RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17738
(316 letters)
>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV,
RNAse H, reverse transcriptase, transcription; 1.50A
{Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A
3v1r_A* 2hb5_A
Length = 165
Score = 44.1 bits (104), Expect = 1e-05
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 11/72 (15%)
Query: 203 IYTDGSKDEEN----AGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNN 258
YTDGS + AG A V + + +L +S EL A+ AL+ N
Sbjct: 26 WYTDGSSFLQEGQRRAGAA-VTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLN 84
Query: 259 TVENYVIISDSQ 270
+ +DS+
Sbjct: 85 ------VYTDSR 90
>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 = 42.9 bits (100), Expect = 1e-04
Identities = 36/277 (12%), Positives = 78/277 (28%), Gaps = 75/277 (27%)
Query: 1 MRSAIDYTSMYRQINQIPRRNAYTWC----SAEQVMELFGDLYL--HTIDI-IKVL---- 49
+ D ++ +N + ++F L + + I +L
Sbjct: 340 GLATWDN---WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW 396
Query: 50 NPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNEPPLE---IRRKILTFNYAA 106
+ + ++N + L T I +++LE + R I+ +Y
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVD-HYNI 455
Query: 107 KVTSVPQHPCYKLLMFPKYVQNY---------KNKKINTINVFLEEKFPLFKKI------ 151
T + P Y+ Y KN + E+ LF+ +
Sbjct: 456 PKTFDSDD------LIPPYLDQYFYSHIGHHLKNIE-------HPERMTLFRMVFLDFRF 502
Query: 152 ------HTLTHPPPPPWTLDT-PDLNF-QLHIFTKKITSSPIIKS--NFLAILQNYETHV 201
H T L+T L F + +I ++ + +F L E ++
Sbjct: 503 LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDF---LPKIEENL 559
Query: 202 RIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIF 238
++ ++ + +IF
Sbjct: 560 ICS----------------KYTDLLRIALMAEDEAIF 580
Score = 33.7 bits (76), Expect = 0.080
Identities = 33/296 (11%), Positives = 83/296 (28%), Gaps = 58/296 (19%)
Query: 36 GDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNEPPLEI 95
G+ DI+ V +N +Q+ + I +
Sbjct: 12 GEHQYQYKDILSVFEDAFVDN-FDC-KDVQDM-PK---SILSKEEIDHI---IMSKDAVS 62
Query: 96 RRKILTFNYAAKVTSVPQ-------HPCYKLLMFPKYVQNYKNKKINTINVFLEEKFPLF 148
L + +K + Q YK LM + + T ++E++ L+
Sbjct: 63 GTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM-SPIKTEQRQPSMMTRM-YIEQRDRLY 120
Query: 149 KKIHTLTHPPPPPWTLDTPDLNFQLHIFTKKITSSPII---------KSNFLAI--LQNY 197
+ + + +L ++ + + K+ ++A+ +Y
Sbjct: 121 N-----DNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT-WVALDVCLSY 174
Query: 198 ETHVR----IY--TDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEY 251
+ + I+ + + P+ + + L + + ++
Sbjct: 175 KVQCKMDFKIFWLNLKNCNS---------PETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225
Query: 252 LHHPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQTLNQGGFKCEILANTK 307
H + + + L + N+ N + N C+IL T+
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQ--------NAKAWNAFNLSCKILLTTR 273
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO
enzyme, structural genomics, protein structure
initiative; NMR {Desulfitobacterium hafniense dcb-2}
PDB: 2kw4_A
Length = 147
Score = 38.5 bits (90), Expect = 8e-04
Identities = 15/82 (18%), Positives = 24/82 (29%), Gaps = 11/82 (13%)
Query: 196 NYETHVRIYTDGSKDEEN--AGCAFVIPDRNITKMFSLDP-----KSSIFACELYAIYAA 248
+ T +YTDGS AFV + + + A E+ A A
Sbjct: 2 DDRTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYA 61
Query: 249 LEYLHHPNNNTVENYVIISDSQ 270
++ I+ D
Sbjct: 62 VKKASQLG----VKIRILHDYA 79
>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 = 36.6 bits (84), Expect = 0.013
Identities = 11/60 (18%), Positives = 23/60 (38%), Gaps = 8/60 (13%)
Query: 228 MFSLDPKSSIFACELYAIYAALEYLHHPNNNTVE--NY------VIISDSQAALQAISNI 279
M +++P + A+ +E + VE NY + + AL ++N+
Sbjct: 1809 MIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNV 1868
Score = 35.8 bits (82), Expect = 0.022
Identities = 32/223 (14%), Positives = 61/223 (27%), Gaps = 90/223 (40%)
Query: 79 TPIQALHLETNEP--PLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKKINT 136
P + + +EP P E+ K L + ++ V ++L
Sbjct: 43 EPTEGFAAD-DEPTTPAELVGKFLGY-VSSLVEPSKVGQFDQVLNL-------------C 87
Query: 137 INVFLEEKFPLFKKIHTLTHPPPPPWTLDTPDLNFQLHIFTKKITSSPIIKSNFLAILQN 196
+ F E + IH L L + + ++K+ +++N
Sbjct: 88 LTEF-ENCYLEGNDIHALAA------KLLQEN-------------DTTLVKTK--ELIKN 125
Query: 197 YETHVRIYTDGSKDEENAGCAFVIPDRNITKMFS--L-----DPKSSIFAC--------- 240
Y T A ++ R K + L + + + A
Sbjct: 126 Y------IT-----------ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDD 168
Query: 241 ------ELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAIS 277
+LY Y L V + +I S L +
Sbjct: 169 YFEELRDLYQTYHVL----------VGD--LIKFSAETLSELI 199
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 30.6 bits (70), Expect = 0.31
Identities = 17/100 (17%), Positives = 28/100 (28%), Gaps = 39/100 (39%)
Query: 200 HVRIYTDGS-------------------KDEENAGCAFVIPDRNIT--KMFSLDPKSSIF 238
V +YTDG N G T +
Sbjct: 7 FVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRL---PGRQTNQRA---------- 53
Query: 239 ACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAISN 278
E++A A+E N N + + ++S + I+N
Sbjct: 54 --EIHAACKAIEQAKTQNINKLV---LYTNSMFTINGITN 88
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded
RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus
tokodaii} PDB: 3aly_A
Length = 149
Score = 29.6 bits (67), Expect = 0.65
Identities = 18/94 (19%), Positives = 34/94 (36%), Gaps = 13/94 (13%)
Query: 201 VRIYTDGSKDEEN----AGCAFVI-PDRNITKMFSLDPKSSIFAC-----ELYAIYAALE 250
+ Y DG + +N A FVI D + + L K E + +E
Sbjct: 2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLME 61
Query: 251 YLHHPNNNTVENYVIISDSQAALQAISNIYTIQN 284
+ ++ I DSQ ++ ++ Y ++
Sbjct: 62 TMLRLGISSPI---IKGDSQLVIKQMNGEYKVKA 92
>3uow_A GMP synthetase; structural genomics consortium, SGC, purine
nucleotide biosy process, ligase; HET: XMP; 2.72A
{Plasmodium falciparum}
Length = 556
Score = 29.5 bits (67), Expect = 1.6
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 4/34 (11%)
Query: 28 AEQVMELFGDLYLHTIDIIKVLNPDASENNLKIL 61
AE V + ++I K+ DASEN L L
Sbjct: 298 AENVYTFLKSTFPD-MNITKI---DASENFLSNL 327
>2gtq_A Aminopeptidase N; alanine aminopeptidase, M1 family peptidas PSI-2,
structural genomics, protein structure initiative; 2.05A
{Neisseria meningitidis}
Length = 867
Score = 29.5 bits (66), Expect = 1.7
Identities = 5/32 (15%), Positives = 13/32 (40%)
Query: 158 PPPPWTLDTPDLNFQLHIFTKKITSSPIIKSN 189
P + + DL+F ++ + S ++
Sbjct: 12 QTPAYHILKTDLHFDINEPQTVVKSRLTVEPQ 43
>2vxo_A GMP synthase [glutamine-hydrolyzing]; proto-oncogene,
phosphoprotein, GMP synthetase, guanine monophosphate
synthetase, chromosomal rearrangement; HET: XMP; 2.5A
{Homo sapiens}
Length = 697
Score = 28.8 bits (65), Expect = 2.9
Identities = 13/72 (18%), Positives = 23/72 (31%), Gaps = 12/72 (16%)
Query: 28 AEQVMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLE 87
++ V E L I + + +A+ N + + L+
Sbjct: 284 SQSVEEALKKL---GIQVKVI---NAAH---SFYNGTTTLPISDEDRTPRKRISKTLN-M 333
Query: 88 TNEPPLEIRRKI 99
T P E +RKI
Sbjct: 334 TTSP--EEKRKI 343
>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif,
hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1
PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A
2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*
Length = 142
Score = 27.1 bits (60), Expect = 5.1
Identities = 17/83 (20%), Positives = 26/83 (31%), Gaps = 11/83 (13%)
Query: 201 VRIYTDG-SKDEEN---AGCAFVIPDRN-ITKMFSLDPKSSIFACELYAIYAALEYLHHP 255
+ D S+ N V + P + E AI L YL
Sbjct: 12 ESLSVDVGSQG--NPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKER 69
Query: 256 NNNTVENYVIISDSQAALQAISN 278
N I S+SQ A++ + +
Sbjct: 70 N----SRKPIYSNSQTAIKWVKD 88
>3p0j_A Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase,
AARS, tyrrs, pseudod translation, ATP-binding,
nucleotide-binding, ligase; HET: TYE; 2.89A {Leishmania
major} PDB: 3p0i_A* 3p0h_A*
Length = 690
Score = 27.9 bits (62), Expect = 6.1
Identities = 11/111 (9%), Positives = 29/111 (26%), Gaps = 4/111 (3%)
Query: 23 YTWCSAEQVMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQ 82
T+ + E + + F + L + +L P++ ++
Sbjct: 304 TTYATYEDLEQAFVSDEVSEDA----LKSCLIDEVNALLEPVRQHFASNEEAHELLEAVK 359
Query: 83 ALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKK 133
+ + PL +P L + ++ K+
Sbjct: 360 SYRKDGATLPLAETALPAAPAKPHACMWMPALLKVPLDVAEGMIKVTKDFI 410
>3tqi_A GMP synthase [glutamine-hydrolyzing]; ligase; 2.84A {Coxiella
burnetii}
Length = 527
Score = 27.4 bits (62), Expect = 7.5
Identities = 6/28 (21%), Positives = 12/28 (42%), Gaps = 5/28 (17%)
Query: 28 AEQVMELFGDLYLHTIDIIKVLNPDASE 55
++V+ +F +I V DA +
Sbjct: 273 VDEVLNVFQKHL--GAKVICV---DAKD 295
>1gpm_A GMP synthetase, XMP aminase; class I glutamine amidotransferase,
N-type ATP pyrophosphata transferase (glutamine
amidotransferase); HET: AMP CIT; 2.20A {Escherichia
coli} SCOP: c.23.16.1 c.26.2.1 d.52.2.1
Length = 525
Score = 27.0 bits (61), Expect = 8.2
Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 5/28 (17%)
Query: 28 AEQVMELFGDLYLHTIDIIKVLNPDASE 55
AEQV+++FGD + ++I+ V A +
Sbjct: 270 AEQVLDMFGDHF--GLNIVHV---PAED 292
>2c36_A Glycoprotein D HSV-1; viral protein, immunoglobulin-like,
transmembrane; HET: NAG MAN BMA NDG; 2.11A {Human
herpesvirus 1} PDB: 2c3a_A* 3sku_A* 3u82_A 1l2g_A*
1jma_A*
Length = 285
Score = 26.8 bits (58), Expect = 8.9
Identities = 6/79 (7%), Positives = 14/79 (17%), Gaps = 13/79 (16%)
Query: 158 PPPPWTLDTPDLNFQLHIFTKKITSSPIIKSNFLAILQNYETHVRIYTDGSKDEENAGCA 217
P D P + HI + F + +
Sbjct: 1 PVLDQLTDPPGVRRVYHI-------QAGLPDPFQPPSLPITVYYAVLERA------CRSV 47
Query: 218 FVIPDRNITKMFSLDPKSS 236
+ ++ +
Sbjct: 48 LLNAPSEAPQIVRGASEDV 66
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
0.321 0.135 0.405
Gapped
Lambda K H
0.267 0.0784 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,760,053
Number of extensions: 274697
Number of successful extensions: 574
Number of sequences better than 10.0: 1
Number of HSP's gapped: 570
Number of HSP's successfully gapped: 29
Length of query: 316
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 222
Effective length of database: 4,077,219
Effective search space: 905142618
Effective search space used: 905142618
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 (21.9 bits)
S2: 57 (25.6 bits)