RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8408
(393 letters)
>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 = 47.9 bits (113), Expect = 5e-06
Identities = 48/371 (12%), Positives = 97/371 (26%), Gaps = 137/371 (36%)
Query: 17 RYLMDKA------IIDNLVFRCHYRITSAMLFVSC-VLVTANNL-IGDPINCIADGAVP- 67
R L K ++ N+ + + +A SC +L+T + D ++ +
Sbjct: 236 RLLKSKPYENCLLVLLNV---QNAKAWNAFNL-SCKILLTTRFKQVTDFLSAATTTHISL 291
Query: 68 GHVINTYC----------WI-TSTFTLPHQAHKPVGSHVIHP------------------ 98
H T ++ LP + +P
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT------TNPRRLSIIAESIRDGLATWD 345
Query: 99 ------------AVGSYVEGEDEKRYHTYYQ---------WVPFMLFFQGILFYVPHWIW 137
+ S + + Y + +P +L ++ W
Sbjct: 346 NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILL--SLI-------W 396
Query: 138 KNLEENKVRMITDGMRGA--------------------IVTSKEDRRERQKRLV-QYII- 175
++ ++ V ++ + + + E+ + +V Y I
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIP 456
Query: 176 ---DTLHMHNVYAAGYFFC-------------EFLNFVNVVGNMILID-SFLG------G 212
D+ + Y YF+ F M+ +D FL
Sbjct: 457 KTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLF-----RMVFLDFRFLEQKIRHDS 511
Query: 213 TFFTYGTEVLK-FTQLN------QENRTDPMVEVFPRVTKCTFHKYGSSGSIQDHDALCI 265
T + +L QL +N DP E K + + L
Sbjct: 512 TAWNASGSILNTLQQLKFYKPYICDN--DPKYERLVNAILDFLPKIEENLICSKYTDLLR 569
Query: 266 LALNILNEKIY 276
+AL +E I+
Sbjct: 570 IALMAEDEAIF 580
Score = 33.3 bits (75), Expect = 0.18
Identities = 44/278 (15%), Positives = 78/278 (28%), Gaps = 71/278 (25%)
Query: 132 VPHWIWKNLEENKVRMITDGMRGAIVTSKE--------DRRERQKRLVQYIIDTLHMHNV 183
+ + ++ + + D + I++ +E D RL TL
Sbjct: 22 LSVFEDAFVDNFDCKDVQDMPKS-ILSKEEIDHIIMSKDAVSGTLRL----FWTLLSKQE 76
Query: 184 YAAGYFFCEFL--NFVNVVGNMILIDSFLGGTFFTY--GTEVLKFTQLNQENRTDPMVEV 239
F E L N+ FL T ++ + Q +R +V
Sbjct: 77 EMVQKFVEEVLRINY-----------KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125
Query: 240 FPRVTKCTFHKYGSSGSIQDHDALCILALNILNEKIYILLWFWFYALAIMSFGAICYSLS 299
F KY S +Q + L AL L +L+ + G +
Sbjct: 126 FA--------KYNVS-RLQPYLKL-RQALLELRPAKNVLI----DGVL--GSGK-----T 164
Query: 300 VITLPSIRETILIRRFRFG----------TPAGVSALIRRTQVGDFLLLHLLGQNMNNMF 349
+ L + + F +P ++ Q LL+ + N
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCNSP---ETVLEMLQ----KLLYQIDPN----- 212
Query: 350 FGEILDELSTNLHLGNNIPTAPSTLELSPIYPSDKLRL 387
+ D S ++I L S Y + L L
Sbjct: 213 WTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL 250
Score = 29.4 bits (65), Expect = 2.8
Identities = 11/62 (17%), Positives = 22/62 (35%), Gaps = 9/62 (14%)
Query: 335 FLLLHLLGQNMNNMFFGEILDE----LSTNLHLGNNIPTAPSTLELSPIYPSDKLRLHKE 390
F L + M F E+L L + + P+ + + Y + RL+ +
Sbjct: 68 FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRM-----YIEQRDRLYND 122
Query: 391 TE 392
+
Sbjct: 123 NQ 124
>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 = 37.3 bits (86), Expect = 0.009
Identities = 24/109 (22%), Positives = 41/109 (37%), Gaps = 20/109 (18%)
Query: 300 VITLPSIRETILIRRF--------------RFGTPAGVSALIRRTQVGDFLLLHLL-GQN 344
L +T L++ R SAL R G+ L+ + GQ
Sbjct: 105 AAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQG 164
Query: 345 MNNMFFGEILDEL-ST-NLHLGNNIPTAPSTL-ELSPIYPSDKLRLHKE 390
+ +F E L +L T ++ +G+ I + TL EL D ++ +
Sbjct: 165 NTDDYFEE-LRDLYQTYHVLVGDLIKFSAETLSELIRT-TLDAEKVFTQ 211
Score = 29.2 bits (65), Expect = 3.2
Identities = 23/118 (19%), Positives = 39/118 (33%), Gaps = 48/118 (40%)
Query: 288 IMSFGAICYSLSV----------------ITLPSIRETI-----------LIRRF-RFGT 319
+S G++ + L V LP E L+ +F +
Sbjct: 10 TLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGY-- 67
Query: 320 PAGVSALIRRTQVGDF--LLLHLLGQNMNNMFFGEILDELSTNLHLGNNIPTAPSTLE 375
VS+L+ ++VG F +L L + F L+ GN+I + L
Sbjct: 68 ---VSSLVEPSKVGQFDQVLNLCLTE-----FENCYLE--------GNDIHALAAKLL 109
Score = 27.7 bits (61), Expect = 8.4
Identities = 52/306 (16%), Positives = 86/306 (28%), Gaps = 114/306 (37%)
Query: 3 VFAMVSAMAG----FVKVRYLMDKAIIDNLVF----RCH--YRITSAMLFVSCVLVTANN 52
V A+ A F + KAI ++F RC+ Y TS L S + + N
Sbjct: 278 VTAVAIAETDSWESFFV---SVRKAI--TVLFFIGVRCYEAYPNTS--LPPSILEDSLEN 330
Query: 53 LIGDP-----INCIADGAVPGHV--INTYCWITSTFTLPHQAHKPVG------SHVI--H 97
G P I+ + V +V N++ LP + + V+
Sbjct: 331 NEGVPSPMLSISNLTQEQVQDYVNKTNSH--------LPAGKQVEISLVNGAKNLVVSGP 382
Query: 98 P----AVGSYVE------GEDEKR--------------------YHTYY-----QWVPFM 122
P + + G D+ R +H++ +
Sbjct: 383 PQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKD 442
Query: 123 LFFQGILFY-----VPHWIWKNLEENKVRMITDGMRGAIVTSKEDRRERQKRLVQYIIDT 177
L + F +P V DG D R + + I+D
Sbjct: 443 LVKNNVSFNAKDIQIP-----------VYDTFDG---------SDLRVLSGSISERIVDC 482
Query: 178 LHMHNVY---AAGYFFCEFLNF----VNVVGNMILIDSFLGGTFFTYGTEVLKFTQLNQE 230
+ V + L+F + +G L GT G V+ L+
Sbjct: 483 IIRLPVKWETTTQFKATHILDFGPGGASGLGV--LTHRNKDGT----GVRVIVAGTLDI- 535
Query: 231 NRTDPM 236
N D
Sbjct: 536 NPDDDY 541
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop,
lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli}
SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A
Length = 327
Score = 30.7 bits (70), Expect = 0.84
Identities = 13/68 (19%), Positives = 19/68 (27%), Gaps = 12/68 (17%)
Query: 318 GTPAGVSALIRRTQVGDFLLLHLLGQNMNNMFFGEILDELSTNLHLGNNIPTAPSTLELS 377
G A V L RR V + + M L+ L + + L
Sbjct: 205 GCGAHVIYL-RRLAVSKYPV--------ERMVT---LEHLRELVEQAEQQDIPAAELLDP 252
Query: 378 PIYPSDKL 385
+ P D
Sbjct: 253 LLMPMDSP 260
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification,
structural genomics, PSI, structure initiative; 1.90A
{Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2
Length = 316
Score = 28.7 bits (65), Expect = 2.8
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 318 GTPAGVSALIRRTQVGDFLL 337
G V+AL RRT+VG F L
Sbjct: 191 GVGGHVTAL-RRTRVGRFEL 209
>3e0j_A DNA polymerase subunit delta-2; DNA polymerase delta, P66 subunit,
P50 subunit, human, DNA replication, DNA-directed DNA
polymerase; HET: DNA; 3.00A {Homo sapiens}
Length = 476
Score = 28.9 bits (64), Expect = 3.1
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 331 QVGDFLLLHLLGQNMNNMF----FGEILDELSTNLHLGNNIPTAPSTLELSPIYPSDKLR 386
+ L GQN++++F + L+ L L + + PTAP TL P Y +D
Sbjct: 342 TIDGVRFLGTSGQNVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFI 401
Query: 387 L 387
Sbjct: 402 F 402
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation,
lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima}
SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A
Length = 309
Score = 28.4 bits (64), Expect = 4.0
Identities = 6/20 (30%), Positives = 7/20 (35%), Gaps = 1/20 (5%)
Query: 318 GTPAGVSALIRRTQVGDFLL 337
G A L R VG +
Sbjct: 183 GCGATAVEL-VRESVGPHTI 201
>2jn4_A Hypothetical protein FIXU, NIFT; structural genomics, PSI-2,
protein structure initiative, northeast ST genomics
consortium, NESG; NMR {Rhodopseudomonas palustris} SCOP:
b.173.1.1
Length = 87
Score = 26.7 bits (59), Expect = 4.2
Identities = 12/32 (37%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 127 GILFYVPHWIWKNLEENKVRMITDGMRGAIVT 158
G YV K+LEE V M + G VT
Sbjct: 32 GHSAYVAK---KDLEELIVEMENPALWGGKVT 60
>3s52_A Putative fumarylacetoacetate hydrolase family Pro; csgid,
structural genomics, center for structural genomics O
infectious diseases; 2.01A {Yersinia pestis} PDB: 1nr9_A
Length = 221
Score = 27.1 bits (61), Expect = 8.5
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 318 GTPAGVSALIRRTQVGDFLLLHLLGQNMNN 347
GTP GV + Q GD L + L G+ +N
Sbjct: 193 GTPQGVGPM----QSGDMLKIMLNGKTVNT 218
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
0.328 0.141 0.443
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,162,450
Number of extensions: 372815
Number of successful extensions: 909
Number of sequences better than 10.0: 1
Number of HSP's gapped: 905
Number of HSP's successfully gapped: 18
Length of query: 393
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 297
Effective length of database: 4,021,377
Effective search space: 1194348969
Effective search space used: 1194348969
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 58 (26.1 bits)