RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780183|ref|YP_003064596.1| single-strand binding protein
(ssb) [Candidatus Liberibacter asiaticus str. psy62]
(159 letters)
>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 = 152 bits (384), Expect = 4e-38
Identities = 64/159 (40%), Positives = 95/159 (59%), Gaps = 16/159 (10%)
Query: 5 LNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEEL 64
LNKV+LIG LG DP+ + G ++VN R+AT +S+ ++ T+++ EKTEWHSV+VF+
Sbjct: 23 LNKVMLIGYLGDDPESKTMTSGAEVVNFRMATFESYMNKNTHQKVEKTEWHSVVVFNPHF 82
Query: 65 CRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMR----SMVMLDGRRDSLQGE 120
+I QYL KGSKVYIEG LQTRKWQD++G++RYTTEI++ + +LD +++
Sbjct: 83 AKIALQYLHKGSKVYIEGKLQTRKWQDKNGHDRYTTEIVLPQYKGELHLLDAKKEQSASS 142
Query: 121 EQRSEQHSNNLKENVVGNRYSSPREESVFSDELDDEIPF 159
+ Q Y+ + D +PF
Sbjct: 143 SSVTSQ------------SYAIASGADDYGISAHDSMPF 169
>1se8_A Single-strand binding protein; DNA binding protein; 1.80A
{Deinococcus radiodurans} SCOP: b.40.4.3
Length = 301
Score = 146 bits (369), Expect = 2e-36
Identities = 35/143 (24%), Positives = 58/143 (40%), Gaps = 1/143 (0%)
Query: 1 MVASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVF 60
M +N V LIG L DP++R+T +G + +A D R +H V +
Sbjct: 1 MARGMNHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIGN-DGRERNLPWYHRVSIL 59
Query: 61 SEELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQGE 120
+ E+ L+ G V +EG+L+ R+W+ G R + M L + + +Q
Sbjct: 60 GKPAEWQAERNLKGGDAVVVEGTLEYRQWEAPEGGKRSAVNVKALRMEQLGTQPELIQDA 119
Query: 121 EQRSEQHSNNLKENVVGNRYSSP 143
+ V+GN P
Sbjct: 120 GGGVRMSGAMNEVLVLGNVTRDP 142
Score = 114 bits (286), Expect = 1e-26
Identities = 39/180 (21%), Positives = 79/180 (43%), Gaps = 24/180 (13%)
Query: 1 MVASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVF 60
M ++N+V+++GN+ DP++R+T G ++++ IA +++++DR +R+EK + ++
Sbjct: 125 MSGAMNEVLVLGNVTRDPEIRYTPAGDAVLSLSIAVNENYQDR-QGQRQEKVHYIDATLW 183
Query: 61 SEELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQGE 120
+ + + LRKG V I G L W D+ GN R +T + + L +
Sbjct: 184 RDLAENM--KELRKGDPVMIMGRLVNEGWTDKDGNKRNSTRVEATRVEALARGAGNANSG 241
Query: 121 EQRS------EQHSNNLKENVVGNRYSSPREESVFS---------------DELDDEIPF 159
+ Q +++ G S P + +D++PF
Sbjct: 242 YAAATPAAPRTQTASSAARPTSGGYQSQPSRAANTGSRSGGLDIDQGLDDFPPEEDDLPF 301
>3k81_C MP18 RNA editing complex protein; krepa6, single domain antibody,
immune system, RNA BIND protein; 3.40A {Trypanosoma
brucei}
Length = 164
Score = 138 bits (348), Expect = 6e-34
Identities = 27/148 (18%), Positives = 56/148 (37%), Gaps = 7/148 (4%)
Query: 1 MVASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVF 60
S+N V L+G + D + + T+ T E + + H++ F
Sbjct: 18 CCKSVNSVTLVGVVH-DIQSGFV-YEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCF 75
Query: 61 SEELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEII-----MRSMVMLDGRRD 115
E V+Q +++G+ V + G L+ + S N + I + ++ G R
Sbjct: 76 GELFSAEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYIQVQPPHGQVAVIHGDRR 135
Query: 116 SLQGEEQRSEQHSNNLKENVVGNRYSSP 143
++ + + + KE G++ P
Sbjct: 136 TVPAAVNPAVEDIKSEKEGSGGDQSGVP 163
>3eiv_A Single-stranded DNA-binding protein 2; DNA damage, DNA repair, DNA
replication, phosphoprotein; 2.14A {Streptomyces
coelicolor}
Length = 199
Score = 137 bits (345), Expect = 1e-33
Identities = 27/124 (21%), Positives = 55/124 (44%)
Query: 3 ASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSE 62
A + ++GNL DP++R T G + R+A++ DR TNE ++
Sbjct: 2 AGETVITVVGNLVDDPELRFTPSGAAVAKFRVASTPRTFDRQTNEWKDGESLFLTCSVWR 61
Query: 63 ELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQGEEQ 122
+ V + L++G +V ++G L+ R ++D+ G R E+ + + + +
Sbjct: 62 QAAENVAESLQRGMRVIVQGRLKQRSYEDREGVKRTVYELDVDEVGASLRSATAKVTKTS 121
Query: 123 RSEQ 126
+
Sbjct: 122 GQGR 125
>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 = 135 bits (340), Expect = 5e-33
Identities = 36/167 (21%), Positives = 66/167 (39%), Gaps = 10/167 (5%)
Query: 3 ASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSE 62
A + ++GNL ADP++R T G +VN +A++ DR + E ++
Sbjct: 2 AGDTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRIYDRQSGEWKDGEALFLRCNIWR 61
Query: 63 ELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQGEEQ 122
E V + L +G++V + G L+ R ++ + G R E+ + + + +
Sbjct: 62 EAAENVAESLTRGARVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKAS 121
Query: 123 RS----------EQHSNNLKENVVGNRYSSPREESVFSDELDDEIPF 159
RS + + VG+ S D+E PF
Sbjct: 122 RSXXXXXXFGSGSRQAPAQMSGGVGDDPWGSAPTSGSFGVGDEEPPF 168
>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 = 134 bits (337), Expect = 1e-32
Identities = 70/175 (40%), Positives = 102/175 (58%), Gaps = 20/175 (11%)
Query: 4 SLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEE 63
+NKVIL+GNLG DP+VR+ +G + NI +ATS+SW+D+ T E +E+TEWH +V +
Sbjct: 5 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHR-VVLFGK 63
Query: 64 LCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMR---SMVMLDGRRDS---- 116
L + +YLRKGS+VYIEG L+TRKW DQSG +RYTTE+++ +M ML GR+
Sbjct: 64 LAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPA 123
Query: 117 ------LQGEEQRSEQHSNNLKENVVGNRYSSPREESVFS------DELDDEIPF 159
Q + + G S P++ + + + DD+IPF
Sbjct: 124 GGNIGGGQPQGGWGQPQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF 178
>3k7u_C MP18 RNA editing complex protein; OB-fold, RNA-editing proteins,
kinetoplastids, system, RNA binding protein; 2.10A
{Trypanosoma brucei} PDB: 3k80_D
Length = 148
Score = 129 bits (325), Expect = 3e-31
Identities = 28/148 (18%), Positives = 57/148 (38%), Gaps = 7/148 (4%)
Query: 1 MVASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVF 60
M S+N V L+G + D + + T+ T E + + H++ F
Sbjct: 2 MSKSVNSVTLVGVVH-DIQSGFV-YEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCF 59
Query: 61 SEELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIM-----RSMVMLDGRRD 115
E V+Q +++G+ V + G L+ + S N + I + ++ G R
Sbjct: 60 GELFSAEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYIQVQPPHGQVAVIHGDRR 119
Query: 116 SLQGEEQRSEQHSNNLKENVVGNRYSSP 143
++ + + + KE G++ P
Sbjct: 120 TVPAAVNPAVEDIKSEKEGSGGDQSGVP 147
>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 = 126 bits (318), Expect = 2e-30
Identities = 35/133 (26%), Positives = 65/133 (48%), Gaps = 3/133 (2%)
Query: 1 MVASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVF 60
M LN+V LIG L A PD+R+T G I+++ +A D++ D + + RE +H V +
Sbjct: 1 MARGLNQVFLIGTLTARPDMRYTPGGLAILDLNLAGQDAFTDE-SGQEREVPWYHRVRLL 59
Query: 61 SEELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQGE 120
+ L KG +++EG L+ R+W ++ G + ++ + L+GR +
Sbjct: 60 -GRQAEMWGDLLEKGQLIFVEGRLEYRQW-EKDGEKKSEVQVRAEFIDPLEGRGRETLED 117
Query: 121 EQRSEQHSNNLKE 133
+ + L +
Sbjct: 118 ARGQPRLRRALNQ 130
Score = 84.8 bits (209), Expect = 8e-18
Identities = 36/159 (22%), Positives = 64/159 (40%), Gaps = 18/159 (11%)
Query: 1 MVASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVF 60
+ +LN+VIL+GNL DPD+R+T G +V + +A ++ + + E+T + V +
Sbjct: 124 LRRALNQVILMGNLTRDPDLRYTPQGTAVVRLGLAVNERRR----GQEEERTHFLEVQAW 179
Query: 61 SEELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQGE 120
E LRKG + + G L W SG R+ T + + G
Sbjct: 180 RE--LAEWASELRKGDGLLVIGRLVNDSWTSSSGERRFQTRVEALRLERPTRGPAQAGGS 237
Query: 121 EQRSEQHSNNLKENVVGNRYSSPREESVFSDELDDEIPF 159
+ Q +E + ++++PF
Sbjct: 238 RPPTVQTG------------GVDIDEGLEDFPPEEDLPF 264
>1x3e_A Single-strand binding protein; oligonucleotide binding fold,
DNA-binding protein, DNA binding protein; 2.15A
{Mycobacterium smegmatis} PDB: 1x3f_A 1x3g_A 1ue1_A
1ue5_A 1ue6_A 1ue7_A
Length = 165
Score = 124 bits (312), Expect = 8e-30
Identities = 39/164 (23%), Positives = 68/164 (41%), Gaps = 7/164 (4%)
Query: 3 ASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSE 62
A + ++GNL ADP++R T G + N +A++ DR + E ++
Sbjct: 2 AGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRMFDRQSGEWKDGEALFLRCNIWR 61
Query: 63 ELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQGEEQ 122
E V + L +GS+V + G L+ R ++ + G R E+ + + + +
Sbjct: 62 EAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKAS 121
Query: 123 RSEQHSNNLKENVVGNRYSSPREESVFS-------DELDDEIPF 159
RS G+R S P+++ S DDE PF
Sbjct: 122 RSXXXXXXFGSGGGGSRQSEPKDDPWGSAPASGSFSGADDEPPF 165
>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 = 118 bits (298), Expect = 4e-28
Identities = 62/116 (53%), Positives = 87/116 (75%), Gaps = 4/116 (3%)
Query: 4 SLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEE 63
+NKVIL+GNLG DP+VR+ +G + NI +ATS+SW+D+ T E +E+TEWH V++F +
Sbjct: 4 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFG-K 62
Query: 64 LCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMR---SMVMLDGRRDS 116
L + +YLRKGS+VYIEG L+TRKW DQSG +RYTTE+++ +M ML GR+
Sbjct: 63 LAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGG 118
>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 = 114 bits (287), Expect = 9e-27
Identities = 18/106 (16%), Positives = 39/106 (36%), Gaps = 9/106 (8%)
Query: 3 ASLNKVILIGNLGADPDVRHTQDGRKIV-NIRIATSDSWKDRVTNERREKTEWHSVIVFS 61
+ +N IL + P +R+ QD + V + + + V+ +
Sbjct: 9 SHMNSCILQATVVEAPQLRYAQDNQTPVAEMVVQFPGLSSK-------DAPARLKVVGWG 61
Query: 62 EELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSM 107
+ + ++ R +V +EG L+ GN TE+ + +
Sbjct: 62 A-VAQELQDRCRLNDEVVLEGRLRINSLLKPDGNREKQTELTVTRV 106
>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 = 108 bits (270), Expect = 8e-25
Identities = 34/123 (27%), Positives = 64/123 (52%), Gaps = 5/123 (4%)
Query: 1 MVASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNE-----RREKTEWH 55
+ SLN+V L+G +G DP +R + + +AT++ W+ + +KT WH
Sbjct: 10 LERSLNRVHLLGRVGQDPVLRQVEGKNPVTIFSLATNEMWRSGDSEVYQLGDVSQKTTWH 69
Query: 56 SVIVFSEELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRD 115
+ VF L + QY++KGS++Y+EG + ++ D++ R T II +++ L +
Sbjct: 70 RISVFRPGLRDVAYQYVKKGSRIYLEGKIDYGEYMDKNNVRRQATTIIADNIIFLSDQTK 129
Query: 116 SLQ 118
+
Sbjct: 130 EKE 132
>1z9f_A Single-strand binding protein; TM0604, single stranded DNA-binding
protein, structural genomics, joint center for
structural genomics, JCSG; 2.30A {Thermotoga maritima}
Length = 153
Score = 106 bits (266), Expect = 2e-24
Identities = 38/157 (24%), Positives = 60/157 (38%), Gaps = 17/157 (10%)
Query: 3 ASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSE 62
+ NK+ILIG L DP+ R+T G + IA + +T IV
Sbjct: 14 SFFNKIILIGRLVRDPEERYTLSGTPVTTFTIAVDRVPRK--NAPDDAQTTDFFRIVTFG 71
Query: 63 ELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQGEEQ 122
L YL KG V +EG ++ R+W+ +G R + E++ + +D + E +
Sbjct: 72 RLAEFARTYLTKGRLVLVEGEMRMRRWETPTGEKRVSPEVVANVVRFMDRKPAETVSETE 131
Query: 123 RSEQHSNNLKENVVGNRYSSPREESVFSDELDDEIPF 159
P E+ +DE PF
Sbjct: 132 EE---------------LEIPEEDFSSDTFSEDEPPF 153
>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 = 97.6 bits (242), Expect = 1e-21
Identities = 36/126 (28%), Positives = 55/126 (43%), Gaps = 2/126 (1%)
Query: 5 LNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEEL 64
NKVI++G L + ++++ G I +ATS +K + E+ + +F
Sbjct: 2 FNKVIMVGRLTRNVELKYLPSGSAAATIGLATSRRFKKQ-DGTLGEEVCFIDARLF-GRT 59
Query: 65 CRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQGEEQRS 124
I QYL KGS V IEG L W DQ+G I S+ +D + D+ Q +
Sbjct: 60 AEIANQYLSKGSSVLIEGRLTYESWMDQTGKKNSRHTITADSLQFMDKKSDNPQANAMQD 119
Query: 125 EQHSNN 130
N
Sbjct: 120 SIMHEN 125
>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 = 87.7 bits (217), Expect = 1e-18
Identities = 13/110 (11%), Positives = 42/110 (38%), Gaps = 7/110 (6%)
Query: 4 SLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEE 63
N+++L G + P + + G + ++ R+ + ++ S
Sbjct: 18 MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEA-GFHRQAWCQMPVIV--SGH 74
Query: 64 LCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGR 113
+ + + GS++ ++G + K ++ G ++ + + ++D
Sbjct: 75 ENQAITHSITVGSRITVQGFISCHKAKN--GLSKM--VLHAEQIELIDSV 120
>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
Length = 104
Score = 86.9 bits (215), Expect = 2e-18
Identities = 12/107 (11%), Positives = 39/107 (36%), Gaps = 7/107 (6%)
Query: 5 LNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEEL 64
N+++L G + P + + G + ++ R+ + ++ S
Sbjct: 2 TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEA-GFHRQAWCQMPVIV--SGHE 58
Query: 65 CRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLD 111
+ + + GS++ ++G + K ++ + + ++D
Sbjct: 59 NQAITHSITVGSRITVQGFISCHKAKNGLS----KMVLHAEQIELID 101
>3k8a_A Putative primosomal replication protein; beta-barrel, OB-fold,
DNA binding protein; 2.70A {Neisseria gonorrhoeae fa
1090}
Length = 103
Score = 83.4 bits (206), Expect = 2e-17
Identities = 12/93 (12%), Positives = 30/93 (32%), Gaps = 5/93 (5%)
Query: 1 MVASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVF 60
+ N V L + +R+T G +++I + ++ ++ +
Sbjct: 3 HMGFTNLVSLAALIEKAFPIRYTPAGIPVLDIILKHESWQEEN--GQQCLVQLEIPARIL 60
Query: 61 SEELCRIVEQYLRKGSKVYIEGSLQTRKWQDQS 93
+ R+G +EG L + +
Sbjct: 61 GRQAEEW---QYRQGDCATVEGFLAQKSRRSLM 90
>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 = 79.6 bits (196), Expect = 3e-16
Identities = 14/91 (15%), Positives = 34/91 (37%), Gaps = 4/91 (4%)
Query: 4 SLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEE 63
++N++ L+ L +R+T G IVN ++ S + R+ + +
Sbjct: 1 AINRLQLVATLVEREVMRYTPAGVPIVNCLLSYSGQAMEA--QAARQVEFSIEALGAGKM 58
Query: 64 LCRIVEQYLRKGSKVYIEGSLQTRKWQDQSG 94
+ + G+ + G L + ++
Sbjct: 59 ASVL--DRIAPGTVLECVGFLARKHRSSKAL 87
>3fhw_A Primosomal replication protein N; PRIB BPR162 X-RAY NESG,
structural genomics, PSI-2, protein structure
initiative; 1.90A {Bordetella parapertussis} PDB:
3dm4_A 3klw_A
Length = 115
Score = 75.4 bits (185), Expect = 6e-15
Identities = 12/90 (13%), Positives = 30/90 (33%), Gaps = 4/90 (4%)
Query: 5 LNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEEL 64
+N + L + +RHT G + + + + R S + +L
Sbjct: 1 MNTLELSARVLECGAMRHTPAGLPALELLLVHESEVVEA--GHPRRVELTISAVALG-DL 57
Query: 65 CRIVEQYLRKGSKVYIEGSLQTRKWQDQSG 94
++ G+++ ++G L +
Sbjct: 58 ALLL-ADTPLGTEMQVQGFLAPARKDSVKV 86
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 41.1 bits (96), Expect = 1e-04
Identities = 41/221 (18%), Positives = 67/221 (30%), Gaps = 101/221 (45%)
Query: 10 LIG------------NLGADP-DVR--------HTQDGRKIVNIRIATSDSWK------- 41
LIG LG P ++R H+Q G + + IA +DSW+
Sbjct: 240 LIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQ-G-LVTAVAIAETDSWESFFVSVR 297
Query: 42 ----------------------------DRVTNERREKTEWHSVIVFS-EELCRIVEQ-- 70
D + N + S+ + E++ V +
Sbjct: 298 KAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTN 357
Query: 71 -YLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQGEEQ--RSEQH 127
+L G +V I SL N +++V + G SL G R +
Sbjct: 358 SHLPAGKQVEI--SLV---------NGA-------KNLV-VSGPPQSLYGLNLTLRKAKA 398
Query: 128 SNNLKEN---------VVGNRY---SSPREESVF-SDELDD 155
+ L ++ NR+ +SP F S L
Sbjct: 399 PSGLDQSRIPFSERKLKFSNRFLPVASP-----FHSHLLVP 434
Score = 28.0 bits (62), Expect = 0.97
Identities = 21/102 (20%), Positives = 36/102 (35%), Gaps = 39/102 (38%)
Query: 18 PDVRHTQDGRKIVNIRIATSDSWKDR----VTNERREKTEW---------HSVIVF---- 60
P V T DG ++R S S +R + R +W H ++ F
Sbjct: 458 P-VYDTFDGS---DLR-VLSGSISERIVDCII---RLPVKWETTTQFKATH-ILDFGPGG 508
Query: 61 SEELC----RIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRY 98
+ L R + G +V + G+L D + ++ Y
Sbjct: 509 ASGLGVLTHRNKDG---TGVRVIVAGTL------DINPDDDY 541
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.2 bits (72), Expect = 0.049
Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 87 RKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQGE-EQRSEQHSNNLKENVVGNRYSSPRE 145
RKW+++ + E+ S VM R+ + + E+ +++ S +++N + NR +
Sbjct: 88 RKWREE--QRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIA---- 141
Query: 146 ESVFSDELDDEI 157
+ F + D +I
Sbjct: 142 DKAFYQQPDADI 153
>1pn2_A Peroxisomal hydratase-dehydrogenase-epimerase; hot-DOG fold,
hydratase 2 motif, lyase; 1.95A {Candida tropicalis}
SCOP: d.38.1.4 d.38.1.4 PDB: 1pn4_A*
Length = 280
Score = 30.0 bits (67), Expect = 0.22
Identities = 9/65 (13%), Positives = 25/65 (38%)
Query: 59 VFSEELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVMLDGRRDSLQ 118
++ E R V+ +L+ W++ + T ++ R + ++ L
Sbjct: 215 ALIDKFGMFNEIKARFTGIVFPGETLRVLAWKESDDTIVFQTHVVDRGTIAINNAAIKLV 274
Query: 119 GEEQR 123
G++ +
Sbjct: 275 GDKAK 279
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 27.1 bits (59), Expect = 1.7
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 8/83 (9%)
Query: 16 ADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEELCRIVEQYLRKG 75
A P++ R++V R A W V NE E + + + SE+ E L +
Sbjct: 1240 ASPNLNMKYRKRQLVT-REAQIKDW---VENEL-EALKLEAEEIPSEDQN---EFLLERT 1291
Query: 76 SKVYIEGSLQTRKWQDQSGNNRY 98
+++ E Q R Q Q GN+ Y
Sbjct: 1292 REIHNEAESQLRAAQQQWGNDFY 1314
>3mz2_A Glycerophosphoryl diester phosphodiesterase; structural genomics,
joint center for structural genomics; HET: MSE PE4;
1.55A {Parabacteroides distasonis}
Length = 292
Score = 25.5 bits (55), Expect = 5.1
Identities = 7/45 (15%), Positives = 16/45 (35%), Gaps = 5/45 (11%)
Query: 2 VASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTN 46
+ + + + D R T+D ++ D +R +N
Sbjct: 50 METFENTLSYTPATFEIDPRLTKDSVIVLF-----HDDTLERTSN 89
>1nv8_A HEMK protein; class I adoMet-dependent methyltransferase; HET: SAM
MEQ; 2.20A {Thermotoga maritima} SCOP: c.66.1.30 PDB:
1nv9_A* 1vq1_A* 1sg9_A*
Length = 284
Score = 25.3 bits (55), Expect = 5.7
Identities = 9/50 (18%), Positives = 16/50 (32%), Gaps = 11/50 (22%)
Query: 62 EELCRIVEQYLRKGSKVYIE-GSLQTRK----------WQDQSGNNRYTT 100
+ +Y G V +E G Q + +D +G R+
Sbjct: 229 DFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLL 278
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.314 0.131 0.371
Gapped
Lambda K H
0.267 0.0511 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,354,748
Number of extensions: 57481
Number of successful extensions: 185
Number of sequences better than 10.0: 1
Number of HSP's gapped: 152
Number of HSP's successfully gapped: 30
Length of query: 159
Length of database: 5,693,230
Length adjustment: 85
Effective length of query: 74
Effective length of database: 3,632,490
Effective search space: 268804260
Effective search space used: 268804260
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 (21.9 bits)
S2: 53 (24.7 bits)