RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10246
(287 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 = 42.7 bits (101), Expect = 2e-05
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 213 PWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSI 255
++ + M R F + +H G N+ VD AK+++
Sbjct: 94 EFTQAYAKLMNQYRG-IYSFEKVKAHSGNEFNDYVDMKAKSAL 135
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 37.9 bits (89), Expect = 0.001
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 228 INIKFLWIPSHCGIVENERVDQAAKNSI 255
++I+++ +P H G + NE D+ A+
Sbjct: 122 MDIQWMHVPGHSGFIGNEEADRLAREGA 149
>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase,
hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB:
3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A
Length = 150
Score = 37.5 bits (88), Expect = 0.001
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 229 NIKFLWIPSHCGIVENERVDQAAKNSI 255
+ W+P+H GI NE+VD+ I
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLVSAGI 145
>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 = 38.7 bits (89), Expect = 0.002
Identities = 31/192 (16%), Positives = 52/192 (27%), Gaps = 86/192 (44%)
Query: 53 NEILEKDSPVSAHRILFLLL----------------NPD-----------CNDPSFFLPD 85
+ I+ VS LF L + PS
Sbjct: 52 DHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPS---MM 108
Query: 86 PGSFEKDNDNISSV------YLVSRSESIARLARYGKSAWFDLQKAGLELPTNAFGVENN 139
+ + D + + Y VSR + + L++A LEL
Sbjct: 109 TRMYIEQRDRLYNDNQVFAKYNVSRLQPYLK-----------LRQALLEL---------- 147
Query: 140 VQCSWILSTQASSGCLLINSATGYAMSGYQDTRLYSG-AILVMKVLQSVQI-----FKIG 193
+ + L+ + G SG + + V S ++ FKI
Sbjct: 148 ---------RPAKNVLI------DGVLG-------SGKTWVALDVCLSYKVQCKMDFKI- 184
Query: 194 KWLEISVLGSPD 205
WL + SP+
Sbjct: 185 FWLNLKNCNSPE 196
Score = 30.6 bits (68), Expect = 0.72
Identities = 21/129 (16%), Positives = 34/129 (26%), Gaps = 30/129 (23%)
Query: 7 KKVGILKATTNITPAYDSLVCLEGRASAFSWPRLAGHSRSACQFQNNEILEKDSPVSAHR 66
K V K TT I + + L E R F + + +
Sbjct: 348 KHVNCDKLTTIIESSLNVLEPAEYRK----------------MFDRLSVFPPSAHIPTIL 391
Query: 67 ILFLLLNPDCNDPSFF---LPDPGSFEKDNDN----ISSVYLVSRSESIAR-------LA 112
+ + + +D L EK I S+YL + + +
Sbjct: 392 LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVD 451
Query: 113 RYGKSAWFD 121
Y FD
Sbjct: 452 HYNIPKTFD 460
>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 = 36.7 bits (86), Expect = 0.002
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 229 NIKFLWIPSHCGIVENERVDQAAKNSI 255
IK+ W+ H G ENER D+ A+ +
Sbjct: 115 QIKWEWVKGHAGHPENERADELARAAA 141
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 35.9 bits (84), Expect = 0.005
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 229 NIKFLWIPSHCGIVENERVDQAAKNSI 255
+ F + H N R D+ A+ +I
Sbjct: 116 RVTFHKVKGHSDNPYNSRADELARLAI 142
>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 = 37.3 bits (86), Expect = 0.005
Identities = 48/230 (20%), Positives = 75/230 (32%), Gaps = 79/230 (34%)
Query: 6 PKKVGILKATTNIT-PAYDSLVCLEGRASAF----SW---PR---LAGHSR---SACQFQ 51
K G+L AT T PA L +E +AF S P AGHS +A
Sbjct: 1722 EK--GLLSATQF-TQPA---LTLME--KAAFEDLKSKGLIPADATFAGHSLGEYAA---- 1769
Query: 52 NNEILEKDSPVSAHRILFLLLNPDCNDPSFFLPDPGSFEKDNDNISSVYLVS-RSESIAR 110
L S ++ S E S V +V R ++
Sbjct: 1770 ----L-----ASLADVM-------------------SIE------SLVEVVFYRGMTMQV 1795
Query: 111 LARYGKSAWFDLQKAGLELPT--NAFGVENNVQCSWILSTQASSGCLL-I---NSATG-Y 163
+ + + P A + +Q + +G L+ I N Y
Sbjct: 1796 AVPRDELGRSNYGMIAIN-PGRVAASFSQEALQ-YVVERVGKRTGWLVEIVNYNVENQQY 1853
Query: 164 AMSGYQDTRLYSGAI-LVMKVLQSVQIFKIGKWLEISVLGSPD-VKKVIF 211
+G D R A+ V VL +++ KI +E+ S + V+ +F
Sbjct: 1854 VAAG--DLR----ALDTVTNVLNFIKLQKI-DIIELQKSLSLEEVEGHLF 1896
Score = 33.5 bits (76), Expect = 0.081
Identities = 45/305 (14%), Positives = 81/305 (26%), Gaps = 104/305 (34%)
Query: 15 TTNITPA--YDSLVCLEGR----------ASAFSWPRLAGHSRSACQFQNNEILEKDSPV 62
TP L G A SW F +
Sbjct: 255 LLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWE----------SFFVSV-------R 297
Query: 63 SAHRILFLL------LNPDCNDPSFFLPDPGSFEKDNDNISSVYLVSRSESIARLARYGK 116
A +LF + P+ + P L D ++N+ + S L + + ++ Y
Sbjct: 298 KAITVLFFIGVRCYEAYPNTSLPPSILED---SLENNEGVPSPMLSISNLTQEQVQDY-- 352
Query: 117 SAWFDLQKAGLELPTNAFGVENNVQCSWILSTQASSGCLLINSATGYAMSGYQDTRLYSG 176
+ K LP V+ S L+N A +SG + LY
Sbjct: 353 -----VNKTNSHLPAG-----KQVEIS------------LVNGAKNLVVSGPPQS-LYGL 389
Query: 177 AILVMKVL------QSVQIF---KI---GKWLEISVLGSPDVKKVIF-SPWSVRNVRAMK 223
+ + K QS F K+ ++L ++ P F S + +
Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVAS---P------FHSHL-LVPASDLI 439
Query: 224 FARDINIKFLWIPSHCGI----VENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNE 279
+ + I + + SI +++ ++ V
Sbjct: 440 NKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPV----------- 488
Query: 280 WKTDW 284
W
Sbjct: 489 ---KW 490
Score = 31.9 bits (72), Expect = 0.26
Identities = 35/207 (16%), Positives = 57/207 (27%), Gaps = 74/207 (35%)
Query: 80 SFF--LPDP-GSFEKDNDNISSVYLVSR-SESIARLARYGKSAWFDLQKAGLELPTNAFG 135
F LP+P F D++ + LV + ++ L K FD L L F
Sbjct: 36 QFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFD---QVLNLCLTEFE 92
Query: 136 VE----NNVQC-----------------SWILS------------TQASSGCLLINSATG 162
N++ I + + S+ L G
Sbjct: 93 NCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEG 152
Query: 163 ----YAMSG-------Y----QDT-RLYSGAI-----LVMKVLQSV------------QI 189
A+ G Y +D + Y + + L + Q
Sbjct: 153 NAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQG 212
Query: 190 FKIGKWLEISVLGSPDVKKVIFSPWSV 216
I +WLE +PD ++ P S
Sbjct: 213 LNILEWLENPS-NTPDKDYLLSIPISC 238
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 35.6 bits (83), Expect = 0.006
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 229 NIKFLWIPSHCGIVENERVDQAAKNSI 255
I + W+ H G ENER DQ A+ +
Sbjct: 117 QIDWRWVKGHAGHAENERCDQLARAAA 143
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 35.6 bits (83), Expect = 0.006
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 229 NIKFLWIPSHCGIVENERVDQAAKNSI 255
++F ++ H G ENERVD+ A+
Sbjct: 120 RVRFHFVKGHTGHPENERVDREARRQA 146
>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 = 31.4 bits (71), Expect = 0.19
Identities = 8/42 (19%), Positives = 16/42 (38%), Gaps = 5/42 (11%)
Query: 229 NIKFLWIPSHCGIVE-----NERVDQAAKNSIYAQLLKSVVV 265
+ + P H N DQAA+ + +L++ +
Sbjct: 123 RLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLETSTL 164
>2dre_A Water-soluble chlorophyll protein; beta-trefoil, tetramer, plant,
singlet oxygen, photooxidation, chlorophyll carrier;
HET: CLA; 2.00A {Lepidium virginicum}
Length = 180
Score = 27.4 bits (60), Expect = 4.8
Identities = 7/31 (22%), Positives = 9/31 (29%)
Query: 209 VIFSPWSVRNVRAMKFARDINIKFLWIPSHC 239
V S S + +I I F C
Sbjct: 62 VTISTPSSSEGNDVLTNTNIAITFDAPIWLC 92
>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular
transport, cytoplasm, cytoplasmic vesicle, exocytosis,
GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae}
SCOP: c.37.1.8
Length = 213
Score = 26.9 bits (60), Expect = 6.9
Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 7/65 (10%)
Query: 176 GAILVMKVLQSVQIFKIGKWL-EISVLGSPDVKKVIF---SPWSVRNV---RAMKFARDI 228
G ILV V I +W ++ + + + ++ S R V + A+++
Sbjct: 95 GIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKEL 154
Query: 229 NIKFL 233
I F+
Sbjct: 155 GIPFI 159
>3s8k_A Latex serine proteinase inhibitor; kunitz-STI fold, protease
inhibitor, hydrolase inhibitor; HET: NAG FUC; 1.70A
{Carica papaya} PDB: 3s8j_A*
Length = 184
Score = 26.5 bits (58), Expect = 7.7
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 209 VIFSPWSVRNVRAMKFARDINIKFLWIPSHCG 240
+IFS ++ + D+N+KF I +C
Sbjct: 60 IIFSAIKNVKDNIVRESVDLNVKFN-ITINCN 90
>3dg3_A Muconate cycloisomerase; muconate lactonizing enzyme, muconolactone
binding; 1.60A {Mycobacterium smegmatis} PDB: 3dg6_A*
3dg7_A*
Length = 367
Score = 26.9 bits (60), Expect = 9.4
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 4/42 (9%)
Query: 210 IFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAA 251
+ +P V A I+IK + G + RV A
Sbjct: 245 VPTPADVTREVLGGSATAISIK----TARTGFTGSTRVHHLA 282
>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: 3is9_A*
3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_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* ...
Length = 557
Score = 27.0 bits (60), Expect = 9.4
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 234 WIPSHCGIVENERVDQ 249
W+P+H GI NE+VD+
Sbjct: 537 WVPAHKGIGGNEQVDK 552
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
0.319 0.133 0.402
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,228,100
Number of extensions: 234297
Number of successful extensions: 450
Number of sequences better than 10.0: 1
Number of HSP's gapped: 446
Number of HSP's successfully gapped: 26
Length of query: 287
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 194
Effective length of database: 4,105,140
Effective search space: 796397160
Effective search space used: 796397160
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 (21.8 bits)
S2: 57 (25.6 bits)