RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy12447
(551 letters)
>d1s5ja1 c.55.3.5 (A:40-449) Exonuclease domain of family B DNA
polymerases {Sulfolobus solfataricus [TaxId: 2287]}
Length = 410
Score = 160 bits (405), Expect = 2e-44
Identities = 65/478 (13%), Positives = 114/478 (23%), Gaps = 148/478 (30%)
Query: 52 PIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDE 111
+ ++F + G PY V + + ++
Sbjct: 26 AVCKLFDKETQKIYALYDNTGHKPYFLVDLEPDKVGKIPKIVRD---------------- 69
Query: 112 IQEAVLMVEIVQKQTVFGFWGEELENFLKITESVFPTFP---THTYKAFESNIDFDIRFM 168
+ +E V K + KI KA+E++I + +M
Sbjct: 70 --PSFDHIETVSKID---PYTWNKFKLTKIVVRDPLAVRRLRNDVPKAYEAHIKYFNNYM 124
Query: 169 VDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVST 228
D ++ + GK + L +D + + A + D T
Sbjct: 125 YDIGLIPGMPYVVKNGKLESVY----------------LSLDEKDVEEIKKAFADSDEMT 168
Query: 229 DDIVSHAPEGEWSKVAPLRILSFDIEC-AGRKGIFPDPNHDPIIQIANMCISQGASENIF 287
+ +++ ++ ++ DIE KG PD I+ + +
Sbjct: 169 RQMAVDWLPIFETEIPKIKRVAIDIEVYTPVKGRIPDSQKAEFPIISIALAGSDGLKKVL 228
Query: 288 VKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPI 347
V N +N +
Sbjct: 229 VLNRNDVN----------------------------------------------EGSVKL 242
Query: 348 VGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
G V TE ELL ++ + + I +N +FD PY+ RA LG
Sbjct: 243 DGISVERFNTEYELLGRFFDILL--EYPIVLTFNGDDFDLPYIYFRALKLG--------- 291
Query: 408 VKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSF 467
I GK E
Sbjct: 292 -------YFPEEIPIDVAGKDE-------------------------------------- 306
Query: 468 IQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSI 525
I+ + E K Y L++V+ L K V I
Sbjct: 307 -----AKYLAGLHIDLYKFFFNKAVRNYAFEGKYNEYNLDAVAKALLGTSKVKVDTLI 359
>d1q8ia1 c.55.3.5 (A:2-389) Exonuclease domain of family B DNA
polymerases {Escherichia coli [TaxId: 562]}
Length = 388
Score = 102 bits (255), Expect = 3e-24
Identities = 41/402 (10%), Positives = 100/402 (24%), Gaps = 128/402 (31%)
Query: 52 PIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDE 111
V + T G + + ++ A + + I+ +G
Sbjct: 18 TEVSFWLATDNG-PLQVTLAPQESVAFIPADQV-----------PRAQHILQGEQG---- 61
Query: 112 IQEAVLMVEIVQKQTVFGFWGEELENFLKITESVFPTFPTHTYKAFESNIDFDIRFMVDN 171
+ L ++ +Q V+G + + + +E+++ R++++
Sbjct: 62 FRLTPLALKDFHRQPVYGLYCRAHRQLMNYEK----RLREGGVTVYEADVRPPERYLMER 117
Query: 172 DIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDI 231
I W+E + + + +
Sbjct: 118 FITSPVWVEG----------------------------------------DMHNGTIVNA 137
Query: 232 VSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNV 291
PL+ +S DIE ++ CI V +
Sbjct: 138 RLKPHPDYR---PPLKWVSIDIETTRHGELY--------------CIGLEGCGQRIVYML 180
Query: 292 FTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQ 351
N A + ++ + +
Sbjct: 181 GPENGDASSLDFELEYVASRPQ-------------------------------------- 202
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDI 411
LL+K +A+ DPD+ G+N+ FD L A+ + +
Sbjct: 203 ---------LLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNSE-- 251
Query: 412 RSVIKDSFIQSKQMGKRENKTINFEGNSD-RRETLGVKNFTF 452
++ ++ + + +G + +F+
Sbjct: 252 -LEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSL 292
>d1tgoa1 c.55.3.5 (A:1-347) Exonuclease domain of family B DNA
polymerases {Archaeon Thermococcus gorgonarius [TaxId:
71997]}
Length = 347
Score = 96.8 bits (240), Expect = 1e-22
Identities = 81/480 (16%), Positives = 128/480 (26%), Gaps = 193/480 (40%)
Query: 51 VPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKD 110
P++R+F G + F PY+Y K+ + + +
Sbjct: 13 KPVIRIFKKE-NGEFKIDYDRNFEPYIYALL------------KDDSAIEDVKKITAERH 59
Query: 111 EIQEAVLMVEIVQKQTVFGFWGEELENFLKITESVFPTFPTHTYKAFESNIDFDIRFMVD 170
V+ E V+K+ F G +E K + F
Sbjct: 60 GTTVRVVRAEKVKKK----FLGRPIE-VWK------------------------LYFTHP 90
Query: 171 NDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDD 230
D+ R + +D+ DI ID
Sbjct: 91 QDVPAI----------------------RDKIKEHPAVVDIYEYDIPFAKRYLIDKGLIP 128
Query: 231 IVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKN 290
L++L+FDIE +G + PI+ I
Sbjct: 129 ---------MEGDEELKMLAFDIETLYHEG--EEFAEGPILMI----------------- 160
Query: 291 VFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGS 350
+ A G++VI K I
Sbjct: 161 -----SYADEEGARVITWK------------------------------------NIDLP 179
Query: 351 QVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKD 410
V TE E++ ++ ++E DPD+ YN NFDF YL R++ LGVK LGR
Sbjct: 180 YVDVVSTEKEMIKRFLKVVKEKDPDVLITYNGDNFDFAYLKKRSEKLGVKF--ILGREGS 237
Query: 411 IRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQS 470
+ + + + +G
Sbjct: 238 EPKIQR----------MGDRFAVEVKG--------------------------------- 254
Query: 471 KQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQ 530
R+ FDL V+ R L +YTL +V + KE V I+
Sbjct: 255 ---------------RIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKVYAEEIAQAW 299
>d1noya_ c.55.3.5 (A:) Exonuclease domain of family B DNA
polymerases {Bacteriophage T4 [TaxId: 10665]}
Length = 372
Score = 57.6 bits (138), Expect = 1e-09
Identities = 33/191 (17%), Positives = 55/191 (28%), Gaps = 27/191 (14%)
Query: 214 DDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQI 273
+DI A D I +R+ + DIE G K P I I
Sbjct: 73 EDIGLEALGMNDFKLAYISDTYGSEIVYDRKFVRVANCDIEVTGDKFPDPMKAEYEIDAI 132
Query: 274 ANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENI 333
+ +F + + + G
Sbjct: 133 THYDSIDD-RFYVFDLLNSMYGSVSKWDAKLAAK--------------LDCEGGDEVPQE 177
Query: 334 FVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINR 393
+ V + E ++L ++ + P IFTG+NI+ FD PY++NR
Sbjct: 178 ILDRV------------IYMPFDNERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNR 225
Query: 394 AKHLGVKNFTF 404
K + +
Sbjct: 226 VKMILGERSMK 236
>d1ih7a1 c.55.3.5 (A:1-375) Exonuclease domain of family B DNA
polymerases {Bacteriophage RB69 [TaxId: 12353]}
Length = 375
Score = 52.2 bits (124), Expect = 8e-08
Identities = 18/71 (25%), Positives = 33/71 (46%)
Query: 334 FVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINR 393
+ I + E ELL ++ F ++ P I TG+N+++FD PY+ NR
Sbjct: 170 LQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNR 229
Query: 394 AKHLGVKNFTF 404
K++ ++
Sbjct: 230 IKNIFGESTAK 240
>d1x9ma1 c.55.3.5 (A:1-210) Exonuclease domain of T7 DNA polymerase
{Bacteriophage T7 [TaxId: 10760]}
Length = 204
Score = 31.5 bits (70), Expect = 0.18
Identities = 7/54 (12%), Positives = 15/54 (27%)
Query: 351 QVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTF 404
+ + + + + +N +D P L AK + F
Sbjct: 30 EYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHL 83
>d1itwa_ c.77.1.2 (A:) Monomeric isocitrate dehydrogenase
{Azotobacter vinelandii [TaxId: 354]}
Length = 740
Score = 30.9 bits (70), Expect = 0.40
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 436 EGNSDRRETLGVKNFTF 452
EGNSDRR L VKN+
Sbjct: 139 EGNSDRRAPLSVKNYAR 155
>d1t1ua2 c.43.1.3 (A:402-616) Choline O-acetyltransferase {Rat
(Rattus norvegicus) [TaxId: 10116]}
Length = 215
Score = 29.5 bits (66), Expect = 0.91
Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 5/64 (7%)
Query: 46 SQLKPVPIVRMFG---VTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAII 102
SQ+ P + V G C + + +S+ T F EA+ +++
Sbjct: 149 SQV-PTTMEMFCCYGPVVPNGYGACYNPQPEAITFCISSFHSCKETSSVEFAEAVGASLV 207
Query: 103 ADMR 106
DMR
Sbjct: 208 -DMR 210
>d1uw4b_ a.118.1.14 (B:) Regulator of nonsense transcripts 2, UPF2
{Human (Homo sapiens) [TaxId: 9606]}
Length = 248
Score = 29.5 bits (66), Expect = 0.98
Identities = 9/81 (11%), Positives = 26/81 (32%), Gaps = 2/81 (2%)
Query: 104 DMRGNKDEIQEAVLMVEIVQKQTVFGFWGEELENFLKITESVFPTFPTHTYKAFESNIDF 163
D + I+ +++ + G +L+ FL + + +
Sbjct: 144 DPPEHLFRIRLVCTILDTCGQYFDRGSSKRKLDCFLVYFQRYVWWKKSLEVWTKDHPFPI 203
Query: 164 DIRFMVDN--DIVGCNWIEIP 182
DI +M+ + +++
Sbjct: 204 DIDYMISDTLELLRPKIKLCN 224
>d1igtb3 b.1.1.2 (B:236-361) Immunoglobulin heavy chain gamma
constant domain 2, CH2-gamma {Mouse (Mus musculus),
gamma2 [TaxId: 10090]}
Length = 119
Score = 27.4 bits (60), Expect = 2.2
Identities = 10/45 (22%), Positives = 13/45 (28%), Gaps = 7/45 (15%)
Query: 39 PIPGMPGSQLKPVPIVRMFGVTME-------GNSVCCHVHGFSPY 76
P P L P V +F ++ V C V S
Sbjct: 3 PPCKCPAPNLLGGPSVFIFPPKIKDVLMISLSPIVTCVVVDVSED 47
>d1bb9a_ b.34.2.1 (A:) Amphiphysin 2 {Rat (Rattus norvegicus)
[TaxId: 10116]}
Length = 83
Score = 26.1 bits (57), Expect = 3.7
Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 1/52 (1%)
Query: 212 STDDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFP 263
TD++ A + + V EG W + E +G+FP
Sbjct: 25 DTDELQLKAGDVVLVIPFQNPEEQDEG-WLMGVKESDWNQHKELEKCRGVFP 75
>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the
epsilon subunit of DNA polymerase III {Escherichia coli
[TaxId: 562]}
Length = 174
Score = 26.9 bits (58), Expect = 4.4
Identities = 8/28 (28%), Positives = 10/28 (35%)
Query: 247 RILSFDIECAGRKGIFPDPNHDPIIQIA 274
R + D E G I II+I
Sbjct: 1 RQIVLDTETTGMNQIGAHYEGHKIIEIG 28
>d1y97a1 c.55.3.5 (A:1-228) Three prime repair exonuclease 2, TREX2
{Human (Homo sapiens) [TaxId: 9606]}
Length = 228
Score = 26.5 bits (57), Expect = 8.7
Identities = 22/154 (14%), Positives = 43/154 (27%), Gaps = 33/154 (21%)
Query: 251 FDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKT 310
D+E G I +++ + + + EN
Sbjct: 13 LDLEATGL-----PSVEPEIAELSLFAVHRSSLENPE---------------HDESGALV 52
Query: 311 ETELLDKWSAFI---RTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367
+LDK + + R ASE + + + ++ A
Sbjct: 53 LPRVLDKLTLCMCPERPFTAKASEITGLSSEGLARCRKA---------GFDGAVVRTLQA 103
Query: 368 FIRELDPD-IFTGYNIQNFDFPYLINRAKHLGVK 400
F+ +N ++DFP L + LG +
Sbjct: 104 FLSRQAGPICLVAHNGFDYDFPLLCAELRRLGAR 137
>d2igia1 c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia coli
[TaxId: 562]}
Length = 180
Score = 26.1 bits (56), Expect = 9.4
Identities = 18/107 (16%), Positives = 36/107 (33%), Gaps = 11/107 (10%)
Query: 247 RILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVI 306
++ D+E G DP D II+IA + A+ NI + + + +
Sbjct: 6 NLIWIDLEMTGL-----DPERDRIIEIA--TLVTDANLNILAEGPTIAVHQSDEQLALMD 58
Query: 307 CCKTE----TELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVG 349
+ L+++ A + + + +PI G
Sbjct: 59 DWNVRTHTASGLVERVKASTMGDREAELATLEFLKQWVPAGKSPICG 105
Database: scop70_1_75
Posted date: Mar 27, 2010 6:21 PM
Number of letters in database: 2,407,596
Number of sequences in database: 13,730
Lambda K H
0.321 0.137 0.418
Gapped
Lambda K H
0.267 0.0436 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 2,135,972
Number of extensions: 104948
Number of successful extensions: 277
Number of sequences better than 10.0: 1
Number of HSP's gapped: 270
Number of HSP's successfully gapped: 30
Length of query: 551
Length of database: 2,407,596
Length adjustment: 90
Effective length of query: 461
Effective length of database: 1,171,896
Effective search space: 540244056
Effective search space used: 540244056
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: 55 (25.7 bits)