RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14498
(171 letters)
>1eqq_A Single stranded DNA binding protein; beta barrel, protein-DNA
complex, replication/RNA complex; HET: 5MU; 3.20A
{Escherichia coli} SCOP: b.40.4.3
Length = 178
Score = 217 bits (553), Expect = 3e-73
Identities = 74/174 (42%), Positives = 106/174 (60%), Gaps = 5/174 (2%)
Query: 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKL 62
VNKVI++GNLG+DPE RYM NG AV N+++AT+E+WRDK +GE +E TEWHR+ + KL
Sbjct: 5 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKL 64
Query: 63 AQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIAD---NMQMLGSRKNTNEKNI 119
A++ +YL+KGSQ+YIEG+L+TRKWT++ G ++Y TEV+ + MQMLG R+
Sbjct: 65 AEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAG 124
Query: 120 SNNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISN--FLEADDDVPF 171
N + ++ P SN ++ DDD+PF
Sbjct: 125 GNIGGGQPQGGWGQPQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF 178
>3tqy_A Single-stranded DNA-binding protein; DNA replication, transferase;
2.60A {Coxiella burnetii}
Length = 158
Score = 214 bits (548), Expect = 9e-73
Identities = 81/169 (47%), Positives = 108/169 (63%), Gaps = 15/169 (8%)
Query: 1 MA-SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFY 59
MA VNKVI+IGNLG+DPE RY NG+AV NV++AT+ WRDK +GE +E TEWHRI F+
Sbjct: 4 MARGVNKVILIGNLGQDPEVRYTPNGNAVANVTLATSTTWRDKQTGELQERTEWHRIAFF 63
Query: 60 RKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNI 119
+LA+IV +YL+KGS+IYIEG L+TRKW +K GV++Y TE+IA+ M ML +R N N
Sbjct: 64 NRLAEIVGEYLRKGSKIYIEGSLRTRKWQDKNGVDRYTTEIIANEMHMLDNRGGGNSGNY 123
Query: 120 SNNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDD 168
N+ E SN + S+ +++F DDD
Sbjct: 124 GNHSEGG-----------ASNKQSAPTSSQTPTAGDDSSVADF---DDD 158
>3pgz_A Single-stranded DNA-binding protein; ssgcid, single-strand binding
protein, structural genomics center for infectious
disease; 2.10A {Bartonella henselae}
Length = 193
Score = 211 bits (538), Expect = 8e-71
Identities = 73/177 (41%), Positives = 108/177 (61%), Gaps = 11/177 (6%)
Query: 1 MA-SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFY 59
MA S+NKVI+IGNLG DPE R +++GD V N+ IAT+E+WRD+N+ E++E TEWH I +
Sbjct: 22 MAGSLNKVILIGNLGADPEIRRLNSGDQVANLRIATSESWRDRNTNERKERTEWHNIVIF 81
Query: 60 -RKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADN----MQMLGSRKNT 114
L ++V+QYLKKGS+IYIEG+LQTRKW ++ G ++Y TE++ +QML R
Sbjct: 82 NENLVKVVEQYLKKGSKIYIEGQLQTRKWQDQNGNDRYTTEIVLQKYRGELQMLDGRAAA 141
Query: 115 NEKNISNNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVPF 171
+ + +++ A + N+ ++ L S + DDDVPF
Sbjct: 142 GGEQMQGANQSS-----GAYSSVGFGDNSANQRDVFGSNNSQLGESFSHKLDDDVPF 193
>1qvc_A Single stranded DNA binding protein monomer; beta-barrel; 2.20A
{Escherichia coli} SCOP: b.40.4.3 PDB: 1kaw_A 1eyg_A
1sru_A
Length = 145
Score = 204 bits (520), Expect = 1e-68
Identities = 66/123 (53%), Positives = 92/123 (74%), Gaps = 3/123 (2%)
Query: 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKL 62
VNKVI++GNLG+DPE RYM NG AV N+++AT+E+WRDK +GE +E TEWHR+ + KL
Sbjct: 4 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKL 63
Query: 63 AQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIAD---NMQMLGSRKNTNEKNI 119
A++ +YL+KGSQ+YIEG+L+TRKWT++ G ++Y TEV+ + MQMLG R+
Sbjct: 64 AEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAG 123
Query: 120 SNN 122
N
Sbjct: 124 GNI 126
>1z9f_A Single-strand binding protein; TM0604, single stranded DNA-binding
protein, structural GENO joint center for structural
genomics, JCSG; 2.30A {Thermotoga maritima}
Length = 153
Score = 201 bits (514), Expect = 1e-67
Identities = 46/171 (26%), Positives = 79/171 (46%), Gaps = 30/171 (17%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYR 60
M+ NK+I+IG L RDPE RY +G VT +IA R N+ + + T++ RI +
Sbjct: 13 MSFFNKIILIGRLVRDPEERYTLSGTPVTTFTIAVDRVPRK-NAPDDAQTTDFFRIVTFG 71
Query: 61 KLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNIS 120
+LA+ + YL KG + +EG ++ R+W G ++ EV+A+ ++ + +
Sbjct: 72 RLAEFARTYLTKGRLVLVEGEMRMRRWETPTGEKRVSPEVVANVVRFMDRKPAET----- 126
Query: 121 NNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVPF 171
S T E E +E+F + ++D+ PF
Sbjct: 127 -----------------VSETEEELEIPEEDFSSDT-------FSEDEPPF 153
>3lgj_A Single-stranded DNA-binding protein; niaid, CAT scratch fever,
rochalimaea, LYME disease, ALS collaborative
crystallography, DNA replication; 2.50A {Bartonella
henselae}
Length = 169
Score = 200 bits (509), Expect = 1e-66
Identities = 54/176 (30%), Positives = 92/176 (52%), Gaps = 31/176 (17%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYR 60
+ +NKV++IG LG DPE++ M++G V N +AT E++ +KN+ +K E TEWH + +
Sbjct: 20 GSMLNKVMLIGYLGDDPESKTMTSGAEVVNFRMATFESYMNKNTHQKVEKTEWHSVVVFN 79
Query: 61 -KLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADN----MQMLGSRKNTN 115
A+I QYL KGS++YIEG+LQTRKW +K G ++Y TE++ + +L ++K +
Sbjct: 80 PHFAKIALQYLHKGSKVYIEGKLQTRKWQDKNGHDRYTTEIVLPQYKGELHLLDAKKEQS 139
Query: 116 EKNISNNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVPF 171
+++++ +S + D +PF
Sbjct: 140 -----------------------ASSSSVTSQSYAIASGADDYGISA---HDSMPF 169
>3ull_A DNA binding protein; DNA replication, mitochondrion, transit
peptide; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3
PDB: 1s3o_A* 2dud_A
Length = 132
Score = 196 bits (501), Expect = 5e-66
Identities = 44/123 (35%), Positives = 72/123 (58%), Gaps = 7/123 (5%)
Query: 1 MA-SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNS-----GEKRELTEWH 54
+ S+N+V ++G +G+DP R + + VT S+AT E WR +S G+ + T WH
Sbjct: 10 LERSLNRVHLLGRVGQDPVLRQVEGKNPVTIFSLATNEMWRSGDSEVYQLGDVSQKTTWH 69
Query: 55 RITFYRK-LAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKN 113
RI+ +R L + QY+KKGS+IY+EG++ ++ +K V + T +IADN+ L +
Sbjct: 70 RISVFRPGLRDVAYQYVKKGSRIYLEGKIDYGEYMDKNNVRRQATTIIADNIIFLSDQTK 129
Query: 114 TNE 116
E
Sbjct: 130 EKE 132
>3afp_A Single-stranded DNA-binding protein; OB-fold, quaternary structure
and stability, changes on oligomerisation,
water-bridges, DNA damage; 2.05A {Mycobacterium leprae}
PDB: 3afq_A 1ue1_A 1ue5_A 1ue6_A 1ue7_A 1x3e_A 1x3f_A
1x3g_A 3a5u_A*
Length = 168
Score = 197 bits (503), Expect = 9e-66
Identities = 42/172 (24%), Positives = 78/172 (45%), Gaps = 5/172 (2%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKREL-TEWHRITFY 59
MA + I+GNL DPE R+ S+G AV N ++A+T D+ SGE ++ + R +
Sbjct: 1 MAGDTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRIYDRQSGEWKDGEALFLRCNIW 60
Query: 60 RKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNI 119
R+ A+ V + L +G+++ + GRL+ R + +EG ++ + EV D +
Sbjct: 61 REAAENVAESLTRGARVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
Query: 120 SNNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVPF 171
S + + + + + + P +F D++ PF
Sbjct: 121 SRSGGGGGGF---GSGSRQAPAQMSGGVGDDPWGSAP-TSGSFGVGDEEPPF 168
>1se8_A Single-strand binding protein; DNA binding protein; 1.80A
{Deinococcus radiodurans} SCOP: b.40.4.3
Length = 301
Score = 199 bits (507), Expect = 1e-64
Identities = 47/178 (26%), Positives = 87/178 (48%), Gaps = 9/178 (5%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYR 60
++N+V+++GN+ RDPE RY GDAV ++SIA EN++D+ G+++E + T +R
Sbjct: 126 SGAMNEVLVLGNVTRDPEIRYTPAGDAVLSLSIAVNENYQDRQ-GQRQEKVHYIDATLWR 184
Query: 61 KLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNIS 120
LA+ + + L+KG + I GRL WT+K+G ++ T V A ++ L +
Sbjct: 185 DLAENM-KELRKGDPVMIMGRLVNEGWTDKDGNKRNSTRVEATRVEALARGAGNANSGYA 243
Query: 121 NNLENNFFNIMSARKNYTSNTNNEKE-------KSKENFKTQPLPISNFLEADDDVPF 171
++ ++ + + S+ + +F +DD+PF
Sbjct: 244 AATPAAPRTQTASSAARPTSGGYQSQPSRAANTGSRSGGLDIDQGLDDFPPEEDDLPF 301
Score = 192 bits (489), Expect = 6e-62
Identities = 42/131 (32%), Positives = 65/131 (49%), Gaps = 3/131 (2%)
Query: 1 MA-SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFY 59
MA +N V +IG L RDPE RY NG AV ++A + N G +R L +HR++
Sbjct: 1 MARGMNHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIG-NDGRERNLPWYHRVSIL 59
Query: 60 RKLAQIV-KQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKN 118
K A+ ++ LK G + +EG L+ R+W EG ++ V A M+ LG++ +
Sbjct: 60 GKPAEWQAERNLKGGDAVVVEGTLEYRQWEAPEGGKRSAVNVKALRMEQLGTQPELIQDA 119
Query: 119 ISNNLENNFFN 129
+ N
Sbjct: 120 GGGVRMSGAMN 130
>2vw9_A Single-stranded DNA binding protein; DNA replication,
single-stranded DNA, single-stranded DNA binding
protein, oligonucleotide/oligosaccharide binding fold,
OB-fold; 2.30A {Helicobacter pylori}
Length = 134
Score = 190 bits (485), Expect = 2e-63
Identities = 34/119 (28%), Positives = 63/119 (52%), Gaps = 1/119 (0%)
Query: 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLA 63
NKVI++G L R+ E +Y+ +G A + +AT+ ++ ++ G E + + + A
Sbjct: 2 FNKVIMVGRLTRNVELKYLPSGSAAATIGLATSRRFKKQD-GTLGEEVCFIDARLFGRTA 60
Query: 64 QIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNISNN 122
+I QYL KGS + IEGRL W ++ G + + AD++Q + + + + N +
Sbjct: 61 EIANQYLSKGSSVLIEGRLTYESWMDQTGKKNSRHTITADSLQFMDKKSDNPQANAMQD 119
>3ulp_A Single-strand binding protein; OB-fold, DNA binding,
single-stranded DNA, apicoplast, DNA B protein-DNA
complex; HET: DNA; 2.10A {Plasmodium falciparum}
Length = 124
Score = 189 bits (483), Expect = 2e-63
Identities = 44/120 (36%), Positives = 75/120 (62%), Gaps = 7/120 (5%)
Query: 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFY-RK 61
S+NK+++IG +G +P+ + ++ GD V S+AT E WRD+N+ E + T+WHRI Y +
Sbjct: 5 SLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTDWHRIVVYDQN 64
Query: 62 LAQIVKQYLKKGSQIYIEGRLQTRKW--TNKEGVEKYITEVIAD----NMQMLGSRKNTN 115
+ ++ +YL+KG ++Y++G L TRKW + K ITE+I ++ L ++N N
Sbjct: 65 IVDLIDKYLRKGRRVYVQGSLHTRKWHTNDMNSQPKQITEIILSYNKGDLIFLDDKRNFN 124
>3eiv_A Single-stranded DNA-binding protein 2; DNA damage, DNA repair, DNA
replication, phosphoprotein; 2.14A {Streptomyces
coelicolor}
Length = 199
Score = 189 bits (482), Expect = 4e-62
Identities = 30/112 (26%), Positives = 63/112 (56%), Gaps = 1/112 (0%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKREL-TEWHRITFY 59
MA + ++GNL DPE R+ +G AV +A+T D+ + E ++ + + + +
Sbjct: 1 MAGETVITVVGNLVDDPELRFTPSGAAVAKFRVASTPRTFDRQTNEWKDGESLFLTCSVW 60
Query: 60 RKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111
R+ A+ V + L++G ++ ++GRL+ R + ++EGV++ + E+ D +
Sbjct: 61 RQAAENVAESLQRGMRVIVQGRLKQRSYEDREGVKRTVYELDVDEVGASLRS 112
>2fxq_A Single-strand binding protein; strand beta-sheet extended loops,
DNA binding protein; 1.85A {Thermus aquaticus} PDB:
2ihe_A 2cwa_A 2ihf_A
Length = 264
Score = 188 bits (480), Expect = 6e-61
Identities = 37/129 (28%), Positives = 70/129 (54%), Gaps = 3/129 (2%)
Query: 1 MA-SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFY 59
MA +N+V +IG L P+ RY G A+ ++++A + + D++ G++RE+ +HR+
Sbjct: 1 MARGLNQVFLIGTLTARPDMRYTPGGLAILDLNLAGQDAFTDES-GQEREVPWYHRVRLL 59
Query: 60 RKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNI 119
+ A++ L+KG I++EGRL+ R+W K+G +K +V A+ + L R ++
Sbjct: 60 GRQAEMWGDLLEKGQLIFVEGRLEYRQWE-KDGEKKSEVQVRAEFIDPLEGRGRETLEDA 118
Query: 120 SNNLENNFF 128
Sbjct: 119 RGQPRLRRA 127
Score = 179 bits (457), Expect = 2e-57
Identities = 39/171 (22%), Positives = 69/171 (40%), Gaps = 31/171 (18%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYR 60
++N+VI++GNL RDP+ RY G AV + +A E R G++ E T + + +R
Sbjct: 125 RRALNQVILMGNLTRDPDLRYTPQGTAVVRLGLAVNERRR----GQEEERTHFLEVQAWR 180
Query: 61 KLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNIS 120
+LA+ L+KG + + GRL WT+ G ++ T V A ++
Sbjct: 181 ELAEWA-SELRKGDGLLVIGRLVNDSWTSSSGERRFQTRVEALRLERPTRGPAQA----- 234
Query: 121 NNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVPF 171
+ ++ + L ++D+PF
Sbjct: 235 ------------------GGSRPPTVQTGGVDIDEGLEDFPP---EEDLPF 264
>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A
{Bacillus subtilis}
Length = 116
Score = 182 bits (464), Expect = 1e-60
Identities = 39/118 (33%), Positives = 70/118 (59%), Gaps = 3/118 (2%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYR 60
N+V+++G L +DP+ RY S G AV +V++A ++++ + GE ++ T +R
Sbjct: 2 HHMFNQVMLVGRLTKDPDLRYTSAGAAVAHVTLAVNRSFKNAS-GEIE--ADYVNCTLWR 58
Query: 61 KLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKN 118
K A+ Y +KGS + + GR+QTR + N+EGV Y+TEV+AD ++ + + +
Sbjct: 59 KTAENTALYCQKGSLVGVSGRIQTRSYENEEGVNVYVTEVLADTVRFMDPKPREKAAD 116
>3koj_A Uncharacterized protein YCF41; single-strand binding protein
family, PF00436, SNR59A, NESG, structural genomics,
PSI-2; 1.90A {Synechococcus elongatus pcc 6301}
Length = 108
Score = 131 bits (331), Expect = 2e-40
Identities = 16/107 (14%), Positives = 38/107 (35%), Gaps = 8/107 (7%)
Query: 1 MASVNKVIIIGNLGRDPETRYM-SNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFY 59
+ +N I+ + P+ RY N V + + ++ +
Sbjct: 8 HSHMNSCILQATVVEAPQLRYAQDNQTPVAEMVVQFPGLSSKDA-------PARLKVVGW 60
Query: 60 RKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQ 106
+AQ ++ + ++ +EGRL+ +G + TE+ +
Sbjct: 61 GAVAQELQDRCRLNDEVVLEGRLRINSLLKPDGNREKQTELTVTRVH 107
>3k7u_C MP18 RNA editing complex protein; OB-fold, RNA-editing proteins,
kinetoplastids, system, RNA binding protein; 2.10A
{Trypanosoma brucei} PDB: 3k80_D 3stb_D
Length = 148
Score = 84.1 bits (207), Expect = 2e-21
Identities = 27/128 (21%), Positives = 54/128 (42%), Gaps = 8/128 (6%)
Query: 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRIT-FYRK 61
SVN V ++G + D ++ ++ DAVT ++ TT + E + H I F
Sbjct: 5 SVNSVTLVGVV-HDIQSGFV-YEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCFGEL 62
Query: 62 LAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVI-----ADNMQMLGSRKNTNE 116
+ VKQ +K+G+ + + GRL+ + + I + ++ + T
Sbjct: 63 FSAEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYIQVQPPHGQVAVIHGDRRTVP 122
Query: 117 KNISNNLE 124
++ +E
Sbjct: 123 AAVNPAVE 130
>3k81_C MP18 RNA editing complex protein; krepa6, single domain antibody,
immune system, RNA BIND protein; 3.40A {Trypanosoma
brucei}
Length = 164
Score = 69.5 bits (169), Expect = 1e-15
Identities = 24/100 (24%), Positives = 46/100 (46%), Gaps = 3/100 (3%)
Query: 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK- 61
SVN V ++G + D ++ ++ DAVT ++ TT + E + H I + +
Sbjct: 21 SVNSVTLVGVV-HDIQSGFV-YEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCFGEL 78
Query: 62 LAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVI 101
+ VKQ +K+G+ + + GRL+ + + I
Sbjct: 79 FSAEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYI 118
>1txy_A Primosomal replication protein N; OB fold, dimer, DNA binding
protein; 2.00A {Escherichia coli} SCOP: b.40.4.3 PDB:
1woc_A 2pnh_A 4apv_A
Length = 104
Score = 59.4 bits (144), Expect = 2e-12
Identities = 17/106 (16%), Positives = 44/106 (41%), Gaps = 6/106 (5%)
Query: 5 NKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQ 64
N++++ G + R P + +G + + + + +G R+ + Q
Sbjct: 3 NRLVLSGTVCRAPLRKVSPSGIPHCQFVLEH-RSVQ-EEAGFHRQAWCQMPVIVSGHENQ 60
Query: 65 IVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110
+ + GS+I ++G + K N K + + A+ ++++ S
Sbjct: 61 AITHSITVGSRITVQGFISCHKAKNGLS--KMV--LHAEQIELIDS 102
>1v1q_A Primosomal replication protein N; primosome, DNA replication, DNA
binding; 2.1A {Escherichia coli} SCOP: b.40.4.3 PDB:
2ccz_A
Length = 134
Score = 57.7 bits (139), Expect = 2e-11
Identities = 17/106 (16%), Positives = 44/106 (41%), Gaps = 6/106 (5%)
Query: 5 NKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQ 64
N++++ G + R P + +G + + + + +G R+ + Q
Sbjct: 20 NRLVLSGTVCRAPLRKVSPSGIPHCQFVLEH-RSVQ-EEAGFHRQAWCQMPVIVSGHENQ 77
Query: 65 IVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110
+ + GS+I ++G + K N K + + A+ ++++ S
Sbjct: 78 AITHSITVGSRITVQGFISCHKAKNGLS--KMV--LHAEQIELIDS 119
>3k8a_A Putative primosomal replication protein; beta-barrel, OB-fold,
DNA binding protein; 2.70A {Neisseria gonorrhoeae fa
1090}
Length = 103
Score = 51.3 bits (123), Expect = 3e-09
Identities = 15/97 (15%), Positives = 33/97 (34%), Gaps = 12/97 (12%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIA----TTENWRDKNSGEKRELTEWHRI 56
M N V + + + RY G V ++ + EN G++ +
Sbjct: 4 MGFTNLVSLAALIEKAFPIRYTPAGIPVLDIILKHESWQEEN------GQQCLVQLEIPA 57
Query: 57 TFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGV 93
+ A+ + ++G +EG L + + +
Sbjct: 58 RILGRQAEEWQ--YRQGDCATVEGFLAQKSRRSLMPM 92
>3fhw_A Primosomal replication protein N; PRIB BPR162 X-RAY NESG,
structural genomics, PSI-2, protein initiative; 1.90A
{Bordetella parapertussis} PDB: 3dm4_A 3klw_A
Length = 115
Score = 51.3 bits (123), Expect = 3e-09
Identities = 10/90 (11%), Positives = 29/90 (32%), Gaps = 3/90 (3%)
Query: 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLA 63
+N + + + R+ G + + +G R + LA
Sbjct: 1 MNTLELSARVLECGAMRHTPAGLPALELLLV--HESEVVEAGHPRRVELTISAVALGDLA 58
Query: 64 QIVKQYLKKGSQIYIEGRLQTRKWTNKEGV 93
++ G+++ ++G L + + +
Sbjct: 59 LLL-ADTPLGTEMQVQGFLAPARKDSVKVK 87
>3en2_A Probable primosomal replication protein N; PRIB RSR213C NESG
X-RAY Q8XZT7 Q8XZT7_ralso, structural genomics, PSI-2;
2.30A {Ralstonia solanacearum}
Length = 101
Score = 39.8 bits (93), Expect = 4e-05
Identities = 14/91 (15%), Positives = 38/91 (41%), Gaps = 3/91 (3%)
Query: 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKL 62
++N++ ++ L RY G + N ++ + + + R++ K+
Sbjct: 1 AINRLQLVATLVEREVMRYTPAGVPIVNCLLSYSG--QAMEAQAARQVEFSIEALGAGKM 58
Query: 63 AQIVKQYLKKGSQIYIEGRLQTRKWTNKEGV 93
A ++ + + G+ + G L + ++K V
Sbjct: 59 ASVLDR-IAPGTVLECVGFLARKHRSSKALV 88
>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 = 31.6 bits (71), Expect = 0.15
Identities = 28/170 (16%), Positives = 48/170 (28%), Gaps = 52/170 (30%)
Query: 18 ETRYMSNGD--AVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGS- 74
E Y+ D A+ A D + +EL + + + + KK +
Sbjct: 92 ENCYLEGNDIHAL----AAKLLQENDTTLVKTKELIK----NYITARIMAKRPFDKKSNS 143
Query: 75 -----------QIYIE--GRLQTRKWTNKEG-VEKYITEVIADNMQMLGSRKNTNEKNIS 120
Q+ G Q G + Y E ++ L
Sbjct: 144 ALFRAVGEGNAQLVAIFGG--Q--------GNTDDYFEE-----LRDLY--------QTY 180
Query: 121 NNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVP 170
+ L + + + T + EK TQ L I +LE + P
Sbjct: 181 HVLVGDLIKFSAETLSELIRTTLDAEK----VFTQGLNILEWLENPSNTP 226
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.1 bits (64), Expect = 0.45
Identities = 6/17 (35%), Positives = 9/17 (52%), Gaps = 5/17 (29%)
Query: 67 KQYLKKGSQIYIEGRLQ 83
KQ LKK ++ L+
Sbjct: 19 KQALKK-----LQASLK 30
Score = 27.2 bits (59), Expect = 1.9
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 8/28 (28%)
Query: 144 EKEKSKENFKTQPLPISNF-LEADDDVP 170
EK+ K K Q ++ L ADD P
Sbjct: 18 EKQALK---KLQ----ASLKLYADDSAP 38
>4f9d_A Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylas; family 4
carbohydrate esterase, TIM barrel, hydrolase, deace
carbohydrate/sugar binding; HET: MES; 1.90A {Escherichia
coli} PDB: 4f9j_A*
Length = 618
Score = 28.8 bits (64), Expect = 1.1
Identities = 9/51 (17%), Positives = 21/51 (41%), Gaps = 2/51 (3%)
Query: 58 FYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQML 108
+ +L +K + + +E LQ + W + ++ +A M +L
Sbjct: 549 WLIQLTNQIKNIPQAKDKSILE--LQAQNWQKNGQHQAISSQQLAHWMSLL 597
>1kqf_A FDH-N alpha, formate dehydrogenase, nitrate-inducible, major S;
oxidoreductase, selenium, selenocysteine, seCys,
molybdenum; HET: MGD HEM CDL; 1.60A {Escherichia coli}
SCOP: b.52.2.2 c.81.1.1 PDB: 1kqg_A*
Length = 1015
Score = 26.8 bits (59), Expect = 4.2
Identities = 10/61 (16%), Positives = 19/61 (31%), Gaps = 11/61 (18%)
Query: 77 YIEGRL-QTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNI----------SNNLEN 125
I + R E E+ +T + ML + +NE + ++N
Sbjct: 132 RIAKLMKADRDANFIEKNEQGVTVNRWLSTGMLCASGASNETGMLTQKFARSLGMLAVDN 191
Query: 126 N 126
Sbjct: 192 Q 192
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 26.3 bits (57), Expect = 4.7
Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 18/73 (24%)
Query: 39 WR--------DKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNK 90
WR + ++ K EW R+ A K+ L++ +Q E +++ K N+
Sbjct: 90 WREEQRKRLQELDAASKVMEQEW------REKA---KKDLEEWNQRQSE-QVEKNKINNR 139
Query: 91 EGVEKYITEVIAD 103
+ + + AD
Sbjct: 140 IADKAFYQQPDAD 152
>3evz_A Methyltransferase; NYSGXRC, NEW YORK SGX research CE structural
genomics, protein structure initiative, pyrococc
furiosus, PSI-2; 2.20A {Pyrococcus furiosus}
Length = 230
Score = 26.4 bits (59), Expect = 5.0
Identities = 5/22 (22%), Positives = 10/22 (45%)
Query: 58 FYRKLAQIVKQYLKKGSQIYIE 79
F KL + +L G ++ +
Sbjct: 157 FSVKLLEEAFDHLNPGGKVALY 178
>4dzr_A Protein-(glutamine-N5) methyltransferase, release specific;
structural genomics, PSI-biology; 2.55A
{Alicyclobacillus acidocaldarius subsp}
Length = 215
Score = 26.3 bits (59), Expect = 5.0
Identities = 7/23 (30%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 58 FYRKLAQIVKQYLKKGS-QIYIE 79
FYR++A + L +G +++E
Sbjct: 142 FYRRMAALPPYVLARGRAGVFLE 164
>1h0h_A Formate dehydrogenase (large subunit); tungsten selenium formate
dehydrogenase, selenocysteine, molybdopterin, MGD,
iron-sulphur cluster; HET: 2MD MGD EPE; 1.8A
{Desulfovibrio gigas} SCOP: b.52.2.2 c.81.1.1
Length = 977
Score = 26.4 bits (58), Expect = 6.3
Identities = 12/61 (19%), Positives = 20/61 (32%), Gaps = 11/61 (18%)
Query: 77 YIEGRL-QTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNI----------SNNLEN 125
I R+ +TR+ T K D + +GS NE+ +E+
Sbjct: 94 TIAERVAKTREATFVTKNAKGQVVNRCDGIASVGSAAMDNEECWIYQAWLRSLGLFYIEH 153
Query: 126 N 126
Sbjct: 154 Q 154
>1wi1_A Calcium-dependent activator protein for secretion, CAPS; PH domain,
PIP2 binding site, structural genomics; NMR {Homo
sapiens} SCOP: b.55.1.1
Length = 126
Score = 25.3 bits (55), Expect = 7.9
Identities = 6/43 (13%), Positives = 17/43 (39%)
Query: 105 MQMLGSRKNTNEKNISNNLENNFFNIMSARKNYTSNTNNEKEK 147
+Q+ G + + FFN + +++E+++
Sbjct: 56 LQLDGYTVDYTDPQPGLEGGRAFFNAVKEGDTVIFASDDEQDR 98
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
0.311 0.128 0.359
Gapped
Lambda K H
0.267 0.0565 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,466,630
Number of extensions: 130951
Number of successful extensions: 268
Number of sequences better than 10.0: 1
Number of HSP's gapped: 228
Number of HSP's successfully gapped: 50
Length of query: 171
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 84
Effective length of database: 4,272,666
Effective search space: 358903944
Effective search space used: 358903944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (24.9 bits)