RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 044732
(250 letters)
>1vs3_A TRNA pseudouridine synthase A; TRUA, tRNA modification, structural
NPPSFA, national project on protein structural and
function analyses; 2.25A {Thermus thermophilus}
Length = 249
Score = 63.6 bits (156), Expect = 2e-12
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 167 VNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGA-DEDALLKLMDATCRRATAP 225
V + G +V + FLR VR +V TL+ E G ++L ++ RR P
Sbjct: 175 VAEGEAGLEV-RLYFRGKSFLRGQVRGMVGTLL-EVGLGKRPPESLKAILKTADRRLAGP 232
Query: 226 PAPPEGLCLVDVGY 239
AP GL V+ Y
Sbjct: 233 TAPAHGLYFVEAAY 246
Score = 49.0 bits (118), Expect = 3e-07
Identities = 12/46 (26%), Positives = 21/46 (45%)
Query: 9 KDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYI 54
+ + +A+N P ++V+ +V+ FH A WR Y Y
Sbjct: 68 SAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYR 113
>1dj0_A Pseudouridine synthase I; alpha/beta fold, RNA-binding motif,
RNA-modifying enzyme, lyase; 1.50A {Escherichia coli}
SCOP: d.265.1.1 PDB: 2nqp_A 2nr0_A 2nre_A
Length = 264
Score = 60.2 bits (147), Expect = 4e-11
Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 179 VELVANRFLRKMVRVLVATLVREAAAGA-DEDALLKLMDATCRRATAPPAPPEGLCLVDV 237
V++ AN F+ MVR +V +L+ E A E + +L+ A R A A EGL LV V
Sbjct: 186 VDIKANAFVHHMVRNIVGSLM-EVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAV 244
Query: 238 GY-TNFD-PQNSLIP 250
Y +D P+ + P
Sbjct: 245 DYPDRYDLPKPPMGP 259
Score = 49.8 bits (120), Expect = 2e-07
Identities = 18/46 (39%), Positives = 21/46 (45%)
Query: 9 KDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYI 54
K + +N+ PG I V V V FH FSA RRY YI
Sbjct: 70 ALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYI 115
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 44.8 bits (105), Expect = 1e-05
Identities = 41/261 (15%), Positives = 75/261 (28%), Gaps = 59/261 (22%)
Query: 2 IILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFH-PNFSAKWRRYLYIFPLNDG 60
+ D + + D++D S ++S ++ + + + R + L+
Sbjct: 24 VFEDAFVDNFDCKDVQDMPKS-------ILSKEEIDHIIMSKDAVSGTLRLFWTL-LSKQ 75
Query: 61 ENREQSIDSEVEVENF-------HTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNF 113
E Q EV N+ T Y + L ND F + R
Sbjct: 76 EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ 135
Query: 114 TICRVNLLLQRL--EGKLLSY------KT-FARDTKASRNIGPPTECFIY-----HARAT 159
++ L L +L KT A D S + + I+ + +
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP 195
Query: 160 EAIL-------------PCPVNDHGEGRKVMCVELVA--NRFL--RKMVRVLVATLVREA 202
E +L +DH K+ + A R L + L LV
Sbjct: 196 ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL---LV--- 249
Query: 203 AAGADE--DA-LLKLMDATCR 220
+A + +C+
Sbjct: 250 ---LLNVQNAKAWNAFNLSCK 267
>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 = 32.3 bits (73), Expect = 0.18
Identities = 39/207 (18%), Positives = 63/207 (30%), Gaps = 74/207 (35%)
Query: 91 ENIENLLINDEGGFGSHEKPRNFT--ICRVNLLLQRLEGKLLSYKTFARDTKASRNI--- 145
N NL I+ GG N++ I + +GKL + K F + S +
Sbjct: 1667 NNPVNLTIH-FGGEKGKRIRENYSAMIFETIV-----DGKLKTEKIFKEINEHSTSYTFR 1720
Query: 146 GPPTECFIYHARATE----AIL--------------PCPVND----H--GE--------G 173
AT+ A+ P + H GE
Sbjct: 1721 SEKGLLS-----ATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLAD 1775
Query: 174 RKVM----CVELVANR--FLRKMVRV---------LVATLVREAAAGADEDALLKLMDAT 218
VM VE+V R ++ V ++A AA ++AL +++
Sbjct: 1776 --VMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERV 1833
Query: 219 CRRATAPPAPPEGLCLVDVGYTNFDPQ 245
+R L + V Y N + Q
Sbjct: 1834 GKRTG-------WLVEI-VNY-NVENQ 1851
>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 = 30.7 bits (68), Expect = 0.23
Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 9/27 (33%)
Query: 122 LQRLEGKLLSYKTFARDT------KAS 142
L++L+ L K +A D+ KA+
Sbjct: 22 LKKLQASL---KLYADDSAPALAIKAT 45
>3h7c_X Agmatine deiminase; structural genomics, protein structure
initiative, center for eukaryotic structural genomics,
CESG; HET: MSE 211 1PE; 1.50A {Arabidopsis thaliana}
PDB: 1vkp_A* 2q3u_A* 3h7k_A*
Length = 383
Score = 28.1 bits (62), Expect = 3.0
Identities = 17/104 (16%), Positives = 36/104 (34%), Gaps = 10/104 (9%)
Query: 11 VKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSE 70
P+ E+A P IRV+ + + +R F + + S++
Sbjct: 64 ASPAQWENAR-KQLPEDIRVVEM--------SMNDSWFRDSGPTFIVRKRPVKLSSLNRN 114
Query: 71 VEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFT 114
+ +++ + G +GCY + + L+ PR
Sbjct: 115 IAGIDWNFNAWGGAN-DGCYNDWSHDLLVSRKILALERIPRFQH 157
>1mr1_C SKI oncogene, SKI, C-SKI; SMAD, cancer, TGF-B signaling, protein
interaction, signaling protein; 2.85A {Homo sapiens}
SCOP: d.217.1.2
Length = 99
Score = 25.2 bits (55), Expect = 8.8
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 37 SRVFHPNF-SAKWRRYLYIFPLNDGENREQSIDSEVE 72
+R H F SA WR Y+ + G+ + + ++
Sbjct: 55 NRTCHWGFDSANWRAYILLSQDYTGKEEQARLGRCLD 91
>2pgs_A Putative deoxyguanosinetriphosphate triphosphohyd;
deoxyguanosinetriphosphate triphsphohydrolase,
pseudomonas S PV. phaseolicola 1448A; 2.35A {Pseudomonas
syringae PV}
Length = 451
Score = 26.6 bits (59), Expect = 9.2
Identities = 6/49 (12%), Positives = 13/49 (26%), Gaps = 6/49 (12%)
Query: 15 DIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENR 63
D+ED + ++ ++V + D R
Sbjct: 251 DLEDGLEM------DLLDYAEVESLLLGLVGDDLPETYRQLGPGDSRRR 293
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
0.320 0.136 0.410
Gapped
Lambda K H
0.267 0.0567 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,826,342
Number of extensions: 219889
Number of successful extensions: 559
Number of sequences better than 10.0: 1
Number of HSP's gapped: 556
Number of HSP's successfully gapped: 15
Length of query: 250
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 159
Effective length of database: 4,160,982
Effective search space: 661596138
Effective search space used: 661596138
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: 56 (25.7 bits)