RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6081
(226 letters)
>3fqd_A Protein DHP1, 5'-3' exoribonuclease 2; protein-protein complex,
exonuclease, hydrolase, mRNA proces nuclease, nucleus,
rRNA processing, transcription; 2.20A
{Schizosaccharomyces pombe}
Length = 899
Score = 179 bits (454), Expect = 4e-52
Identities = 103/196 (52%), Positives = 131/196 (66%), Gaps = 19/196 (9%)
Query: 31 PQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECI 90
+ +G +I D S PNPNG+E DNLYLDMNGI+HPC+HPED+PAP+ EDEMMVA+FE
Sbjct: 30 EKLPDGTEIEPDLSLPNPNGVECDNLYLDMNGIVHPCSHPEDRPAPETEDEMMVAVFEYT 89
Query: 91 DRLFRIVRPRKLLYMAIDGVAPRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKETA 150
DR+ +VRPR+LL++AIDGVAPRAKMNQ RSRRFR+S+E A
Sbjct: 90 DRILAMVRPRQLLFIAIDGVAPRAKMNQ-------------------QRSRRFRSSREAA 130
Query: 151 EKIAEVARIREKLLADGCILPPEKEKGSHFDSNCITPGTPFMACLSACLHYYIHDRLNND 210
K E+ E+ G + K +DSNCITPGTPFM L+ L YYI ++LN+D
Sbjct: 131 LKEEELQAFIEEAKQQGIPIDENATKKKSWDSNCITPGTPFMDTLAKSLRYYIINKLNSD 190
Query: 211 PGWKGIKVILSDANVP 226
P W+ ++ ILSDA+VP
Sbjct: 191 PCWRNVRFILSDASVP 206
>3pie_A 5'->3' exoribonuclease (XRN1); beta berrel, tudor domain, chromo
domain, mRNA turnover, RRN processing, RNA binding, DNA
binding; 2.90A {Kluyveromyces lactis} PDB: 3pif_A
Length = 1155
Score = 153 bits (388), Expect = 3e-43
Identities = 74/177 (41%), Positives = 95/177 (53%), Gaps = 32/177 (18%)
Query: 52 EFDNLYLDMNGIIHPCTHPEDKPAPK--DEDEMMVAIFECIDRLFRIVRPRKLLYMAIDG 109
EFDNLYLDMN I+H CTH + E+E+ IF ID LF ++P++ YMAIDG
Sbjct: 28 EFDNLYLDMNSILHNCTHGDGSEVNSRLSEEEVYSKIFSYIDHLFHTIKPKQTFYMAIDG 87
Query: 110 VAPRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKETAEKIAEVARIREKLLADGCI 169
VAPRAKMNQ R+RRFR + + + + + +
Sbjct: 88 VAPRAKMNQ-------------------QRARRFRTAMDAEKALQKAIENGD-------- 120
Query: 170 LPPEKEKGSHFDSNCITPGTPFMACLSACLHYYIHDRLNNDPGWKGIKVILSDANVP 226
E KG FDSN ITPGT FMA L+ L Y+IHD++ ND W+ +KVI S VP
Sbjct: 121 ---ELPKGEPFDSNAITPGTEFMAKLTENLKYFIHDKITNDTRWQNVKVIFSGHEVP 174
>2y35_A LD22664P; hydrolase-DNA complex, RNA degradation, exonuclease
5'-3', R interference; 3.20A {Drosophila melanogaster}
Length = 1140
Score = 148 bits (373), Expect = 5e-41
Identities = 68/177 (38%), Positives = 99/177 (55%), Gaps = 33/177 (18%)
Query: 52 EFDNLYLDMNGIIHPCTHPEDK--PAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDG 109
EFDNLYLDMNGI+H C+HP+D +E+++ IF +D+LF +++P++L ++++DG
Sbjct: 28 EFDNLYLDMNGIVHNCSHPDDNNIHFHLEEEQIFQEIFNYVDKLFYLIKPQRLFFLSVDG 87
Query: 110 VAPRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKETAEKIAEVARIREKLLADGCI 169
VAPRAKMNQ RSRRFR ++E ++ A+ A+ E
Sbjct: 88 VAPRAKMNQ-------------------QRSRRFRTAREAEQQEAKAAQRGEL------- 121
Query: 170 LPPEKEKGSHFDSNCITPGTPFMACLSACLHYYIHDRLNNDPGWKGIKVILSDANVP 226
+ FDSNCITPGT FM L L ++ +++ DP W+ VILS P
Sbjct: 122 -----REHERFDSNCITPGTEFMVRLQEGLRAFLKTKISTDPLWQRCTVILSGQEAP 173
>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 = 49.7 bits (118), Expect = 3e-07
Identities = 40/240 (16%), Positives = 74/240 (30%), Gaps = 72/240 (30%)
Query: 17 QDSKPYSFASLVSLPQEVNGQKIPFDSSKPNPNGM------------EFDNLYLDMNGII 64
D +P + A LV G+ + + SS P+ + EF+N YL+ N I
Sbjct: 50 ADDEPTTPAELV-------GKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGND-I 101
Query: 65 H--PCTHPEDKPAPKDEDEMMVAIF----ECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQ 118
H ++ + + ++ + R F L +G A
Sbjct: 102 HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNA------- 154
Query: 119 PLTVYSVLYDRGN-----------YSTWQLMRSRRFRASKETAEKIAEVARIREKLLADG 167
+ ++ +GN Y T+ ++ + S ET ++ EK+ G
Sbjct: 155 --QLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQG 212
Query: 168 C-----ILPPEKEKGSHFDSNCITPGTPFMA---------CLSACLHYYIHDR-LNNDPG 212
+ P TP ++ + HY + + L PG
Sbjct: 213 LNILEWLENPSN-----------TPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPG 261
Score = 42.3 bits (99), Expect = 8e-05
Identities = 37/234 (15%), Positives = 69/234 (29%), Gaps = 79/234 (33%)
Query: 50 GMEF--------------DNLYLDMNG--IIH-----PCT---HPEDKPAPKDEDEMMVA 85
GM+ DN + D G I+ P H + + +
Sbjct: 1632 GMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAM 1691
Query: 86 IFE-CID------RLFRIVRPRKLLYMAIDGVAPRAKMN-----QP--LTVYSVLYDRGN 131
IFE +D ++F+ + Y + ++ QP +
Sbjct: 1692 IFETIVDGKLKTEKIFKEINEHSTSYT-FRS--EKGLLSATQFTQPALTLM--------E 1740
Query: 132 YSTWQLMRSRRFRASK---------E-TA----------EKIAEVARIREKLLADGCILP 171
+ ++ ++S+ + E A E + EV R +
Sbjct: 1741 KAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQV---AV 1797
Query: 172 PEKEKG-SHFDSNCITPGTPFMACLSACLHYYIHDRLNNDPGWKGIKVILSDAN 224
P E G S++ I PG + L Y + +R+ GW ++ N
Sbjct: 1798 PRDELGRSNYGMIAINPGRVAASFSQEALQYVV-ERVGKRTGW-----LVEIVN 1845
Score = 31.2 bits (70), Expect = 0.31
Identities = 39/222 (17%), Positives = 63/222 (28%), Gaps = 91/222 (40%)
Query: 25 ASLVSL---------PQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPA 75
SL L P ++ +IPF K +F N +L P +
Sbjct: 384 QSLYGLNLTLRKAKAPSGLDQSRIPFSERKL-----KFSNRFL-------PVA------S 425
Query: 76 PKDEDEMMVAIF------ECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQPLTVYSVLYDR 129
P F D + + + + + A D P VY
Sbjct: 426 P----------FHSHLLVPASDLINKDLVKNNVSFNAKDIQIP---------VYDT---- 462
Query: 130 GNYSTWQLMRSRRFRASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDSNCIT--- 186
+R S +E+I + LP + E + F + I
Sbjct: 463 ---FDGSDLRV----LSGSISERIVDCI----------IRLPVKWETTTQFKATHILDFG 505
Query: 187 PG-TPFMACLSACLHYYIHDRLNNDPGWKGIKVILS---DAN 224
PG + L+ N G G++VI++ D N
Sbjct: 506 PGGASGLGVLTH----------RNKDG-TGVRVIVAGTLDIN 536
>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 = 34.1 bits (77), Expect = 0.035
Identities = 17/117 (14%), Positives = 36/117 (30%), Gaps = 21/117 (17%)
Query: 27 LVSLPQEVNGQKIPFDS--SKPNPNGMEFDNLYLDMN-GIIHPCTHPEDKPAPKDEDEMM 83
++ V+G F + SK +F L +N + E + P M
Sbjct: 54 IIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQR-QPSMMTRMY 112
Query: 84 VAIFECIDRLFRIVR-------PRKLLYMAIDGVAPRAKMNQPLTVY-------SVL 126
+ E DRL+ + R Y+ + + + + + + +
Sbjct: 113 I---EQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWV 166
Score = 29.4 bits (65), Expect = 1.2
Identities = 25/211 (11%), Positives = 56/211 (26%), Gaps = 65/211 (30%)
Query: 55 NLYLDMNGIIHP-CTHPEDKPAPKDEDEMMVAIFECIDRLFRI-VRPRKLLYM------- 105
L ++ H + + + RL + LL +
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQ------AELRRLLKSKPYENCLLVLLNVQNAK 257
Query: 106 AIDGVAPRAKMNQPL--TVYSVLYDRGNYSTWQLMRSRRFRAS---KETAEKIAEVARIR 160
A + K+ L T + + D + +T + + E + + R
Sbjct: 258 AWNAFNLSCKI---LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314
Query: 161 EKLLADGCILPPEKEKGSHFDSNCITPGTPF-MACLSACLH----------YYIHDRLNN 209
+ D LP E + P ++ ++ + + D+L
Sbjct: 315 PQ---D---LPREVLTTN-----------PRRLSIIAESIRDGLATWDNWKHVNCDKLTT 357
Query: 210 ---------DPG-----WKGIKVILSDANVP 226
+P + + V A++P
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPPSAHIP 388
>1hw1_A FADR, fatty acid metabolism regulator protein; helix-turn-helix,
helix bundle, transcription; 1.50A {Escherichia coli}
SCOP: a.4.5.6 a.78.1.1 PDB: 1hw2_A 1e2x_A 1h9g_A* 1h9t_A
Length = 239
Score = 28.1 bits (63), Expect = 1.8
Identities = 11/38 (28%), Positives = 14/38 (36%), Gaps = 2/38 (5%)
Query: 138 MRSRRFRASKETAEKIAEVARIREKLLADGCILPPEKE 175
M + + E I E I G ILP E+E
Sbjct: 1 MVIKAQSPAGFAEEYIIE--SIWNNRFPPGTILPAERE 36
>3k40_A Aromatic-L-amino-acid decarboxylase; PLP dependent protein, alpha
beta protein, alternative splicing, catecholamine
biosynthesis, lyase; HET: LLP; 1.75A {Drosophila
melanogaster}
Length = 475
Score = 27.4 bits (61), Expect = 3.8
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 131 NYSTWQLMRSRRFRASK 147
+Y WQ+ RRFRA K
Sbjct: 342 DYRHWQIPLGRRFRALK 358
>4e1o_A HDC, histidine decarboxylase; lyase; HET: PLP PVH; 1.80A {Homo
sapiens}
Length = 481
Score = 27.4 bits (61), Expect = 4.4
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 131 NYSTWQLMRSRRFRASK 147
++ WQ+ SRRFR+ K
Sbjct: 349 DFMHWQIPLSRRFRSVK 365
>1js3_A DDC;, DOPA decarboxylase; carbidopa, parkinson'S disease, vitamin;
HET: PLP 142; 2.25A {Sus scrofa} SCOP: c.67.1.6 PDB:
1js6_A* 3rch_A* 3rbl_A 3rbf_A*
Length = 486
Score = 27.0 bits (60), Expect = 5.1
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 131 NYSTWQLMRSRRFRASK 147
+Y WQL RRFR+ K
Sbjct: 345 DYRHWQLPLGRRFRSLK 361
>1epw_A Bontoxilysin B, botulinum neurotoxin type B; zinc, metalloprotease,
transmembrane, hydrolase; 1.90A {Clostridium botulinum}
SCOP: b.29.1.6 b.42.4.2 d.92.1.7 h.4.2.1 PDB: 1f31_A*
1g9a_A* 1g9b_A* 1g9c_A* 1g9d_A* 1i1e_A* 1s0b_A 1s0c_A
1s0d_A 1s0e_A 1s0f_A 1s0g_A 2np0_A 3zuq_A 2etf_A 2xhl_A
1z0h_A 2nm1_A 3g94_A 1f82_A ...
Length = 1290
Score = 27.1 bits (59), Expect = 6.5
Identities = 9/48 (18%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 35 NGQKIPFDS-SKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDE 81
++I +++ S N + L LD + I E+ + D +
Sbjct: 468 KNERIEYNTQSNYIENDFPINELILDTDLISKIELPSENTESLTDFNV 515
>1e8c_A UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diaminopimelate
ligase; peptidoglycan biosynthesis; HET: KCX UAG API;
2.00A {Escherichia coli} SCOP: c.98.1.1 c.59.1.1
c.72.2.1
Length = 498
Score = 26.4 bits (59), Expect = 9.3
Identities = 3/11 (27%), Positives = 6/11 (54%)
Query: 32 QEVNGQKIPFD 42
Q V Q++ +
Sbjct: 471 QIVGNQRLDYS 481
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
0.318 0.135 0.414
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,525,289
Number of extensions: 209834
Number of successful extensions: 453
Number of sequences better than 10.0: 1
Number of HSP's gapped: 445
Number of HSP's successfully gapped: 19
Length of query: 226
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 136
Effective length of database: 4,188,903
Effective search space: 569690808
Effective search space used: 569690808
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 (21.7 bits)
S2: 55 (25.1 bits)