RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13344
(155 letters)
>2i7x_A Protein CFT2; polyadenylation, metallo-B-lactamase, PRE-mRNA
processing, artemis, V(D)J recombination, double-strand
break repair; 2.50A {Saccharomyces cerevisiae} SCOP:
d.157.1.10
Length = 717
Score = 92.2 bits (228), Expect = 1e-22
Identities = 29/142 (20%), Positives = 56/142 (39%), Gaps = 11/142 (7%)
Query: 17 KQFPMFPFHETKIKYDEYGNHSSWAYGEEIFTG-PIWKIVKEGEEEIVYGVDFNLKKERH 75
+ + Y + AY + G IW I E++VY +N ++
Sbjct: 129 DHIVPLKYSQLVDLRSRYDGLTLLAYNAGVCPGGSIWCI-STYSEKLVYAKRWNHTRDNI 187
Query: 76 LNGC--------VLDRFIRPTVVITDTMSAIYQQARRRTRDERLMTNILQTLRNNGNVLV 127
LN L +RP+ +IT Q ++ R + + + L ++G+V++
Sbjct: 188 LNAASILDATGKPLSTLMRPSAIITTLDRFGSSQPFKK-RSKIFKDTLKKGLSSDGSVII 246
Query: 128 AVDTAGRVLELTHMLEQLWRNK 149
VD +G+ L+L + +L
Sbjct: 247 PVDMSGKFLDLFTQVHELLFES 268
Score = 41.3 bits (96), Expect = 5e-05
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 8 NSRFFKSNKKQFPMFPFHETKIKYDEYGNHS 38
+ S + MFPF+ KIK D+YG
Sbjct: 523 DIIIQPSAASKHKMFPFNPAKIKKDDYGTVV 553
>2i7t_A Cleavage and polyadenylation specificity factor 73 kDa subunit;
metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J
recombination; 2.10A {Homo sapiens} SCOP: d.157.1.10
PDB: 2i7v_A
Length = 459
Score = 49.5 bits (119), Expect = 6e-08
Identities = 24/109 (22%), Positives = 49/109 (44%), Gaps = 11/109 (10%)
Query: 55 VKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITDTMSAIYQQARRRTRDERLMTN 114
++ +++Y DF+ +++RHL + I+P ++I ++ + +R R+ R
Sbjct: 167 IEIAGVKLLYTGDFSRQEDRHLMAAEIP-NIKPDILIIESTYGTHIHEKREEREARFCNT 225
Query: 115 ILQTLRNNGNVLVAVDTAGRVLELTHMLEQLWRNK----------DSGL 153
+ + G L+ V GR EL +L++ W+N S L
Sbjct: 226 VHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHPELHDIPIYYASSL 274
>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp
family, KH domain, ribonuclease, ME beta-lactamase
superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB:
3af6_A*
Length = 651
Score = 47.7 bits (114), Expect = 2e-07
Identities = 26/100 (26%), Positives = 40/100 (40%), Gaps = 9/100 (9%)
Query: 55 VKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITDTM--SAIYQQARRRTRDERLM 112
+ G I DF R L F R ++ ++ A Q R ++RL+
Sbjct: 355 IGNGLHNIAITGDFKFIPTRLLEPANAK-FPRLETLVMESTYGGANDIQMPREEAEKRLI 413
Query: 113 TNILQTLRNNGNVLV---AVDTAGRVLELTHMLEQLWRNK 149
I T++ G VL+ AV GR E+ +LE+ R
Sbjct: 414 EVIHNTIKRGGKVLIPAMAV---GRAQEVMMVLEEYARIG 450
>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor;
hydrolase, KH, metallo-beta-lactamase; 3.10A
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 636
Score = 47.3 bits (113), Expect = 4e-07
Identities = 27/101 (26%), Positives = 44/101 (43%), Gaps = 9/101 (8%)
Query: 55 VKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITDTM--SAIYQQARRRTRDERLM 112
+ +G+ +VY DF ++ R L F R ++ ++ Q R ++ L+
Sbjct: 340 IGDGQHNMVYTGDFKYEQSRLLEAAANR-FPRIETLVMESTYGGHEDVQPSRNRAEKELV 398
Query: 113 TNILQTLRNNGNVLV---AVDTAGRVLELTHMLEQLWRNKD 150
I TLR G +L+ AV GR EL +LE+ R
Sbjct: 399 KTIYSTLRRGGKILIPVFAV---GRAQELMIVLEEYIRTGI 436
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit;
hydrolase, metallo-beta-lactamase, beta-CAsp, RNA
processing; 2.59A {Methanosarcina mazei}
Length = 640
Score = 46.9 bits (112), Expect = 5e-07
Identities = 23/101 (22%), Positives = 43/101 (42%), Gaps = 9/101 (8%)
Query: 55 VKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITDT--MSAIYQQARRRTRDERLM 112
+ +G +V+ D+ +K R + V F R VI++ +A Q + ++ L
Sbjct: 343 IGDGLHNVVFTGDYKYEKTRLFDPAVNK-FPRVETVISEATYGNANAFQPALKDAEKHLQ 401
Query: 113 TNILQTLRNNGNVLV---AVDTAGRVLELTHMLEQLWRNKD 150
+ T+ G ++ AV GR E+ +LE+ R
Sbjct: 402 MVVKNTIERGGIAVIPAFAV---GRSQEVMIVLEESIRKGL 439
>3iek_A Ribonuclease TTHA0252; metallo beta lactamase fold, endonuclease,
hydrolase, metal- nuclease, RNA-binding, rRNA
processing; HET: FLC; 2.05A {Thermus thermophilus} PDB:
2dkf_A* 3iel_A* 3iem_A* 2zdf_A* 3idz_A* 2zdd_A* 3ie0_A*
2zde_A* 3ie1_A* 2zdw_A* 3a4y_A* 2yvd_A* 3ie2_A*
Length = 431
Score = 36.7 bits (86), Expect = 0.001
Identities = 16/95 (16%), Positives = 31/95 (32%), Gaps = 8/95 (8%)
Query: 55 VKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITDTMSAIYQQARRRTRDERLMTN 114
+ +VY D +++ L +V+ + R +
Sbjct: 150 AQGEGRTLVYSGDLGNREKDVLPD--PSLPPLADLVLAEGTYGDRPHRPYRETVREFLEI 207
Query: 115 ILQTLRNNGNVLV---AVDTAGRVLELTHMLEQLW 146
+ +TL G VL+ AV R E+ ++L
Sbjct: 208 LEKTLSQGGKVLIPTFAV---ERAQEILYVLYTHG 239
>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 = 34.3 bits (78), Expect = 0.011
Identities = 26/162 (16%), Positives = 44/162 (27%), Gaps = 71/162 (43%)
Query: 32 DEYGNHSS----W---------AYGEEI--------------FTGPIWKIVKEGEEEIVY 64
D Y + W YG I F G K ++E +++
Sbjct: 1634 DLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIF 1693
Query: 65 --GVDFNLKKER-------HLNGCVLDRFIRPTVVITDTMSAIYQQARRRTRDERLMT-- 113
VD LK E+ H F +++ T Q A L
Sbjct: 1694 ETIVDGKLKTEKIFKEINEHSTSYT---FRSEKGLLSATQFT--QPA--------LTLME 1740
Query: 114 -NILQTLRNNGNV----------------LVAVDTAGRVLEL 138
+ L++ G + L ++ A V+ +
Sbjct: 1741 KAAFEDLKSKGLIPADATFAGHSLGEYAALASL--AD-VMSI 1779
Score = 30.4 bits (68), Expect = 0.28
Identities = 20/91 (21%), Positives = 32/91 (35%), Gaps = 37/91 (40%)
Query: 14 SNKK-----QF-PMF-PFH-------ETKIKYDEYGNHSSWAYGEEIFTGPIWKIVKEGE 59
S +K +F P+ PFH I D N+ S+ ++ +I
Sbjct: 410 SERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFN-AKD------IQIP---- 458
Query: 60 EEIVY----GVDFNLKKERHLNGCVLDRFIR 86
VY G D R L+G + +R +
Sbjct: 459 ---VYDTFDGSDL-----RVLSGSISERIVD 481
>3nem_A Aspartyl-tRNA synthetase; rossmann fold, OB fold, ligase; HET: AMO
ATP; 1.89A {Thermococcus kodakarensis} PDB: 3nel_A*
3nen_A 1b8a_A*
Length = 438
Score = 30.6 bits (70), Expect = 0.17
Identities = 11/78 (14%), Positives = 26/78 (33%), Gaps = 17/78 (21%)
Query: 16 KKQFPMFPFHETKIKYDEYGNHSSWAYGEEIFTGPIWKIVKEGEEEIVYGVDFNLKKERH 75
+ ++ YD+ +I+ + +EI +G D + + ER
Sbjct: 270 NFELEEPKLPFPRVSYDK-----------------ALEILGDLGKEIPWGEDIDTEGERL 312
Query: 76 LNGCVLDRFIRPTVVITD 93
L +++ P +
Sbjct: 313 LGKYMMENENAPLYFLYQ 330
>1eov_A ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA synthetase, tRNA
ligase, APO-enzyme, OB-fold,; 2.30A {Saccharomyces
cerevisiae} SCOP: b.40.4.1 d.104.1.1 PDB: 1asy_A*
1asz_A*
Length = 487
Score = 30.0 bits (68), Expect = 0.30
Identities = 7/41 (17%), Positives = 19/41 (46%)
Query: 53 KIVKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITD 93
++++ +EI D + + E+ L V D++ ++
Sbjct: 337 EMLRAAGKEIGDFEDLSTENEKFLGKLVRDKYDTDFYILDK 377
>2dc1_A L-aspartate dehydrogenase; NAD, oxidoreductase; HET: CIT NAD; 1.90A
{Archaeoglobus fulgidus}
Length = 236
Score = 28.5 bits (63), Expect = 0.73
Identities = 9/95 (9%), Positives = 28/95 (29%), Gaps = 12/95 (12%)
Query: 51 IWKIVKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITDTMSAIYQQARRRTRDER 110
+ + ++ EI +D + E+ + G V +
Sbjct: 15 LAEWLERNGFEIAAILDVRGEHEKMVRGIDEFLQREMDVAVEAASQQA------------ 62
Query: 111 LMTNILQTLRNNGNVLVAVDTAGRVLELTHMLEQL 145
+ + L+ +++V A + + ++
Sbjct: 63 VKDYAEKILKAGIDLIVLSTGAFADRDFLSRVREV 97
>3i7f_A Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-binding,
aminoacyl-tRNA synthetase, LI nucleotide-binding,
protein biosynthesis; 2.80A {Entamoeba histolytica}
Length = 548
Score = 28.6 bits (64), Expect = 0.77
Identities = 6/41 (14%), Positives = 16/41 (39%)
Query: 53 KIVKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITD 93
++++ E I DF +E L + ++ ++
Sbjct: 400 EMLRASGETIGDYDDFTTPQEVKLGELIKAKYNTDFYILDK 440
>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 = 28.3 bits (62), Expect = 1.1
Identities = 18/108 (16%), Positives = 35/108 (32%), Gaps = 28/108 (25%)
Query: 44 EEIFTGP---------IWKIVKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITDT 94
+ I W ++ + EE + V+ L+ ++ I+
Sbjct: 52 DHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINY---KFLMSP-IKTEQRQPSM 107
Query: 95 MSAIYQQARRR-------------TRDERLMT--NILQTLRNNGNVLV 127
M+ +Y + R R +R + + L LR NVL+
Sbjct: 108 MTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI 155
Score = 27.9 bits (61), Expect = 1.7
Identities = 22/95 (23%), Positives = 39/95 (41%), Gaps = 11/95 (11%)
Query: 19 FPM----FPFHETKIKYDEYGNHSSWAYGEEIFTGPIWK--IVKEGE--EEIVYGV-DFN 69
F M F F E KI++D ++S + + +K I E +V + DF
Sbjct: 493 FRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFL 552
Query: 70 LKKERHLNGCVLDRFIRPTVVITDTMSAIYQQARR 104
K E +L +R + + AI+++A +
Sbjct: 553 PKIEENLICSKYTDLLR--IALMAEDEAIFEEAHK 585
>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A
{Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB:
1j8y_F
Length = 297
Score = 27.5 bits (62), Expect = 1.8
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 116 LQTLRNNGNVLVAVDTAGR--VLELTHMLEQLWRNKD 150
++ + ++ VDTAGR E +LE++ +
Sbjct: 173 VEKFLSEKMEIIIVDTAGRHGYGEEAALLEEMKNIYE 209
>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition
particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A
{Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A
Length = 433
Score = 27.5 bits (62), Expect = 2.1
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 116 LQTLRNNGNVLVAVDTAGR--VLELTHMLEQL 145
+ N ++ VDTAGR E T +LE++
Sbjct: 172 VDIFVKNKMDIIIVDTAGRHGYGEETKLLEEM 203
>2gez_A L-asparaginase alpha subunit; isoaspartyl aminopeptidase,
NTN-hydrolase, autoproteolysis, taspase, sodium binding,
hydrolase; 2.60A {Lupinus luteus}
Length = 195
Score = 25.5 bits (56), Expect = 7.4
Identities = 10/51 (19%), Positives = 18/51 (35%), Gaps = 9/51 (17%)
Query: 91 ITDTMSAIYQQARRRTRDERLMTNILQT----LRNNGNVLVAVDTAGRVLE 137
I ++ ++ R + + LQ L+ L V+ R LE
Sbjct: 18 IPFSLPPERRKPREEG-----LRHCLQIGVEALKAQKPPLDVVELVVRELE 63
>1wyd_A Hypothetical aspartyl-tRNA synthetase; archaea, LIGA; HET: EPE;
2.30A {Sulfolobus tokodaii}
Length = 429
Score = 25.6 bits (57), Expect = 8.0
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 4/41 (9%)
Query: 53 KIVKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITD 93
+I++ I +G D + R LN + I D
Sbjct: 285 EILRSKGYNIKFGDDIGTPELRILN----EELKEDLYFIVD 321
>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity
A; hydrolase inhibitor-hydrolase complex, DEAD box RNA
helicase; 2.90A {Escherichia coli}
Length = 170
Score = 25.2 bits (56), Expect = 9.2
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 13/45 (28%)
Query: 100 QQARRRTRDERLMTNILQTLRNNG-NVLVAVDTAGR---VLELTH 140
Q R ++ L NVLVA D A R + +++H
Sbjct: 66 QGKRNEA---------IKRLTEGRVNVLVATDVAARGIDIPDVSH 101
>3c17_A L-asparaginase precursor; isoaspartyl peptidase, NTN-hydrolase,
autoprot precursor, hydrolase; 1.95A {Escherichia coli}
PDB: 2zak_A
Length = 320
Score = 25.4 bits (56), Expect = 9.6
Identities = 12/64 (18%), Positives = 21/64 (32%), Gaps = 17/64 (26%)
Query: 86 RPTVVI--------TDTMSAIYQQARRRTRDERLMTNILQT----LRNNGNVLVAVDTAG 133
+ + I MS + ++ I++T L + L V A
Sbjct: 2 KAVIAIHGGAGAISRAQMSLQQELRYIEA-----LSAIVETGQKMLEAGESALDVVTEAV 56
Query: 134 RVLE 137
R+LE
Sbjct: 57 RLLE 60
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase;
HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5
Length = 189
Score = 25.0 bits (55), Expect = 9.8
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 7/28 (25%)
Query: 66 VDFNLKKERHLNGCVLDRFIRPTVVITD 93
V+ + + D+FIRP ITD
Sbjct: 31 VNVHGA-------VLYDKFIRPEGEITD 51
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 0.137 0.413
Gapped
Lambda K H
0.267 0.0536 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,457,198
Number of extensions: 143045
Number of successful extensions: 381
Number of sequences better than 10.0: 1
Number of HSP's gapped: 371
Number of HSP's successfully gapped: 38
Length of query: 155
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 69
Effective length of database: 4,300,587
Effective search space: 296740503
Effective search space used: 296740503
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: 53 (24.6 bits)