BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 029710
(189 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KIO|A Chain A, Mouse Rnase H2 Complex
Length = 301
Score = 144 bits (364), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 69/136 (50%), Positives = 90/136 (66%), Gaps = 3/136 (2%)
Query: 13 IFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 72
+ QV++DTVG E YQA+L Q FP I+ V KADSL+PVVS ASI AKV RD+ ++ W
Sbjct: 136 VTQVFVDTVGXPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQ 195
Query: 73 FEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLW 131
F E +++ ++GSGYP DP+TKAWL H +FGFP VRFSW T + K+ +V+W
Sbjct: 196 FVENLQDLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAEDVIW 255
Query: 132 ESDEMDEDVSSRRSGK 147
E E +ED R GK
Sbjct: 256 EDSEAEED--PERPGK 269
>pdb|3P5J|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
Length = 301
Score = 144 bits (362), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 69/136 (50%), Positives = 90/136 (66%), Gaps = 3/136 (2%)
Query: 13 IFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 72
+ QV++DTVG E YQA+L Q FP I+ V KADSL+PVVS ASI AKV RD+ ++ W
Sbjct: 136 VTQVFVDTVGMPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQ 195
Query: 73 FEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLW 131
F E +++ ++GSGYP DP+TKAWL H +FGFP VRFSW T + K+ +V+W
Sbjct: 196 FVENLQDLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAEDVIW 255
Query: 132 ESDEMDEDVSSRRSGK 147
E E +ED R GK
Sbjct: 256 EDSEAEED--PERPGK 269
>pdb|3PUF|A Chain A, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|D Chain D, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|G Chain G, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|J Chain J, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|M Chain M, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|P Chain P, Crystal Structure Of Human Rnase H2 Complex
Length = 302
Score = 138 bits (347), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 66/139 (47%), Positives = 91/139 (65%), Gaps = 6/139 (4%)
Query: 13 IFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 72
+ QV++DTVG E YQA+L Q FP I+ V KAD+LYPVVS ASI AKV RD+ ++ W
Sbjct: 138 VTQVFVDTVGMPETYQARLQQSFPGIEVTVKAKADALYPVVSAASICAKVARDQAVKKWQ 197
Query: 73 FEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLW 131
F E +++ ++GSGYP DP+TKAWL +H +FGFP VRFSW T + K+ +V+W
Sbjct: 198 FVEKLQDLDTDYGSGYPNDPKTKAWLKEHVEPVFGFPQFVRFSWRTAQTILEKEAEDVIW 257
Query: 132 ESDEMDEDVSSRRSGKRQL 150
E + S + G R++
Sbjct: 258 E-----DSASENQEGLRKI 271
>pdb|3P56|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
pdb|3P56|D Chain D, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
Length = 299
Score = 135 bits (340), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 65/139 (46%), Positives = 90/139 (64%), Gaps = 6/139 (4%)
Query: 13 IFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 72
+ QV++DTVG E YQA+L Q FP I+ V KA +LYPVVS ASI AKV RD+ ++ W
Sbjct: 135 VTQVFVDTVGMPETYQARLQQSFPGIEVTVKAKAAALYPVVSAASICAKVARDQAVKKWQ 194
Query: 73 FEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLW 131
F E +++ ++GSGYP DP+TKAWL +H +FGFP VRFSW T + K+ +V+W
Sbjct: 195 FVEKLQDLDTDYGSGYPNDPKTKAWLKEHVEPVFGFPQFVRFSWRTAQTILEKEAEDVIW 254
Query: 132 ESDEMDEDVSSRRSGKRQL 150
E + S + G R++
Sbjct: 255 E-----DSASENQEGLRKI 268
>pdb|2DFF|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-204)-C
Length = 213
Score = 73.6 bits (179), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 44/114 (38%), Positives = 64/114 (56%), Gaps = 8/114 (7%)
Query: 16 VYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIF 73
+Y D D E++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR +
Sbjct: 102 IYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV----- 156
Query: 74 EETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIV 127
E + + GSGYP DP T+A+L ++ FP +VR W T +D++
Sbjct: 157 -EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTLKKITQDMI 209
>pdb|1IO2|A Chain A, Crystal Structure Of Type 2 Ribonuclease H From
Hyperthermophilic Archaeon, Thermococcus Kodakaraensis
Kod1
Length = 213
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 43/106 (40%), Positives = 60/106 (56%), Gaps = 8/106 (7%)
Query: 16 VYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIF 73
+Y D D E++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR +
Sbjct: 102 IYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV----- 156
Query: 74 EETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 119
E + + GSGYP DP T+A+L ++ FP +VR W T
Sbjct: 157 -EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTL 201
>pdb|2DFH|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-212)-C
Length = 221
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 43/106 (40%), Positives = 60/106 (56%), Gaps = 8/106 (7%)
Query: 16 VYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIF 73
+Y D D E++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR +
Sbjct: 102 IYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV----- 156
Query: 74 EETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 119
E + + GSGYP DP T+A+L ++ FP +VR W T
Sbjct: 157 -EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTL 201
>pdb|2DFE|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-200)-C
Length = 209
Score = 71.6 bits (174), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 43/106 (40%), Positives = 60/106 (56%), Gaps = 8/106 (7%)
Query: 16 VYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIF 73
+Y D D E++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR +
Sbjct: 102 IYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV----- 156
Query: 74 EETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 119
E + + GSGYP DP T+A+L ++ FP +VR W T
Sbjct: 157 -EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTT 201
>pdb|1UAX|A Chain A, Crystal Structure Of The Ribonuclease H2 From Pyrococcus
Horikoshii Ot3
pdb|1UAX|B Chain B, Crystal Structure Of The Ribonuclease H2 From Pyrococcus
Horikoshii Ot3
Length = 220
Score = 71.2 bits (173), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 35/79 (44%), Positives = 46/79 (58%), Gaps = 6/79 (7%)
Query: 41 VVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTD 100
+ KAD+ Y +VS ASI+AKVTRDR + E + + FGSGYP DP TK WL +
Sbjct: 129 IAEHKADAKYEIVSAASIIAKVTRDREI------EKLKQKYGEFGSGYPSDPRTKEWLEE 182
Query: 101 HKHIIFGFPSLVRFSWGTC 119
+ FP +VR +W T
Sbjct: 183 YYKQYGDFPPIVRRTWETA 201
>pdb|1X1P|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-197)-A(28-42)
Length = 212
Score = 67.8 bits (164), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 42/106 (39%), Positives = 59/106 (55%), Gaps = 8/106 (7%)
Query: 16 VYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIF 73
+Y D D E++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR +
Sbjct: 102 IYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV----- 156
Query: 74 EETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 119
E + + GSGYP DP T+A+L ++ FP +VR G
Sbjct: 157 -EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGAGAI 201
>pdb|1EKE|A Chain A, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii)
With Mes Ligand
pdb|1EKE|B Chain B, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii)
With Mes Ligand
Length = 230
Score = 67.4 bits (163), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 36/97 (37%), Positives = 54/97 (55%), Gaps = 10/97 (10%)
Query: 25 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 84
+K + + +R +IK + KAD+ YPVVS ASI+AK RD + + + ++ +
Sbjct: 127 DKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYY------KKIYGDI 180
Query: 85 GSGYPGDPETKAWLTDH--KHIIFGFPSLVRFSWGTC 119
GSGYP DP+T +L D+ KH P + R W TC
Sbjct: 181 GSGYPSDPKTIKFLEDYFKKH--KKLPDIARTHWKTC 215
>pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus
pdb|1I3A|A Chain A, Rnase Hii From Archaeoglobus Fulgidus With Cobalt
Hexammine Chloride
Length = 225
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 34/109 (31%), Positives = 53/109 (48%), Gaps = 15/109 (13%)
Query: 17 YLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEET 76
Y+D+ + ++ + ++ V KAD YP+V+ ASI+AKV R+R + E
Sbjct: 119 YVDSPDVIPERLSRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREI------ER 172
Query: 77 AENMHRNFGSGYPGDPET----KAWLTDHKHIIFGFPSLVRFSWGTCTS 121
+ +FGSGY DP T K W+ + PS VR W T ++
Sbjct: 173 LKEKFGDFGSGYASDPRTREVLKEWIASGR-----IPSCVRMRWKTVSN 216
>pdb|3P83|D Chain D, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|E Chain E, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|F Chain F, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus
Length = 217
Score = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 34/109 (31%), Positives = 53/109 (48%), Gaps = 15/109 (13%)
Query: 17 YLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEET 76
Y+D+ + ++ + ++ V KAD YP+V+ ASI+AKV R+R + E
Sbjct: 111 YVDSPDVIPERLSRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREI------ER 164
Query: 77 AENMHRNFGSGYPGDPET----KAWLTDHKHIIFGFPSLVRFSWGTCTS 121
+ +FGSGY DP T K W+ + PS VR W T ++
Sbjct: 165 LKEKFGDFGSGYASDPRTREVLKEWIASGR-----IPSCVRMRWKTVSN 208
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.322 0.136 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,343,144
Number of Sequences: 62578
Number of extensions: 204547
Number of successful extensions: 459
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 435
Number of HSP's gapped (non-prelim): 14
length of query: 189
length of database: 14,973,337
effective HSP length: 93
effective length of query: 96
effective length of database: 9,153,583
effective search space: 878743968
effective search space used: 878743968
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)