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= psy12553
(401 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 259 bits (663), Expect = 2e-69, Method: Compositional matrix adjust.
Identities = 127/259 (49%), Positives = 174/259 (67%), Gaps = 17/259 (6%)
Query: 20 NDNSRNLIISSTIPESCKSQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCA 79
DN+ +SS +P C+ +PCVLG+DEAGRGPVLGPMVY YCP +L + L A
Sbjct: 11 RDNTGRCRLSSPVPAVCRKEPCVLGVDEAGRGPVLGPMVYAICYCPLPRLADL-EALKVA 69
Query: 80 DSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLI 139
DSK L E +R+ + + ++ ++GW ++++SPN+I SML R KY+LN +SHD A GLI
Sbjct: 70 DSKTLLESERERLFAKM-EDTDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLI 128
Query: 140 RKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADS 199
+ + GVNV +V+VDTVG PE+Y+ +L + FP + +TV +KAD+ YPV
Sbjct: 129 QYALDQGVNVTQVFVDTVGMPETYQARLQQSFPGIEVTVKAKADALYPV----------- 177
Query: 200 TYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGF 259
V AASICAKV+RD A+K W F E +Q + +GSGYP DP TK +L E+++PVFGF
Sbjct: 178 ----VSAASICAKVARDQAVKKWQFVEKLQDLDTDYGSGYPNDPKTKAWLKEHVEPVFGF 233
Query: 260 PQLVRFSWSTASKILKEKA 278
PQ VRFSW TA IL+++A
Sbjct: 234 PQFVRFSWRTAQTILEKEA 252
>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 = 257 bits (657), Expect = 8e-69, Method: Compositional matrix adjust.
Identities = 127/258 (49%), Positives = 175/258 (67%), Gaps = 16/258 (6%)
Query: 21 DNSRNLIISSTIPESCKSQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCAD 80
DN+ +SS +P C +PCVLG+DEAGRGPVLGPMVY YCP +L + L AD
Sbjct: 9 DNTGRCRLSSPVPAVCLKEPCVLGVDEAGRGPVLGPMVYAICYCPLSRLADL-EALKVAD 67
Query: 81 SKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIR 140
SK LTE +R+ + + ++ ++GW ++++SPN+I SML R KY+LN +SHD A GLI+
Sbjct: 68 SKTLTENERERLFAKMEEDGDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQ 127
Query: 141 KVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADST 200
+ VNV +V+VDTVG PE+Y+ +L + FP + +TV +KA DS
Sbjct: 128 YALDQNVNVTQVFVDTVGMPETYQARLQQHFPGIEVTVKAKA---------------DSL 172
Query: 201 YPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFP 260
+PVV AASI AKV+RD A+K+W F E +Q ++ +GSGYP DP TK +L +++DPVFGFP
Sbjct: 173 FPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDYGSGYPNDPKTKAWLRKHVDPVFGFP 232
Query: 261 QLVRFSWSTASKILKEKA 278
Q VRFSWSTA IL+++A
Sbjct: 233 QFVRFSWSTAQAILEKEA 250
>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 = 254 bits (649), Expect = 6e-68, Method: Compositional matrix adjust.
Identities = 127/259 (49%), Positives = 174/259 (67%), Gaps = 17/259 (6%)
Query: 20 NDNSRNLIISSTIPESCKSQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCA 79
DN+ +SS +P C+ +PCVLG+ EAGRGPVLGPMVY YCP +L + L A
Sbjct: 8 RDNTGRCRLSSPVPAVCRKEPCVLGVAEAGRGPVLGPMVYAICYCPLPRLADL-EALKVA 66
Query: 80 DSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLI 139
DSK L E +R+ + + ++ ++GW ++++SPN+I SML R KY+LN +SHD A GLI
Sbjct: 67 DSKTLLESERERLFAKM-EDTDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLI 125
Query: 140 RKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADS 199
+ + GVNV +V+VDTVG PE+Y+ +L + FP + +TV +KA AA+
Sbjct: 126 QYALDQGVNVTQVFVDTVGMPETYQARLQQSFPGIEVTVKAKA--------AAL------ 171
Query: 200 TYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGF 259
YPVV AASICAKV+RD A+K W F E +Q + +GSGYP DP TK +L E+++PVFGF
Sbjct: 172 -YPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDYGSGYPNDPKTKAWLKEHVEPVFGF 230
Query: 260 PQLVRFSWSTASKILKEKA 278
PQ VRFSW TA IL+++A
Sbjct: 231 PQFVRFSWRTAQTILEKEA 249
>pdb|3KIO|A Chain A, Mouse Rnase H2 Complex
Length = 301
Score = 251 bits (640), Expect = 7e-67, Method: Compositional matrix adjust.
Identities = 125/258 (48%), Positives = 172/258 (66%), Gaps = 16/258 (6%)
Query: 21 DNSRNLIISSTIPESCKSQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCAD 80
DN+ +SS +P C +PCVLG+DEAGRGPVLGP VY YCP +L + L AD
Sbjct: 9 DNTGRCRLSSPVPAVCLKEPCVLGVDEAGRGPVLGPXVYAICYCPLSRLADL-EALKVAD 67
Query: 81 SKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIR 140
SK LTE +R+ + ++ ++GW ++++SPN+I S L R KY+LN +SHD A GLI+
Sbjct: 68 SKTLTENERERLFAKXEEDGDFVGWALDVLSPNLISTSXLGRVKYNLNSLSHDTAAGLIQ 127
Query: 141 KVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADST 200
+ VNV +V+VDTVG PE+Y+ +L + FP + +TV +K ADS
Sbjct: 128 YALDQNVNVTQVFVDTVGXPETYQARLQQHFPGIEVTVKAK---------------ADSL 172
Query: 201 YPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFP 260
+PVV AASI AKV+RD A+K+W F E +Q ++ +GSGYP DP TK +L +++DPVFGFP
Sbjct: 173 FPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDYGSGYPNDPKTKAWLRKHVDPVFGFP 232
Query: 261 QLVRFSWSTASKILKEKA 278
Q VRFSWSTA IL+++A
Sbjct: 233 QFVRFSWSTAQAILEKEA 250
>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 = 105 bits (262), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 79/234 (33%), Positives = 119/234 (50%), Gaps = 34/234 (14%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
V G+DEAGRGPV+GP+V G A + N E L+++G DSK LT +R+ + + +
Sbjct: 3 VAGVDEAGRGPVIGPLVIGVAVI-DEKNIERLRDIGVKDSKQLTPGQREKLFSKLI--DI 59
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDT--VGP 159
+ V +++P I + +S+NE+ A + + + + +++YVD+ V P
Sbjct: 60 LDDYYVLLVTPKEIDE-----RHHSMNELE---AEKFVVALNSLRIKPQKIYVDSADVDP 111
Query: 160 PESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSAL 219
F LI KA Y A KAD+ Y +V AASI AKV+RD +
Sbjct: 112 KR---------FASLI-----KAGLKYEATVIA-EHKADAKYEIVSAASIIAKVTRDREI 156
Query: 220 KSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKI 273
E ++ + +GSGYP DP TK++L E FP +VR +W TA KI
Sbjct: 157 ------EKLKQKYGEFGSGYPSDPRTKEWLEEYYKQYGDFPPIVRRTWETARKI 204
>pdb|2DFF|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-204)-C
Length = 213
Score = 92.0 bits (227), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 76/236 (32%), Positives = 111/236 (47%), Gaps = 32/236 (13%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
+ GIDEAGRGPV+GPMV A +N+ L+ L DSK LT K+R+ + + I
Sbjct: 3 IAGIDEAGRGPVIGPMVIA-AVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEIL--GV 59
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVG-PP 160
+++ + P+VI + ++ +LNE + + + + V +Y D
Sbjct: 60 LDDYVILELPPDVIGS-----REGTLNEFEVE---NFAKALNSLKVKPDVIYADAADVDE 111
Query: 161 ESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALK 220
E + ++L E VA KAD +PVV AASI AKV+RD A+
Sbjct: 112 ERFARELGERLNFEAEVVAK--------------HKADDIFPVVSAASILAKVTRDRAV- 156
Query: 221 SWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKE 276
E ++ E GSGYP DP T+ FL FP +VR W T KI ++
Sbjct: 157 -----EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTLKKITQD 207
>pdb|2DFH|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-212)-C
Length = 221
Score = 92.0 bits (227), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 76/233 (32%), Positives = 109/233 (46%), Gaps = 32/233 (13%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
+ GIDEAGRGPV+GPMV A +N+ L+ L DSK LT K+R+ + + I
Sbjct: 3 IAGIDEAGRGPVIGPMVIA-AVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEIL--GV 59
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVG-PP 160
+++ + P+VI + ++ +LNE + + + + V +Y D
Sbjct: 60 LDDYVILELPPDVIGS-----REGTLNEFEVE---NFAKALNSLKVKPDVIYADAADVDE 111
Query: 161 ESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALK 220
E + ++L E VA KAD +PVV AASI AKV+RD A+
Sbjct: 112 ERFARELGERLNFEAEVVAK--------------HKADDIFPVVSAASILAKVTRDRAV- 156
Query: 221 SWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKI 273
E ++ E GSGYP DP T+ FL FP +VR W T KI
Sbjct: 157 -----EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTLKKI 204
>pdb|1IO2|A Chain A, Crystal Structure Of Type 2 Ribonuclease H From
Hyperthermophilic Archaeon, Thermococcus Kodakaraensis
Kod1
Length = 213
Score = 91.7 bits (226), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 76/233 (32%), Positives = 109/233 (46%), Gaps = 32/233 (13%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
+ GIDEAGRGPV+GPMV A +N+ L+ L DSK LT K+R+ + + I
Sbjct: 3 IAGIDEAGRGPVIGPMVI-AAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEIL--GV 59
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVG-PP 160
+++ + P+VI + ++ +LNE + + + + V +Y D
Sbjct: 60 LDDYVILELPPDVIGS-----REGTLNEFEVE---NFAKALNSLKVKPDVIYADAADVDE 111
Query: 161 ESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALK 220
E + ++L E VA KAD +PVV AASI AKV+RD A+
Sbjct: 112 ERFARELGERLNFEAEVVAK--------------HKADDIFPVVSAASILAKVTRDRAV- 156
Query: 221 SWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKI 273
E ++ E GSGYP DP T+ FL FP +VR W T KI
Sbjct: 157 -----EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTLKKI 204
>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 = 91.7 bits (226), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 84/246 (34%), Positives = 120/246 (48%), Gaps = 42/246 (17%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
++GIDEAGRGPVLGP V A+ + EE LK LG DSK LT+ KR + + EN
Sbjct: 3 IIGIDEAGRGPVLGPXVV-CAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLL--EN- 58
Query: 102 WLGW----MVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVR----EVY 153
LG+ ++E N + NS+ +LN++ +A + + +I +N+R E+Y
Sbjct: 59 -LGYVEKRILEAEEINQLXNSI------NLNDIEINAFSKVAKNLIEK-LNIRDDEIEIY 110
Query: 154 VDTVGP-----PESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAAS 208
+D +S+K K+ +I E + + A+ KAD+ YPVV AAS
Sbjct: 111 IDACSTNTKKFEDSFKDKIEDIIKERNLNIKIIAE-----------HKADAKYPVVSAAS 159
Query: 209 ICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWS 268
I AK RD + + G GSGYP DP T KFL + P + R W
Sbjct: 160 IIAKAERDEIIDYYKKIYG------DIGSGYPSDPKTIKFLEDYFKKHKKLPDIARTHWK 213
Query: 269 TASKIL 274
T +IL
Sbjct: 214 TCKRIL 219
>pdb|2DFE|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-200)-C
Length = 209
Score = 89.7 bits (221), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 74/234 (31%), Positives = 109/234 (46%), Gaps = 32/234 (13%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
+ GIDEAGRGPV+GPMV A +N+ L+ L DSK LT K+R+ + + I
Sbjct: 3 IAGIDEAGRGPVIGPMVIA-AVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEIL--GV 59
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVG-PP 160
+++ + P+VI + ++ +LNE + + + + V +Y D
Sbjct: 60 LDDYVILELPPDVIGS-----REGTLNEFEVE---NFAKALNSLKVKPDVIYADAADVDE 111
Query: 161 ESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALK 220
E + ++L E VA KAD +PVV AASI AKV+RD A+
Sbjct: 112 ERFARELGERLNFEAEVVAK--------------HKADDIFPVVSAASILAKVTRDRAV- 156
Query: 221 SWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKIL 274
E ++ E GSGYP DP T+ FL FP +VR W T ++
Sbjct: 157 -----EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTTQDMI 205
>pdb|1X1P|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-197)-A(28-42)
Length = 212
Score = 82.0 bits (201), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 72/224 (32%), Positives = 105/224 (46%), Gaps = 32/224 (14%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
+ GIDEAGRGPV+GPMV A +N+ L+ L DSK LT K+R+ + + I
Sbjct: 3 IAGIDEAGRGPVIGPMVI-AAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEIL--GV 59
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVG-PP 160
+++ + P+VI + ++ +LNE + + + + V +Y D
Sbjct: 60 LDDYVILELPPDVIGS-----REGTLNEFEVE---NFAKALNSLKVKPDVIYADAADVDE 111
Query: 161 ESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALK 220
E + ++L E VA KAD +PVV AASI AKV+RD A+
Sbjct: 112 ERFARELGERLNFEAEVVAK--------------HKADDIFPVVSAASILAKVTRDRAV- 156
Query: 221 SWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVR 264
E ++ E GSGYP DP T+ FL FP +VR
Sbjct: 157 -----EKLKEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVR 195
>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 = 80.5 bits (197), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 73/236 (30%), Positives = 110/236 (46%), Gaps = 48/236 (20%)
Query: 44 GIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWL 103
GIDEAG+G V+GP+V C ++E+ L+ LG DSK L++ +R+++ + I K
Sbjct: 24 GIDEAGKGCVIGPLVVAGVAC---SDEDRLRKLGVKDSKKLSQGRREELAEEIRK----- 75
Query: 104 GWMVEIISPNVICNS-MLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVR---EV-YVDTVG 158
IC + +L+ +L+E I I K A + +R E+ YVD+
Sbjct: 76 -----------ICRTEVLKVSPENLDERMAAKTINEILKECYAEIILRLKPEIAYVDSPD 124
Query: 159 P-PESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDS 217
PE ++L EI ++ KAD YP+V AASI AKV R+
Sbjct: 125 VIPERLSRELEEITGLRVVA----------------EHKADEKYPLVAAASIIAKVERER 168
Query: 218 ALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKI 273
+ E ++ + +GSGY DP T++ L E I P VR W T S +
Sbjct: 169 EI------ERLKEKFGDFGSGYASDPRTREVLKEWI-ASGRIPSCVRMRWKTVSNL 217
>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 = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 73/236 (30%), Positives = 110/236 (46%), Gaps = 48/236 (20%)
Query: 44 GIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWL 103
GIDEAG+G V+GP+V C ++E+ L+ LG DSK L++ +R+++ + I K
Sbjct: 16 GIDEAGKGCVIGPLVVAGVAC---SDEDRLRKLGVKDSKKLSQGRREELAEEIRK----- 67
Query: 104 GWMVEIISPNVICNS-MLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVR---EV-YVDTVG 158
IC + +L+ +L+E I I K A + +R E+ YVD+
Sbjct: 68 -----------ICRTEVLKVSPENLDERMAAKTINEILKECYAEIILRLKPEIAYVDSPD 116
Query: 159 P-PESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDS 217
PE ++L EI ++ KAD YP+V AASI AKV R+
Sbjct: 117 VIPERLSRELEEITGLRVVA----------------EHKADEKYPLVAAASIIAKVERER 160
Query: 218 ALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKI 273
+ E ++ + +GSGY DP T++ L E I P VR W T S +
Sbjct: 161 EI------ERLKEKFGDFGSGYASDPRTREVLKEWI-ASGRIPSCVRMRWKTVSNL 209
>pdb|3O3F|A Chain A, T. Maritima Rnase H2 D107n In Complex With Nucleic Acid
Substrate And Magnesium Ions
pdb|3O3H|A Chain A, T. Maritima Rnase H2 D107n In Complex With Nucleic Acid
Substrate And Manganese Ions
Length = 222
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 46/182 (25%), Positives = 71/182 (39%), Gaps = 48/182 (26%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
V G+DEAGRG + GP+V K+ G DSK L+ KR+ +LD I E A
Sbjct: 13 VAGVDEAGRGCLAGPVVAAAVVLEKEIE-------GINDSKQLSPAKRERLLDEIM-EKA 64
Query: 102 WLGWMVEIISPNVI-CNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPP 160
+G + I SP I ++ K ++N + ++
Sbjct: 65 AVG--IGIASPEEIDLYNIFNATKLAMNRALENLSVK----------------------- 99
Query: 161 ESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALK 220
P ++ + + P G + K D ++GAASI AKV RD +
Sbjct: 100 -----------PSFVLVNGKGIELSVP--GTCLV-KGDQKSKLIGAASIVAKVFRDRLMS 145
Query: 221 SW 222
+
Sbjct: 146 EF 147
>pdb|3O3G|A Chain A, T. Maritima Rnase H2 In Complex With Nucleic Acid
Substrate And Calcium Ions
Length = 222
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 46/182 (25%), Positives = 71/182 (39%), Gaps = 48/182 (26%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
V G+DEAGRG + GP+V K+ G DSK L+ KR+ +LD I E A
Sbjct: 13 VAGVDEAGRGCLAGPVVAAAVVLEKEIE-------GINDSKQLSPAKRERLLDEIM-EKA 64
Query: 102 WLGWMVEIISPNVI-CNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPP 160
+G + I SP I ++ K ++N + ++
Sbjct: 65 AVG--IGIASPEEIDLYNIFNATKLAMNRALENLSVK----------------------- 99
Query: 161 ESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALK 220
P ++ + + P G + K D ++GAASI AKV RD +
Sbjct: 100 -----------PSFVLVDGKGIELSVP--GTCLV-KGDQKSKLIGAASIVAKVFRDRLMS 145
Query: 221 SW 222
+
Sbjct: 146 EF 147
>pdb|4HHT|A Chain A, T. Maritima Rnase H2 G21s In Complex With Nucleic Acid
Substrate And Calcium Ions
Length = 237
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 45/182 (24%), Positives = 70/182 (38%), Gaps = 48/182 (26%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
V G+DEA RG + GP+V K+ G DSK L+ KR+ +LD I E A
Sbjct: 13 VAGVDEASRGCLAGPVVAAAVVLEKEIE-------GINDSKQLSPAKRERLLDEIM-EKA 64
Query: 102 WLGWMVEIISPNVI-CNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPP 160
+G + I SP I ++ K ++N + ++
Sbjct: 65 AVG--IGIASPEEIDLYNIFNATKLAMNRALENLSVK----------------------- 99
Query: 161 ESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALK 220
P ++ + + P G + K D ++GAASI AKV RD +
Sbjct: 100 -----------PSFVLVDGKGIELSVP--GTCLV-KGDQKSKLIGAASIVAKVFRDRLMS 145
Query: 221 SW 222
+
Sbjct: 146 EF 147
>pdb|2ETJ|A Chain A, Crystal Structure Of Ribonuclease Hii (ec 3.1.26.4) (rnase
Hii) (tm0915) From Thermotoga Maritima At 1.74 A
Resolution
Length = 250
Score = 37.0 bits (84), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 46/176 (26%), Positives = 68/176 (38%), Gaps = 48/176 (27%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
V G+DEAGRG + GP+V K+ G DSK L+ KR+ +LD I E A
Sbjct: 26 VAGVDEAGRGCLAGPVVAAAVVLEKEIE-------GINDSKQLSPAKRERLLDEIX-EKA 77
Query: 102 WLGWMVEIISPNVI-CNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPP 160
+G + I SP I ++ K + N + ++
Sbjct: 78 AVG--IGIASPEEIDLYNIFNATKLAXNRALENLSVK----------------------- 112
Query: 161 ESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRD 216
P ++ + + P G + K D ++GAASI AKV RD
Sbjct: 113 -----------PSFVLVDGKGIELSVP--GTCLV-KGDQKSKLIGAASIVAKVFRD 154
>pdb|2D0A|A Chain A, Crystal Structure Of Bst-Rnase Hiii
pdb|2D0B|A Chain A, Crystal Structure Of Bst-Rnase Hiii In Complex With Mg2+
pdb|2D0C|A Chain A, Crystal Structure Of Bst-Rnase Hiii In Complex With Mn2+
Length = 310
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 12/65 (18%)
Query: 34 ESCKSQPCVL-----------GIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSK 82
E+ QP L G DE G G GP+V AY + + + + LG DSK
Sbjct: 74 ETADHQPSALAAHQLGSLSAIGSDEVGTGDYFGPIVVAAAYVDRPHIAK-IAALGVKDSK 132
Query: 83 ALTEK 87
L ++
Sbjct: 133 QLNDE 137
>pdb|3ASM|A Chain A, Crystal Structure Of Q54a Mutant Protein Of Bst-Rnase Hiii
Length = 310
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 12/65 (18%)
Query: 34 ESCKSQPCVL-----------GIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSK 82
E+ QP L G DE G G GP+V AY + + + + LG DSK
Sbjct: 74 ETADHQPSALAAHQLGSLSAIGSDEVGTGDYFGPIVVAAAYVDRPHIAK-IAALGVKDSK 132
Query: 83 ALTEK 87
L ++
Sbjct: 133 QLNDE 137
>pdb|2ZIW|B Chain B, Crystal Structure Of The Mus81-Eme1 Complex
Length = 341
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 73 LKNLGCADSKALTE----KKRDDILDSICKENAWLGWM-VEIISPNVICNSMLRRQKYSL 127
L + CA +KA+ E K RD+ S C E+ W G + V++ + + RRQ L
Sbjct: 203 LADFTCAFTKAVAEAPFKKLRDETTFSFCLESDWAGGVKVDLAGRGLAL--VWRRQIQQL 260
Query: 128 NEVSHDAAIGLI 139
N VS + A ++
Sbjct: 261 NRVSLEXASAVV 272
>pdb|2ZIU|B Chain B, Crystal Structure Of The Mus81-Eme1 Complex
pdb|2ZIX|B Chain B, Crystal Structure Of The Mus81-Eme1 Complex
Length = 341
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 73 LKNLGCADSKALTE----KKRDDILDSICKENAWLGWM-VEIISPNVICNSMLRRQKYSL 127
L + CA +KA+ E K RD+ S C E+ W G + V++ + + RRQ L
Sbjct: 203 LADFTCAFTKAVAEAPFKKLRDETTFSFCLESDWAGGVKVDLAGRGLAL--VWRRQIQQL 260
Query: 128 NEVSHDAAIGLI 139
N VS + A ++
Sbjct: 261 NRVSLEMASAVV 272
>pdb|2Z39|A Chain A, Crystal Structure Of Brassica Juncea Chitinase Catalytic
Module Glu234ala Mutant (bjchi3-e234a)
pdb|2Z39|B Chain B, Crystal Structure Of Brassica Juncea Chitinase Catalytic
Module Glu234ala Mutant (bjchi3-e234a)
Length = 246
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 22/49 (44%)
Query: 40 PCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKK 88
PC G GRGP++ Y C +D ELLKN A S + K
Sbjct: 107 PCAPGKFYYGRGPMMLSWNYNYGPCGRDLGLELLKNPDVASSDPVIAFK 155
>pdb|2Z37|A Chain A, Crystal Structure Of Brassica Juncea Chitinase Catalytic
Module (Bjchi3)
pdb|2Z37|B Chain B, Crystal Structure Of Brassica Juncea Chitinase Catalytic
Module (Bjchi3)
pdb|2Z37|C Chain C, Crystal Structure Of Brassica Juncea Chitinase Catalytic
Module (Bjchi3)
pdb|2Z37|D Chain D, Crystal Structure Of Brassica Juncea Chitinase Catalytic
Module (Bjchi3)
Length = 244
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 21/45 (46%)
Query: 40 PCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKAL 84
PC G GRGP++ Y C +D ELLKN A S +
Sbjct: 105 PCAPGKFYYGRGPMMLSWNYNYGPCGRDLGLELLKNPDVASSDPV 149
>pdb|2Z38|A Chain A, Crystal Structure Of Chloride Bound Brassica Juncea
Chitinase Catalytic Module (Bjchi3)
Length = 247
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 21/45 (46%)
Query: 40 PCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKAL 84
PC G GRGP++ Y C +D ELLKN A S +
Sbjct: 108 PCAPGKFYYGRGPMMLSWNYNYGPCGRDLGLELLKNPDVASSDPV 152
>pdb|2WA1|A Chain A, Structure Of The Methyltransferase Domain From Modoc
Virus, A Flavivirus With No Known Vector (Nkv)
pdb|2WA1|B Chain B, Structure Of The Methyltransferase Domain From Modoc
Virus, A Flavivirus With No Known Vector (Nkv)
pdb|2WA2|A Chain A, Structure Of The Methyltransferase Domain From Modoc
Virus, A Flavivirus With No Known Vector (Nkv)
pdb|2WA2|B Chain B, Structure Of The Methyltransferase Domain From Modoc
Virus, A Flavivirus With No Known Vector (Nkv)
Length = 276
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 20/38 (52%)
Query: 148 NVREVYVDTVGPPESYKKKLSEIFPELIITVASKADST 185
NVREV T+G K +L E F +IT SK D T
Sbjct: 105 NVREVKAYTLGTSGHEKPRLVETFGWNLITFKSKVDVT 142
>pdb|2ZIV|B Chain B, Crystal Structure Of The Mus81-Eme1 Complex
Length = 351
Score = 28.9 bits (63), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 73 LKNLGCADSKALTE----KKRDDILDSICKENAWLGWM-VEIISPNVICNSMLRRQKYSL 127
L + CA +KA+ E K RD+ S C E+ W G + V++ + + RRQ L
Sbjct: 213 LADFTCAFTKAVAEAPFKKLRDETTFSFCLESDWAGGVKVDLAGRGLAL--VWRRQIQQL 270
Query: 128 NEVSHDAAIGLI 139
N VS + A ++
Sbjct: 271 NRVSLEMASAVV 282
>pdb|1EY3|A Chain A, Structure Of Enoyl-Coa Hydratase Complexed With The
Substrate Dac-Coa
pdb|1EY3|B Chain B, Structure Of Enoyl-Coa Hydratase Complexed With The
Substrate Dac-Coa
pdb|1EY3|C Chain C, Structure Of Enoyl-Coa Hydratase Complexed With The
Substrate Dac-Coa
pdb|1EY3|D Chain D, Structure Of Enoyl-Coa Hydratase Complexed With The
Substrate Dac-Coa
pdb|1EY3|E Chain E, Structure Of Enoyl-Coa Hydratase Complexed With The
Substrate Dac-Coa
pdb|1EY3|F Chain F, Structure Of Enoyl-Coa Hydratase Complexed With The
Substrate Dac-Coa
Length = 258
Score = 28.1 bits (61), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 113 NVICNSMLRRQKYSLNEVSHDAAIGLI-----RKVIAAGVNVREV 152
N +CN ++ +L D A+G I K AAG +++E+
Sbjct: 27 NALCNGLIEELNQALETFEEDPAVGAIVLTGGEKAFAAGADIKEM 71
>pdb|1MJ3|A Chain A, Crystal Structure Analysis Of Rat Enoyl-Coa Hydratase In
Complex With Hexadienoyl-Coa
pdb|1MJ3|B Chain B, Crystal Structure Analysis Of Rat Enoyl-Coa Hydratase In
Complex With Hexadienoyl-Coa
pdb|1MJ3|C Chain C, Crystal Structure Analysis Of Rat Enoyl-Coa Hydratase In
Complex With Hexadienoyl-Coa
pdb|1MJ3|D Chain D, Crystal Structure Analysis Of Rat Enoyl-Coa Hydratase In
Complex With Hexadienoyl-Coa
pdb|1MJ3|E Chain E, Crystal Structure Analysis Of Rat Enoyl-Coa Hydratase In
Complex With Hexadienoyl-Coa
pdb|1MJ3|F Chain F, Crystal Structure Analysis Of Rat Enoyl-Coa Hydratase In
Complex With Hexadienoyl-Coa
Length = 260
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 113 NVICNSMLRRQKYSLNEVSHDAAIGLI-----RKVIAAGVNVREV 152
N +CN ++ +L D A+G I K AAG +++E+
Sbjct: 29 NALCNGLIEELNQALETFEEDPAVGAIVLTGGEKAFAAGADIKEM 73
>pdb|1DUB|A Chain A, 2-Enoyl-Coa Hydratase, Data Collected At 100 K, Ph 6.5
pdb|1DUB|B Chain B, 2-Enoyl-Coa Hydratase, Data Collected At 100 K, Ph 6.5
pdb|1DUB|C Chain C, 2-Enoyl-Coa Hydratase, Data Collected At 100 K, Ph 6.5
pdb|1DUB|D Chain D, 2-Enoyl-Coa Hydratase, Data Collected At 100 K, Ph 6.5
pdb|1DUB|E Chain E, 2-Enoyl-Coa Hydratase, Data Collected At 100 K, Ph 6.5
pdb|1DUB|F Chain F, 2-Enoyl-Coa Hydratase, Data Collected At 100 K, Ph 6.5
pdb|2DUB|A Chain A, Enoyl-Coa Hydratase Complexed With Octanoyl-Coa
pdb|2DUB|B Chain B, Enoyl-Coa Hydratase Complexed With Octanoyl-Coa
pdb|2DUB|C Chain C, Enoyl-Coa Hydratase Complexed With Octanoyl-Coa
pdb|2DUB|D Chain D, Enoyl-Coa Hydratase Complexed With Octanoyl-Coa
pdb|2DUB|E Chain E, Enoyl-Coa Hydratase Complexed With Octanoyl-Coa
pdb|2DUB|F Chain F, Enoyl-Coa Hydratase Complexed With Octanoyl-Coa
Length = 261
Score = 28.1 bits (61), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 113 NVICNSMLRRQKYSLNEVSHDAAIGLI-----RKVIAAGVNVREV 152
N +CN ++ +L D A+G I K AAG +++E+
Sbjct: 30 NALCNGLIEELNQALETFEEDPAVGAIVLTGGEKAFAAGADIKEM 74
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
0.317 0.134 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,426,358
Number of Sequences: 62578
Number of extensions: 461824
Number of successful extensions: 1167
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1100
Number of HSP's gapped (non-prelim): 43
length of query: 401
length of database: 14,973,337
effective HSP length: 101
effective length of query: 300
effective length of database: 8,652,959
effective search space: 2595887700
effective search space used: 2595887700
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)