNDIVGTLCSVL 143
+ L S I + +
Sbjct: 458 PVYDTFDGSDLR-----VLSGSISERIVDCI 483
Score = 31.9 bits (72), Expect = 0.085
Identities = 29/166 (17%), Positives = 46/166 (27%), Gaps = 76/166 (45%)
Query: 8 HSL--F--LEETFRKQDVAPLIAKTM----ALETINTRYPSDDWLHIYTDGSLIN---PE 56
HSL + L + +A M +E + R G + P
Sbjct: 1762 HSLGEYAAL--------AS--LADVMSIESLVEVVFYR------------GMTMQVAVPR 1799
Query: 57 DGAGAGIF--CELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAA 114
D G + + G +F E A++ + ++ RT V
Sbjct: 1800 DELGRSNYGMIAI-----NPGRVAASFSQE--ALQYVVERVGKRTGWLVEIV-------- 1844
Query: 115 IHPMNSVHLNSCP-----------ALEASNDIVGTLCSVLNKIKTN 149
N N AL+ T+ +VLN IK
Sbjct: 1845 ----N---YN-VENQQYVAAGDLRALD-------TVTNVLNFIKLQ 1875
>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 = 33.3 bits (75), Expect = 0.031
Identities = 22/131 (16%), Positives = 39/131 (29%), Gaps = 34/131 (25%)
Query: 20 DVAPLIAKTMALETINTRYPSDDWLHIYTD-------GSL--INPEDGAGAGIFCELFSF 70
P +A + D+W H+ D SL + P E
Sbjct: 324 TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA---------EYRKM 374
Query: 71 YKRLGTFTTNFDGEIAAIKIALLQIL----------NRTNQFE-RAVILSDSKAAIHPMN 119
+ RL F + I LL ++ N+ +++ K + +
Sbjct: 375 FDRLSVFPPSAH-----IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIP 429
Query: 120 SVHLNSCPALE 130
S++L LE
Sbjct: 430 SIYLELKVKLE 440
>1xdi_A RV3303C-LPDA; reductase, FAD, NAD, NADP, unkno function; HET: FAD;
2.81A {Mycobacterium tuberculosis} SCOP: c.3.1.5
d.87.1.1
Length = 499
Score = 30.2 bits (69), Expect = 0.26
Identities = 9/40 (22%), Positives = 11/40 (27%), Gaps = 11/40 (27%)
Query: 58 GAGAGIFCELFSFYKRLGTFTT----------NFDGEIAA 87
G+G E Y LG T D + A
Sbjct: 189 GSGV-TGAEFVDAYTELGVPVTVVASQDHVLPYEDADAAL 227
>1mo9_A ORF3; nucleotide binding motifs, nucleotide binding domain, oxidor;
HET: FAD KPC; 1.65A {Xanthobacter autotrophicus} SCOP:
c.3.1.5 c.3.1.5 d.87.1.1 PDB: 1mok_A* 2c3c_A* 2c3d_A*
3q6j_A*
Length = 523
Score = 30.0 bits (68), Expect = 0.29
Identities = 8/40 (20%), Positives = 9/40 (22%), Gaps = 11/40 (27%)
Query: 58 GAGAGIFCELFSFYKRLGTFTT----------NFDGEIAA 87
G E F+ G T D E A
Sbjct: 221 GGSK-TAVEYGCFFNATGRRTVMLVRTEPLKLIKDNETRA 259
>2a8x_A Dihydrolipoyl dehydrogenase, E3 component of alpha; lipoamide
dehydrogenase, pyruvate dehydrogenase, alpha keto acid
dehydrogenase; HET: FAD; 2.40A {Mycobacterium
tuberculosis} PDB: 3ii4_A*
Length = 464
Score = 30.2 bits (69), Expect = 0.31
Identities = 11/40 (27%), Positives = 14/40 (35%), Gaps = 11/40 (27%)
Query: 58 GAGAGIFCELFSFYKRLGTFTT----------NFDGEIAA 87
GAGA I E K G T N D +++
Sbjct: 178 GAGA-IGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSK 216
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.8 bits (63), Expect = 0.57
Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 6/27 (22%)
Query: 112 KAAIHPM-NSVHL---NSCPAL--EAS 132
K A+ + S+ L +S PAL +A+
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKAT 45
Score = 27.6 bits (60), Expect = 1.2
Identities = 6/23 (26%), Positives = 11/23 (47%), Gaps = 2/23 (8%)
Query: 12 LEETFRK--QDVAPLIAKTMALE 32
L+ + + D AP +A +E
Sbjct: 25 LQASLKLYADDSAPALAIKATME 47
>1onf_A GR, grase, glutathione reductase; oxidoreductase; HET: FAD; 2.60A
{Plasmodium falciparum} SCOP: c.3.1.5 c.3.1.5 d.87.1.1
Length = 500
Score = 28.4 bits (64), Expect = 1.0
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 11/38 (28%)
Query: 60 GAG-IFCELFSFYKRLGTFTT----------NFDGEIA 86
G+G I EL + KRLG + FD +
Sbjct: 183 GSGYIAVELINVIKRLGIDSYIFARGNRILRKFDESVI 220
>2yqu_A 2-oxoglutarate dehydrogenase E3 component; lipoamide dehydrogenase,
2-oxoglutarate dehydrogenase comple pyruvate
dehydrogenase complex; HET: FAD; 1.70A {Thermus
thermophilus} PDB: 2eq7_A*
Length = 455
Score = 28.2 bits (64), Expect = 1.3
Identities = 10/39 (25%), Positives = 13/39 (33%), Gaps = 11/39 (28%)
Query: 58 GAGAGIFCELFSFYKRLGT----------FTTNFDGEIA 86
G G I EL + RLG D E++
Sbjct: 174 GGGV-IGLELGVVWHRLGAEVIVLEYMDRILPTMDLEVS 211
>3ic9_A Dihydrolipoamide dehydrogenase; APC62701, colwellia psychrer 34H,
structural genomics, PSI-2; HET: FAD; 2.15A {Colwellia
psychrerythraea}
Length = 492
Score = 27.9 bits (63), Expect = 1.4
Identities = 10/40 (25%), Positives = 11/40 (27%), Gaps = 11/40 (27%)
Query: 58 GAGAGIFCELFSFYKRLGTFTT----------NFDGEIAA 87
G G I EL RLG D E+
Sbjct: 181 GPGV-IGLELGQALSRLGVIVKVFGRSGSVANLQDEEMKR 219
>1dxl_A Dihydrolipoamide dehydrogenase; oxidoreductase, multienzyme complex
protein, pyruvate dehydrogenase complex, glycine
decarboxylase complex; HET: FAD; 3.15A {Pisum sativum}
SCOP: c.3.1.5 c.3.1.5 d.87.1.1
Length = 470
Score = 27.9 bits (63), Expect = 1.7
Identities = 11/39 (28%), Positives = 15/39 (38%), Gaps = 11/39 (28%)
Query: 58 GAGAGIFCELFSFYKRLGT----------FTTNFDGEIA 86
GAG I E+ S + R+G+ D EI
Sbjct: 184 GAGY-IGLEMGSVWGRIGSEVTVVEFASEIVPTMDAEIR 221
>3urh_A Dihydrolipoyl dehydrogenase; PSI-biology, structural genomics,
protein structure initiati YORK structural genomics
research consortium; HET: FAD; 1.90A {Sinorhizobium
meliloti}
Length = 491
Score = 27.5 bits (62), Expect = 2.2
Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 11/39 (28%)
Query: 58 GAGAGIFCELFSFYKRLGT----------FTTNFDGEIA 86
G G I EL S + RLG DGE+A
Sbjct: 205 GGGV-IGLELGSVWARLGAKVTVVEFLDTILGGMDGEVA 242
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of
RNA/DNA hybrid; 1.40A {Uncultured organism}
Length = 140
Score = 26.7 bits (60), Expect = 2.3
Identities = 21/77 (27%), Positives = 29/77 (37%), Gaps = 9/77 (11%)
Query: 44 LHIYTDG-SLINP-EDGAGAGIFCELFSFYKRLGTF---TTNFDGEIAAIKIALLQILNR 98
+ IYTDG + NP G G I E + + TTN E A+ I L+ L
Sbjct: 4 IIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEAL-IRALEDLQM 62
Query: 99 T---NQFERAVILSDSK 112
+ DS+
Sbjct: 63 FGDKLVDMEVEVRMDSE 79
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 26.3 bits (59), Expect = 3.2
Identities = 26/77 (33%), Positives = 35/77 (45%), Gaps = 19/77 (24%)
Query: 45 HIYTDGS-LINPEDGA-GAGIFC-----ELFSFYKRLGTFTTNFDGEI-AAIKIALLQIL 96
HI+TDGS L NP G G + E+ + TTN E+ A I A L+ L
Sbjct: 8 HIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGFSL----TTNNRMELLAPIV-A-LEAL 61
Query: 97 NRTNQFERAVIL-SDSK 112
+ +IL SDS+
Sbjct: 62 KEPCK----IILTSDSQ 74
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 26.4 bits (59), Expect = 3.2
Identities = 22/76 (28%), Positives = 31/76 (40%), Gaps = 19/76 (25%)
Query: 46 IYTDGS-LINPEDGA-GAGIFC-----ELFSFYKRLGTFTTNFDGEI-AAIKIALLQILN 97
++TDG+ L NP G A + L TTN E+ AAI+ L+ L
Sbjct: 11 LFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEAC----TTNNRMELKAAIE-G-LKALK 64
Query: 98 RTNQFERAVIL-SDSK 112
+ V L +DS
Sbjct: 65 EPCE----VDLYTDSH 76
>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability,
hydrogen exchange, cooperativity, hydrolase; 1.30A
{Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A
1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A
1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A
3aa5_X 1rbv_A ...
Length = 155
Score = 26.3 bits (59), Expect = 3.6
Identities = 27/76 (35%), Positives = 35/76 (46%), Gaps = 19/76 (25%)
Query: 46 IYTDGS-LINPEDGA-GAGIFC-----ELFSFYKRLGTFTTNFDGEI-AAIKIALLQILN 97
I+T GS L NP G GA + + Y R TTN E+ AAI A L+ L
Sbjct: 7 IFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTR----TTNNRMELMAAIV-A-LEALK 60
Query: 98 RTNQFERAVIL-SDSK 112
+ VIL +DS+
Sbjct: 61 EHAE----VILSTDSQ 72
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 25.9 bits (58), Expect = 4.2
Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 17/75 (22%)
Query: 46 IYTDGS-LINPEDGA-GAGIFC-----ELFSFYKRLGTFTTNFDGEI-AAIKIALLQILN 97
IYTDG+ NP G GA + E+ + TTN E+ AAIK L+ L
Sbjct: 7 IYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPA----TTNNRMELMAAIK-G-LEALK 60
Query: 98 RTNQFERAVILSDSK 112
+ + + SDS
Sbjct: 61 EPARVQ---LYSDSA 72
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 26.8 bits (59), Expect = 4.4
Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 23/77 (29%)
Query: 29 MALETINTRYPSDDW--------LHI-YTDG-SLINPEDGAGAGIFCELFSFYKRLG--T 76
++LET+ R+ S+ W I +T G L++ + GI +++G T
Sbjct: 645 LSLETLFNRWHSESWANQLTVCGAIIGWTRGTGLMSANNIIAEGI--------EKMGVRT 696
Query: 77 FTTNFDGEIAAIKIALL 93
F+ E+A + LL
Sbjct: 697 FSQK---EMAFNLLGLL 710
>1v59_A Dihydrolipoamide dehydrogenase; 2-oxoacid dehydroganese complex,
pyruvate dehydrogenase complex; HET: FAD NAD; 2.20A
{Saccharomyces cerevisiae} SCOP: c.3.1.5 c.3.1.5
d.87.1.1 PDB: 1jeh_A*
Length = 478
Score = 25.6 bits (57), Expect = 9.8
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 11/38 (28%)
Query: 60 GAG-IFCELFSFYKRLGT----------FTTNFDGEIA 86
G G I E+ S Y RLG+ + DGE+A
Sbjct: 190 GGGIIGLEMGSVYSRLGSKVTVVEFQPQIGASMDGEVA 227
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
0.320 0.134 0.395
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,436,576
Number of extensions: 139170
Number of successful extensions: 224
Number of sequences better than 10.0: 1
Number of HSP's gapped: 223
Number of HSP's successfully gapped: 27
Length of query: 160
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 74
Effective length of database: 4,300,587
Effective search space: 318243438
Effective search space used: 318243438
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: 53 (24.0 bits)