RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy3154
(101 letters)
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein
LSM5 {Cryptosporidium parvum [TaxId: 5807]}
Length = 92
Score = 87.6 bits (217), Expect = 6e-25
Identities = 20/87 (22%), Positives = 43/87 (49%), Gaps = 2/87 (2%)
Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
++ PL LI + R++V M+ ++ G L +D+++NMVL DV+E + ++ +
Sbjct: 2 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGG 61
Query: 70 EIYKTT--KRSIPMLFVRGDGVILVSP 94
+ + + G+ V ++ P
Sbjct: 62 NKKLKRVMVNRLETILLSGNNVAMLVP 88
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 93
Score = 84.2 bits (208), Expect = 1e-23
Identities = 29/85 (34%), Positives = 48/85 (56%), Gaps = 3/85 (3%)
Query: 14 PLDLIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
PL ++ S+ + +V + RN + L G++ A+D+H NMVL +V+E T V + ++
Sbjct: 3 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKS 62
Query: 72 YKTTK-RSIPMLFVRGDGVILVSPP 95
K R I +F+RGD VI+V
Sbjct: 63 KPVNKDRYISKMFLRGDSVIVVLRN 87
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein
{Archaeon Methanobacterium thermoautotrophicum [TaxId:
145262]}
Length = 74
Score = 76.7 bits (189), Expect = 7e-21
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 13/86 (15%)
Query: 9 ISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETY 68
++V+ PLD + SL+ V +K++ +R RG L ++D H+N+VL D EE
Sbjct: 2 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEV------ 55
Query: 69 EEIYKTTKRSIPMLFVRGDGVILVSP 94
R + + +RGD ++ +SP
Sbjct: 56 -------TRRLGTVLIRGDNIVYISP 74
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein
{Archaeon Pyrococcus abyssi [TaxId: 29292]}
Length = 71
Score = 74.0 bits (182), Expect = 8e-20
Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 13/83 (15%)
Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
+ PLD+I SLD+ V V ++ RG+L YD HLN+VL D E
Sbjct: 1 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEV--------- 51
Query: 72 YKTTKRSIPMLFVRGDGVILVSP 94
+ + +RGD V+ +SP
Sbjct: 52 ----VKRYGKIVIRGDNVLAISP 70
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein
{Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]}
Length = 72
Score = 73.2 bits (180), Expect = 1e-19
Identities = 28/81 (34%), Positives = 39/81 (48%), Gaps = 13/81 (16%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
PLD++ SL V V+++ R RG L YD H+N+VL D EE
Sbjct: 4 PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEV----------- 52
Query: 74 TTKRSIPMLFVRGDGVILVSP 94
R + + +RGD V+ VSP
Sbjct: 53 --VRKVGSVVIRGDTVVFVSP 71
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 81
Score = 70.6 bits (173), Expect = 2e-18
Identities = 16/73 (21%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
+D R+ +++ R+ G A+D+H+N++L D +E I + ++ + KR + +
Sbjct: 7 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRK---IKPKNSKQAEREEKRVLGL 63
Query: 82 LFVRGDGVILVSP 94
+ +RG+ ++ ++
Sbjct: 64 VLLRGENLVSMTV 76
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein
{Sulfolobus solfataricus [TaxId: 2287]}
Length = 76
Score = 70.1 bits (172), Expect = 3e-18
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 13/83 (15%)
Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
+ ++ SL+ V VK++ + +RG L +YDQH+N+VL D EE +
Sbjct: 6 ETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGS--------- 56
Query: 72 YKTTKRSIPMLFVRGDGVILVSP 94
+ + + +RGD VIL+SP
Sbjct: 57 ----GKKLGTIVIRGDNVILISP 75
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein
{Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}
Length = 75
Score = 66.3 bits (162), Expect = 8e-17
Identities = 19/86 (22%), Positives = 40/86 (46%), Gaps = 14/86 (16%)
Query: 10 SVKEPLDLIRLSLDERVHVKMRN-ERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETY 68
++ P +++ + + + V+M+ E L GKL D ++N+ L + E +
Sbjct: 2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEK------ 55
Query: 69 EEIYKTTKRSIPMLFVRGDGVILVSP 94
RS+ + +RG+ V+L+ P
Sbjct: 56 -------VRSLGEIVLRGNNVVLIQP 74
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein
{Archaeon Pyrobaculum aerophilum [TaxId: 13773]}
Length = 71
Score = 65.5 bits (160), Expect = 2e-16
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 14/75 (18%)
Query: 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIP 80
S+ ++V VK+R+ +RG L ++DQH+N++L D EE +
Sbjct: 10 SIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII--------------DGNVYKRG 55
Query: 81 MLFVRGDGVILVSPP 95
+ VRG+ V+ +SP
Sbjct: 56 TMVVRGENVLFISPV 70
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 72
Score = 59.8 bits (145), Expect = 3e-14
Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 13/83 (15%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
P+ ++ + V + V RGKL + ++N + ++ T
Sbjct: 3 PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR----------- 51
Query: 74 TTKRSIPMLFVRGDGVILVSPPN 96
+ +++RG + + P+
Sbjct: 52 --VAQLEQVYIRGCKIRFLILPD 72
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf
{Baker's yeast (Saccharomyces cerevisiae) [TaxId:
4932]}
Length = 68
Score = 51.6 bits (124), Expect = 4e-11
Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 14/74 (18%)
Query: 22 LDERVHVKMR-NERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIP 80
++ RV VK++ N RG L + D + N+ L + EE + + ++
Sbjct: 5 VNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEF-------------VAGVSHGTLG 51
Query: 81 MLFVRGDGVILVSP 94
+F+R + V+ +
Sbjct: 52 EIFIRCNNVLYIRE 65
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon
Pyrobaculum aerophilum [TaxId: 13773]}
Length = 127
Score = 47.0 bits (112), Expect = 9e-09
Identities = 16/77 (20%), Positives = 25/77 (32%), Gaps = 17/77 (22%)
Query: 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIP 80
L V V + N V +G LHA D LN+VL +
Sbjct: 8 LLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA-----------------GEKFN 50
Query: 81 MLFVRGDGVILVSPPNR 97
+F+ ++ + R
Sbjct: 51 RVFIMYRYIVHIDSTER 67
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 80
Score = 41.6 bits (98), Expect = 4e-07
Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 13/76 (17%)
Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
E V ++++N + G + D +N L V+ T+ E +
Sbjct: 10 SHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE-------------PVQLET 56
Query: 82 LFVRGDGVILVSPPNR 97
L +RG+ + P+
Sbjct: 57 LSIRGNNIRYFILPDS 72
>d4ubpc2 c.1.9.2 (C:132-434,C:484-570) alpha-subunit of urease,
catalytic domain {Bacillus pasteurii [TaxId: 1474]}
Length = 390
Score = 27.0 bits (60), Expect = 0.40
Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 26/77 (33%)
Query: 19 RLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRS 78
+L L R+ ++N R + K +M D T ++I+ ETYE
Sbjct: 327 KLGLKRRI-GTVKNCRNIGKK--------DMKWND---VTTDIDINPETYE--------- 365
Query: 79 IPMLFVRGDGVILVSPP 95
V+ DG +L P
Sbjct: 366 -----VKVDGEVLTCEP 377
>d1jyaa_ d.198.1.1 (A:) YopE chaperone SycE {Yersinia pestis
[TaxId: 632]}
Length = 117
Score = 26.0 bits (57), Expect = 0.66
Identities = 7/29 (24%), Positives = 13/29 (44%)
Query: 40 LHAYDQHLNMVLGDVEETVTTVEIDEETY 68
+ Q L++ + D E V V++ E
Sbjct: 7 ITQLFQQLSLSIPDTIEPVIGVKVGEFAC 35
>d1e9yb2 c.1.9.2 (B:132-431,B:481-569) alpha-subunit of urease,
catalytic domain {Helicobacter pylori [TaxId: 210]}
Length = 389
Score = 26.2 bits (58), Expect = 0.74
Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 17/48 (35%)
Query: 48 NMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP 95
+M + T +E++ ETY V DG + S P
Sbjct: 346 DMQFNN---TTAHIEVNPETYH--------------VFVDGKEVTSKP 376
>d1h75a_ c.47.1.1 (A:) Glutaredoxin-like NRDH-redoxin {Escherichia
coli [TaxId: 562]}
Length = 76
Score = 25.0 bits (54), Expect = 0.88
Identities = 5/35 (14%), Positives = 12/35 (34%)
Query: 53 DVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGD 87
+ + V+ E E + R +P++
Sbjct: 25 GFDFEMINVDRVPEAAEALRAQGFRQLPVVIAGDL 59
>d1r7ha_ c.47.1.1 (A:) Glutaredoxin-like NRDH-redoxin
{Corynebacterium ammoniagenes [TaxId: 1697]}
Length = 74
Score = 24.6 bits (53), Expect = 1.5
Identities = 5/34 (14%), Positives = 14/34 (41%)
Query: 54 VEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGD 87
+ + +D+E + + P++ V G+
Sbjct: 26 LAYNTVDISLDDEARDYVMALGYVQAPVVEVDGE 59
>d3lada1 c.3.1.5 (A:1-158,A:278-348) Dihydrolipoamide dehydrogenase
{Azotobacter vinelandii [TaxId: 354]}
Length = 229
Score = 24.6 bits (52), Expect = 2.6
Identities = 8/30 (26%), Positives = 14/30 (46%)
Query: 61 VEIDEETYEEIYKTTKRSIPMLFVRGDGVI 90
V +DE + + S+P ++ GD V
Sbjct: 173 VTLDERGFIYVDDYCATSVPGVYAIGDVVR 202
>d1v59a1 c.3.1.5 (A:1-160,A:283-355) Dihydrolipoamide dehydrogenase
{Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Length = 233
Score = 24.5 bits (52), Expect = 2.8
Identities = 7/30 (23%), Positives = 11/30 (36%)
Query: 61 VEIDEETYEEIYKTTKRSIPMLFVRGDGVI 90
+E+D+ I P + V GD
Sbjct: 177 LEVDKRGRLVIDDQFNSKFPHIKVVGDVTF 206
>d2gjca1 c.3.1.6 (A:16-326) Thiazole biosynthetic enzyme Thi4
{Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Length = 311
Score = 24.5 bits (52), Expect = 3.0
Identities = 12/95 (12%), Positives = 23/95 (24%)
Query: 3 DEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVE 62
D + ++ + LS V + G A +
Sbjct: 192 DPNVIELAGYKNDGTRDLSQKHGVILSTTGHDGPFGAFCAKRIVDIDQNQKLGGMKGLDM 251
Query: 63 IDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNR 97
E I+ + ++ G V + NR
Sbjct: 252 NHAEHDVVIHSGAYAGVDNMYFAGMEVAELDGLNR 286
>d3brda1 b.1.18.1 (A:542-660) DNA-binding protein LAG-1 (CSL)
{Caenorhabditis elegans [TaxId: 6239]}
Length = 119
Score = 23.6 bits (51), Expect = 4.1
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 72 YKTTKRSIPMLFVRGDGVI 90
T +P+ VR DGV+
Sbjct: 90 RTTGDVEVPISLVRDDGVV 108
>d1cmca_ a.43.1.5 (A:) Met repressor, MetJ (MetR) {Escherichia
coli [TaxId: 562]}
Length = 104
Score = 23.4 bits (50), Expect = 4.3
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 2 EDEQIPTISVKEPLDLIRLSLDERVHVKMRNER 34
+ EQ+ I+V PL ++++ DER ++ N R
Sbjct: 17 KSEQVKKITVSIPLKVLKILTDERTRRQVNNLR 49
>d1l1la_ c.7.1.4 (A:) B12-dependent (class II) ribonucleotide
reductase {Lactobacillus leichmannii [TaxId: 28039]}
Length = 721
Score = 23.7 bits (50), Expect = 5.6
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 62 EIDEETYEEIYKTTKRSIP 80
ID+ETYE+ + ++
Sbjct: 689 PIDKETYEKRSQEITGNVE 707
>d2nn6a1 d.14.1.4 (A:1-184) Exosome complex exonuclease RRP45 {Human
(Homo sapiens) [TaxId: 9606]}
Length = 184
Score = 23.6 bits (50), Expect = 5.7
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 79 IPMLFVRGDGVILVSPPNRTP 99
P + V+GD V L +P R P
Sbjct: 162 RPDVSVQGDEVTLYTPEERDP 182
>d1gx5a_ e.8.1.4 (A:) Viral RNA polymerase {Hepatitis C virus
[TaxId: 11103]}
Length = 530
Score = 23.2 bits (50), Expect = 7.3
Identities = 13/46 (28%), Positives = 23/46 (50%)
Query: 30 MRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTT 75
+R ++V +L D H VL +++ +TV+ + EE K T
Sbjct: 47 LRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLT 92
>d1knva_ c.52.1.7 (A:) Restriction endonuclease Bse634I {Bacillus
stearothermophilus [TaxId: 1422]}
Length = 290
Score = 23.4 bits (50), Expect = 7.5
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 3 DEQIPTISVKEPLDLIR 19
Q PT S+KE LD +
Sbjct: 32 HHQTPTGSIKENLDKLE 48
>d2gg2a1 d.127.1.1 (A:3-264) Methionine aminopeptidase
{Escherichia coli [TaxId: 562]}
Length = 262
Score = 22.9 bits (48), Expect = 9.7
Identities = 11/53 (20%), Positives = 18/53 (33%)
Query: 44 DQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPN 96
+ L M+ V+ V+T E+D + I L G + N
Sbjct: 20 AEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISIN 72
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
0.317 0.136 0.376
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 371,310
Number of extensions: 16114
Number of successful extensions: 89
Number of sequences better than 10.0: 1
Number of HSP's gapped: 76
Number of HSP's successfully gapped: 33
Length of query: 101
Length of database: 2,407,596
Length adjustment: 62
Effective length of query: 39
Effective length of database: 1,556,336
Effective search space: 60697104
Effective search space used: 60697104
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.0 bits)