RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780796|ref|YP_003065209.1| ribonuclease H [Candidatus
Liberibacter asiaticus str. psy62]
(152 letters)
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum} (A:)
Length = 146
Score = 139 bits (351), Expect = 2e-34
Identities = 72/139 (51%), Positives = 95/139 (68%), Gaps = 1/139 (0%)
Query: 8 EVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPC 67
+ YTDGA SGNPG GGWG LL Y K ISG + TTNNRMELMAAIK L ALK P
Sbjct: 4 TITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKEPA 63
Query: 68 KVLLYTDSSYVHKGFSQ-WIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIK 126
+V LY+DS+Y+ ++ W+K+W +NGWKT+ KK V+NIDLW + ++ + H+V + +K
Sbjct: 64 RVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFHKVK 123
Query: 127 GHAGNQENEKVDRIARNAA 145
GH+ N N + D +AR A
Sbjct: 124 GHSDNPYNSRADELARLAI 142
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease;
2.00A {Shewanella oneidensis mr-1} PDB: 2zqb_A (A:)
Length = 158
Score = 130 bits (327), Expect = 1e-31
Identities = 72/137 (52%), Positives = 101/137 (73%)
Query: 9 VHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPCK 68
+H +TDG+C GNPGPGG+G+++ YKG K +S G TTNNRMEL+A I AL ALK PCK
Sbjct: 7 IHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGFSLTTNNRMELLAPIVALEALKEPCK 66
Query: 69 VLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKGH 128
++L +DS Y+ +G WI W++ GW TS++ VKN+DLW + +A+ H++D W+KGH
Sbjct: 67 IILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQIDWRWVKGH 126
Query: 129 AGNQENEKVDRIARNAA 145
AG+ ENE+ D++AR AA
Sbjct: 127 AGHAENERCDQLARAAA 143
>1jl1_A Ribonuclease HI; RNAse HI, protein stability,
thermostability, hydrogen exchange, cooperativity,
hydrolase; 1.30A {Escherichia coli} (A:)
Length = 155
Score = 128 bits (322), Expect = 3e-31
Identities = 78/138 (56%), Positives = 100/138 (72%)
Query: 8 EVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPC 67
+V +T G+ GNPGPGG+G +LRY+G+EK S G TTNNRMELMAAI AL ALK
Sbjct: 4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHA 63
Query: 68 KVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKG 127
+V+L TDS YV +G +QWI W++ GWKT+DKK VKN+DLW + A QH++ W+KG
Sbjct: 64 EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKG 123
Query: 128 HAGNQENEKVDRIARNAA 145
HAG+ ENE+ D +AR AA
Sbjct: 124 HAGHPENERADELARAAA 141
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} (A:)
Length = 166
Score = 120 bits (301), Expect = 1e-28
Identities = 79/146 (54%), Positives = 104/146 (71%), Gaps = 1/146 (0%)
Query: 1 MDSKHLREVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKAL 60
M+ + V +TDGAC GNPGPGGW LLR+ EK++SGGE TTNNRMEL AAI+ L
Sbjct: 1 MNPSPRKRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGL 60
Query: 61 TALKYPCKVLLYTDSSYVHKGFSQ-WIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHK 119
ALK PC+V LYTDS Y+ K F++ W++ W++ GW+T++ K VKN DLW + A A H+
Sbjct: 61 KALKEPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHR 120
Query: 120 VDLYWIKGHAGNQENEKVDRIARNAA 145
V +++KGH G+ ENE+VDR AR A
Sbjct: 121 VRFHFVKGHTGHPENERVDREARRQA 146
>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE
motif, hydrolase; 1.50A {Bacillus halodurans c-125} (A:)
Length = 142
Score = 119 bits (298), Expect = 2e-28
Identities = 24/143 (16%), Positives = 46/143 (32%), Gaps = 5/143 (3%)
Query: 1 MDSKHLREVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKAL 60
M + + D GNPG + + G+ TNN E +A + L
Sbjct: 4 MAKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGL 63
Query: 61 -TALKYPCKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHK 119
+ + +Y++S +W+K + +++T L + E H
Sbjct: 64 RYLKERNSRKPIYSNSQTAI----KWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHT 119
Query: 120 VDLYWIKGHAGNQENEKVDRIAR 142
+ +K K D +
Sbjct: 120 YETPILKWQTDKWGEIKADYGRK 142
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid;
2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A* (A:)
Length = 154
Score = 105 bits (263), Expect = 2e-24
Identities = 47/142 (33%), Positives = 70/142 (49%), Gaps = 5/142 (3%)
Query: 9 VHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGG---EKETTNNRMELMAAIKALTALKY 65
V YTDG CS N + Y G ++ G TN R E+ AA KA+ K
Sbjct: 8 VVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKT 67
Query: 66 PC--KVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLY 123
K++LYT+S + G + W++ W++NGWKTS K V N + ++ + +
Sbjct: 68 QNINKLVLYTNSXFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGXDIQWX 127
Query: 124 WIKGHAGNQENEKVDRIARNAA 145
+ GH+G NE+ DR+AR A
Sbjct: 128 HVPGHSGFIGNEEADRLAREGA 149
>2hb5_A Reverse transcriptase/ribonuclease H; RNAse H, hydrolase;
1.59A {Moloney murine leukemia virus} (A:)
Length = 164
Score = 100 bits (249), Expect = 1e-22
Identities = 27/143 (18%), Positives = 47/143 (32%), Gaps = 16/143 (11%)
Query: 8 EVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPC 67
+ YTDG+ G G + + + T+ R EL+A +AL +
Sbjct: 22 DHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKXAE-GK 80
Query: 68 KVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKG 127
K+ +YTDS Y + + ++ ++ + G
Sbjct: 81 KLNVYTDSRYAFATAHLTSEGKEIKNKD----------EILALLKALFLPKRLSIIHCPG 130
Query: 128 HAGN-----QENEKVDRIARNAA 145
H + N D+ AR AA
Sbjct: 131 HQKGHSAEARGNRXADQAARKAA 153
>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase,
drug design, transferase; 2.35A {Human immunodeficiency
virus 2} (A:427-555)
Length = 129
Score = 76.9 bits (188), Expect = 1e-15
Identities = 26/136 (19%), Positives = 44/136 (32%), Gaps = 18/136 (13%)
Query: 9 VHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPCK 68
YTDG+C+ G G + + +TTN + EL A + K
Sbjct: 11 ETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE---QTTNQQAELEAFA--MALTDSGPK 65
Query: 69 VLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKGH 128
V + DS YV + + + E + + + W+ H
Sbjct: 66 VNIIVDSQYVMGIVASQPTESESKIV-------------NQIIEEMIKKEAIYVAWVPAH 112
Query: 129 AGNQENEKVDRIARNA 144
G N++VD +
Sbjct: 113 KGIGGNQEVDHLVSQG 128
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon,
double-stranded RNA-dependent RNAse, hydrolase; 1.60A
{Sulfolobus tokodaii str} (A:)
Length = 149
Score = 74.5 bits (182), Expect = 7e-15
Identities = 32/144 (22%), Positives = 54/144 (37%), Gaps = 20/144 (13%)
Query: 9 VHAYTDGACS-GNPG-PGGWGVLLRYKGKEKI-----ISGGEKETTNNRMELMAAIKALT 61
+ Y DG C NPG +G ++ ++ +TNN E I +
Sbjct: 2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLM- 60
Query: 62 ALKYPCKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVD 121
+L SS + KG SQ + K +K K+ + + + E +
Sbjct: 61 -----ETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAI---ELKKKLNAT 112
Query: 122 LYWIKGHAGNQENEKVDRIARNAA 145
L W+ EN++ DR++R A
Sbjct: 113 LIWVPRE----ENKEADRLSRVAY 132
>3hyf_A Reverse transcriptase/rnaseh; HIV-1, hydrolase, DI-valent
metal nucleic acid cleavage mechanism, DI-valent metal
coordination; HET: ON1; 1.70A {Human immunodeficiency
virus 1} PDB: 1o1w_A 1hrh_A 1rdh_A (A:)
Length = 150
Score = 71.6 bits (174), Expect = 5e-14
Identities = 44/139 (31%), Positives = 65/139 (46%), Gaps = 6/139 (4%)
Query: 8 EVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPC 67
Y DGA + G G + ++ + +TTN + EL A L
Sbjct: 12 AETFYVDGAANRETKLGKAGYVTNRGRQKVV---TLTDTTNQKTELQAIY--LALQDSGL 66
Query: 68 KVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMK-FVEASAQHKVDLYWIK 126
+V + TDS Y +QWI W++ GWKT+DKK VKN+DL + + + KV L W+
Sbjct: 67 EVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVP 126
Query: 127 GHAGNQENEKVDRIARNAA 145
H G NE+VD++
Sbjct: 127 AHKGIGGNEQVDKLVSAGI 145
>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer,
NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine,
diarylpyrimidine, DAPY, DNA recombination; HET: T27;
1.80A {Human immunodeficiency virus 1} PDB: 2ze2_A*
3bgr_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A*
1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A*
1tvr_A* 2hmi_A* 2vg5_A* 2vg6_A* 2vg7_A* ... (A:430-557)
Length = 128
Score = 65.8 bits (159), Expect = 2e-12
Identities = 30/136 (22%), Positives = 43/136 (31%), Gaps = 18/136 (13%)
Query: 9 VHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPCK 68
Y DGA + G G + + TTN + EL A AL +
Sbjct: 11 ETFYVDGAANRETKLGKAGYVTNK---GRQKVVPLTNTTNQKTELQAIYLALQ--DSGLE 65
Query: 69 VLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKGH 128
V + TDS Y K + + + KV L W+ H
Sbjct: 66 VNIVTDSQYALGIIQAQPDKSESELV-------------NQIIEQLIKKEKVYLAWVPAH 112
Query: 129 AGNQENEKVDRIARNA 144
G NE+VD++
Sbjct: 113 KGIGGNEQVDKLVSAG 128
>3c4h_A Poly(ADP-ribose) polymerase 3; enzyme-inhibitor complex,
catalytic fragment, structural genomics, structural
genomics consortium, SGC; HET: DRL; 2.10A {Homo sapiens}
PDB: 3c49_A* 2pa9_A* 3ce0_A* 3fhb_A* (A:148-357)
Length = 210
Score = 28.2 bits (62), Expect = 0.48
Identities = 11/66 (16%), Positives = 20/66 (30%), Gaps = 11/66 (16%)
Query: 84 QWIKKWQQNGWKTSDKKTVKNI------DLWMKFVEASAQHKVDLYWIKGHAGNQENEKV 137
+ I+ + + T+++I +F S L W H N V
Sbjct: 15 KVIQTYLEQTGSNHRCPTLQHIWKVNQEGEEDRFQAHSKLGNRKLLW---HGTNMAV--V 69
Query: 138 DRIARN 143
I +
Sbjct: 70 AAILTS 75
>2cvx_A Ribonucleoside-diphosphate reductase large chain 1;
eukaryotic, ribonucleotide reductase, DNTP regulation,
oxidoreductase; HET: DGT ADP; 2.20A {Saccharomyces
cerevisiae} PDB: 1zyz_A 2cvs_A 2cvt_A* 2cvu_A* 2cvv_A*
1zzd_A* 2cvw_A* 2cvy_A* 2eud_A* 2zlf_A 2zlg_A*
(A:167-616,A:689-888)
Length = 650
Score = 27.1 bits (59), Expect = 1.1
Identities = 8/41 (19%), Positives = 14/41 (34%)
Query: 74 DSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEA 114
+ + + + K KT+K LW +EA
Sbjct: 189 SAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEA 229
>1d5t_A Guanine nucleotide dissociation inhibitor; ultra-high
resolution; 1.04A {Bos taurus} (A:108-122,A:289-395)
Length = 122
Score = 25.9 bits (57), Expect = 2.4
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 33 KGKEKIISGGEKETTNNRMELMAAIKAL 60
+GK I+ ETT+ E+ A+ L
Sbjct: 75 QGKYIAIASTTVETTDPEKEVEPALGLL 102
>2r9f_A Calpain-1 catalytic subunit; protease, peptidase, inhibitor,
alpha-ketoamide, calcium, cytoplasm, hydrolase,
membrane, thiol protease; HET: K2Z; 1.60A {Rattus
norvegicus} (A:1-194)
Length = 194
Score = 24.8 bits (53), Expect = 6.0
Identities = 9/42 (21%), Positives = 17/42 (40%)
Query: 53 LMAAIKALTALKYPCKVLLYTDSSYVHKGFSQWIKKWQQNGW 94
L+AAI +LT + ++ S+ + + Q G
Sbjct: 92 LLAAIASLTLNETILHRVVPYGQSFQEGYAGIFHFQLWQFGE 133
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.315 0.131 0.408
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,175,880
Number of extensions: 48056
Number of successful extensions: 178
Number of sequences better than 10.0: 1
Number of HSP's gapped: 161
Number of HSP's successfully gapped: 24
Length of query: 152
Length of database: 4,956,049
Length adjustment: 81
Effective length of query: 71
Effective length of database: 2,217,844
Effective search space: 157466924
Effective search space used: 157466924
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: 51 (24.3 bits)