RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy14489
(284 letters)
>d1xo1a2 c.120.1.2 (A:19-185) T5 5'-exonuclease {Bacteriophage T5
[TaxId: 10726]}
Length = 167
Score = 110 bits (275), Expect = 2e-30
Identities = 32/175 (18%), Positives = 61/175 (34%), Gaps = 21/175 (12%)
Query: 2 QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
+ L++VDG++ +R + N + ++ L K+Y A + D
Sbjct: 1 RRNLMIVDGTNLGFRFKHN--------NSKKPFASSYVSTIQSLAKSYSARTTIVLGDKG 52
Query: 62 GKNFRNILYPSYKATRKKMPYNL-----ILQINLIHQMVKAIG-----WPILIIKGVEAD 111
FR P Y R + L + A +P I+GVEAD
Sbjct: 53 KSVFRLEHLPEYAGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEAD 112
Query: 112 DVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--NNKIHDRTTIISRF 164
D+ + K V + + D D L+++K++ + + + +
Sbjct: 113 DMAAYIVKLIGHL-YDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHH 166
>d1cmwa2 c.120.1.2 (A:10-173) 5' to 3' exonuclease domain of DNA
polymerase Taq {Thermus aquaticus [TaxId: 271]}
Length = 164
Score = 104 bits (260), Expect = 3e-28
Identities = 58/165 (35%), Positives = 89/165 (53%), Gaps = 3/165 (1%)
Query: 2 QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
+ +LLVDG YR F+AL + PV A+YG K L K K + +FDAK
Sbjct: 2 KGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKEDG-DAVIVVFDAK 60
Query: 62 GKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQA 121
+FR+ Y YKA R P + Q+ LI ++V +G L + G EADDV+ +LAK+A
Sbjct: 61 APSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKA 120
Query: 122 VTKHNLKVIISTNDKDMAQLVSNKIALIN-NNKIHDRTTIISRFG 165
+ +V I T DKD+ QL+S++I +++ + + ++G
Sbjct: 121 EKEG-YEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYG 164
>d1tfra2 c.120.1.2 (A:12-180) T4 RNase H {Bacteriophage T4 [TaxId:
10665]}
Length = 169
Score = 96.6 bits (240), Expect = 3e-25
Identities = 30/156 (19%), Positives = 51/156 (32%), Gaps = 16/156 (10%)
Query: 3 NTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALY----GTIKMLRKLYKNYRATYIACIF 58
+ L+D S + + + + +IK K K T I
Sbjct: 2 EGICLIDFSQIALSTALVN--FPDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCI 59
Query: 59 DAKGKNF-RNILYPSYKATRKKM--------PYNLILQINLIHQMVKAIGWPILIIKGVE 109
D + R YK R K +I ++ + + ++ I E
Sbjct: 60 DNAKSGYWRRDFAYYYKKNRGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYE 119
Query: 110 ADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNK 145
ADD I L K+ + K++I ++D D QL
Sbjct: 120 ADDHIAVLVKK-FSLEGHKILIISSDGDFTQLHKYP 154
>d1cmwa1 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain of DNA
polymerase Taq {Thermus aquaticus [TaxId: 271]}
Length = 116
Score = 70.2 bits (171), Expect = 6e-16
Identities = 35/114 (30%), Positives = 57/114 (50%), Gaps = 6/114 (5%)
Query: 166 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLR 225
+ P++ DY +L GD SDNLPGVK IG KTA KLL ++ SLE ++ N + +K I + +
Sbjct: 1 LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKIL 60
Query: 226 FALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKL 279
++ L + ++TD L + + D + L + + L
Sbjct: 61 AHMDDLKLSWDLAKVRTDLPLEVDF------AKRREPDRERLRAFLERLEFGSL 108
>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease)
{Human (Homo sapiens) [TaxId: 9606]}
Length = 140
Score = 67.7 bits (165), Expect = 8e-15
Identities = 24/116 (20%), Positives = 51/116 (43%), Gaps = 12/116 (10%)
Query: 166 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLR 225
++ E+ VD L+G SD ++ IGPK AV L+ ++ S+E I+ + K + +N
Sbjct: 1 LNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWL 58
Query: 226 FALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKLNF 281
L+ + +L + +P +E+L+ + + + ++
Sbjct: 59 HKEAHQLFLEPEVLDPESVELKWS----------EPNEEELIKFMCGEKQFSEERI 104
>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5
[TaxId: 10726]}
Length = 105
Score = 62.3 bits (151), Expect = 3e-13
Identities = 18/100 (18%), Positives = 42/100 (42%), Gaps = 1/100 (1%)
Query: 168 PEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGV-IGKNLRF 226
E+ + +++GD+ DN+ GV+ IG K ++ ++ ++ +II+ +NL
Sbjct: 4 VEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNA 63
Query: 227 ALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKL 266
+ L + ++ + T C V ++
Sbjct: 64 SEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEI 103
>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease)
{Archaeon Archaeoglobus fulgidus [TaxId: 2234]}
Length = 105
Score = 52.2 bits (125), Expect = 2e-09
Identities = 17/113 (15%), Positives = 41/113 (36%), Gaps = 20/113 (17%)
Query: 166 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLR 225
++ E+++D L+G +D GVK +G K A+ + Y + +
Sbjct: 1 LTREQLIDIAILVG--TDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNI-------- 50
Query: 226 FALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNK 278
+ + +++ D + +P EK + L ++ ++
Sbjct: 51 ---DHVEEIRNFFLNPPVTDDYRIEFR-------EPDFEKAIEFLCEEHDFSR 93
>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease)
{Archaeon Methanococcus jannaschii [TaxId: 2190]}
Length = 108
Score = 47.5 bits (113), Expect = 6e-08
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 166 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGV 219
+S + ++D +G N GVK IG K A +L+ + + + +
Sbjct: 1 ISLDDLIDIAIFMGT-DYNPGGVKGIGFKRAYELVRSGVAKDVLKKEVEYYDEI 53
>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease)
{Archaeon Pyrococcus furiosus [TaxId: 2261]}
Length = 120
Score = 38.3 bits (89), Expect = 2e-04
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 166 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENII 210
++ EK+++ L+G N G+K IG K A++++
Sbjct: 1 LTREKLIELAILVG-TDYNPGGIKGIGLKKALEIVRHSKDPLAKF 44
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human
(Homo sapiens) [TaxId: 9606]}
Length = 62
Score = 29.0 bits (65), Expect = 0.095
Identities = 5/32 (15%), Positives = 12/32 (37%), Gaps = 3/32 (9%)
Query: 180 DMSDNLPGVKKIGPKTAVKLLNQYNSLENIIN 211
D +PG + K L++ ++ +
Sbjct: 3 DFLLKMPG---VNAKNCRSLMHHVKNIAELAA 31
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain
{Escherichia coli [TaxId: 562]}
Length = 56
Score = 28.5 bits (64), Expect = 0.13
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
Query: 183 DNLPGVKKIGPKTAVKLLNQYNSLENIINN 212
+ + GV GPK LL L+ + N
Sbjct: 5 ETIEGV---GPKRRQMLLKYMGGLQGLRNA 31
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015
{Pyrococcus furiosus [TaxId: 2261]}
Length = 68
Score = 27.8 bits (62), Expect = 0.32
Identities = 7/39 (17%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 185 LPGVKKIGPKTAVKLLNQYNSLENIINNAN----NIKGV 219
+ G+ + A +LL + S+E + + ++G+
Sbjct: 12 VEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGI 50
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum
pernix [TaxId: 56636]}
Length = 70
Score = 27.9 bits (62), Expect = 0.33
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 185 LPGVKKIGPKTAVKLLNQYNSLENIIN 211
L IG +TA ++L ++ SLE
Sbjct: 15 LQSFPGIGRRTAERILERFGSLERFFT 41
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal
domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}
Length = 61
Score = 26.9 bits (60), Expect = 0.55
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 183 DNLPGVKKIGPKTAVKLLNQ-YNSLENIIN-NANNIKGVIGKNLRFALNWLPKLKKILTI 240
++LPG +GP TA KL Y++LE I + +K V G + AL + +K +
Sbjct: 4 EDLPG---VGPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAARKAANL 60
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal
domain {Archaeon Methanococcus voltae [TaxId: 2188]}
Length = 60
Score = 26.6 bits (59), Expect = 0.65
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 5/60 (8%)
Query: 183 DNLPGVKKIGPKTAVKLLNQ-YNSLENIIN-NANNIKGVIGKNLRFALNWLPKLKKILTI 240
+LPG +GP TA KL+ Y I + + G + + A + + + +
Sbjct: 2 TDLPG---VGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARDLCDL 58
>d1uvqa2 d.19.1.1 (A:2-84) Class II MHC alpha chain, N-terminal
domain {Human (Homo sapiens), HLA-DQ6 [TaxId: 9606]}
Length = 83
Score = 25.0 bits (55), Expect = 3.4
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 115 GTLAKQAVTKHNLKVII 131
G L AV KHNL ++I
Sbjct: 60 GALRNMAVAKHNLNIMI 76
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1
{Human (Homo sapiens) [TaxId: 9606]}
Length = 78
Score = 24.9 bits (54), Expect = 3.7
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 185 LPGVKKIGPKTAVKLLNQYNSLENIINN 212
L VK + + LL + SLE +I
Sbjct: 21 LTTVKSVNKTDSQTLLTTFGSLEQLIAA 48
>d2tbva_ b.121.4.7 (A:) Tombusvirus coat protein {TBSV (Tomato bushy
stunt virus) [TaxId: 12145]}
Length = 287
Score = 26.4 bits (58), Expect = 3.9
Identities = 10/51 (19%), Positives = 17/51 (33%), Gaps = 6/51 (11%)
Query: 237 ILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQL------FNKYKLNKLNF 281
+ + N + SL L P + L L F++Y N +
Sbjct: 12 LTQVNNSSGFVVNGGIVGNSLQLNPSNGTLFSWLPALASNFDQYSFNSVVL 62
>d1gqea_ e.38.1.1 (A:) Polypeptide chain release factor 2 (RF2)
{Escherichia coli [TaxId: 562]}
Length = 362
Score = 26.1 bits (57), Expect = 5.5
Identities = 12/92 (13%), Positives = 31/92 (33%), Gaps = 8/92 (8%)
Query: 193 PKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVS 252
P+ A L + +SLE +++ + +K + L L + +T + +
Sbjct: 47 PERAQALGKERSSLEAVVDTLDQMK----QGLEDVSGLLELAVEADDEETFNEAVAEL-- 100
Query: 253 IPESLILQPKDEKLLMQLFNKYKLNKLNFLMH 284
++L + + +Y +
Sbjct: 101 --DALEEKLAQLEFRRMFSGEYDSADCYLDIQ 130
>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo
sapiens) [TaxId: 9606]}
Length = 460
Score = 25.7 bits (54), Expect = 7.7
Identities = 8/58 (13%), Positives = 20/58 (34%), Gaps = 5/58 (8%)
Query: 180 DMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKI 237
D+ ++ +LL + + + + K++ AL P L ++
Sbjct: 8 DIQCE-----ELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAEL 60
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
0.322 0.139 0.401
Gapped
Lambda K H
0.267 0.0592 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,030,081
Number of extensions: 48366
Number of successful extensions: 175
Number of sequences better than 10.0: 1
Number of HSP's gapped: 162
Number of HSP's successfully gapped: 34
Length of query: 284
Length of database: 2,407,596
Length adjustment: 84
Effective length of query: 200
Effective length of database: 1,254,276
Effective search space: 250855200
Effective search space used: 250855200
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 (21.9 bits)
S2: 52 (24.1 bits)