RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4846
(279 letters)
>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA
degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A
{Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5
b.40.4.5 b.40.4.16
Length = 760
Score = 223 bits (570), Expect = 7e-68
Identities = 89/275 (32%), Positives = 119/275 (43%), Gaps = 55/275 (20%)
Query: 4 AMLRRHPVPPPANFEPLLHAAR-RQGFELSVGTGKELATSLDAA---------------- 46
AMLRRH PP NFE L R+ +S+ + K LA SLD
Sbjct: 509 AMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMS 568
Query: 47 ------AVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYP 100
A YF SG DF HYGLA IYTHFTSPIRRY D++ HR LA IG +
Sbjct: 569 TRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSL 628
Query: 101 SLLDKKASTALCYNLNYRNRQAQYAGRASVALHTHLFFRSRVQDEDGYVLYVRKNALQIL 160
+ DK +C N+N ++R AQ+AGRAS+ +
Sbjct: 629 THRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVM---------------------- 666
Query: 161 IPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRC-DSPSVSWTYNEK------EQS 213
++ E GYV+ V N + +L+PK+G+EG + L S ++E +
Sbjct: 667 --RNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPT 724
Query: 214 QSCGSVVFHSFDPVTVQL-SLDRSNVQHEKLVLRL 247
S + FD V VQ+ S+ K L L
Sbjct: 725 NSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLL 759
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding,
exonucle binding, mitochondrion, rRNA processing; 3.00A
{Saccharomyces cerevisiae}
Length = 977
Score = 222 bits (568), Expect = 1e-66
Identities = 89/275 (32%), Positives = 119/275 (43%), Gaps = 55/275 (20%)
Query: 4 AMLRRHPVPPPANFEPLLHAAR-RQGFELSVGTGKELATSLDAA---------------- 46
AMLRRH PP NFE L R+ +S+ + K LA SLD
Sbjct: 726 AMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMS 785
Query: 47 ------AVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYP 100
A YF SG DF HYGLA IYTHFTSPIRRY D++ HR LA IG +
Sbjct: 786 TRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSL 845
Query: 101 SLLDKKASTALCYNLNYRNRQAQYAGRASVALHTHLFFRSRVQDEDGYVLYVRKNALQIL 160
+ DK +C N+N ++R AQ+AGRAS+ +
Sbjct: 846 THRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVM---------------------- 883
Query: 161 IPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRC-DSPSVSWTYNEK------EQS 213
++ E GYV+ V N + +L+PK+G+EG + L S ++E +
Sbjct: 884 --RNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPT 941
Query: 214 QSCGSVVFHSFDPVTVQL-SLDRSNVQHEKLVLRL 247
S + FD V VQ+ S+ K L L
Sbjct: 942 NSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLL 976
>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2,
structure initiative, northeast structural genomics
consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP:
b.40.4.5 b.40.4.16 PDB: 2r7f_A
Length = 469
Score = 100 bits (252), Expect = 2e-24
Identities = 36/160 (22%), Positives = 55/160 (34%), Gaps = 30/160 (18%)
Query: 7 RRHPVPPP---ANFEPLLHAARRQGFELSVGTGKELATSLDAAAVYFSSGMLQQSDFHHY 63
P + P + A R+ +L A + Q S H+
Sbjct: 291 ATQDYPTREVAGDTLPAMWARRK---------------TL-ARTRF------QPSPGPHH 328
Query: 64 GLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNLNYRNRQAQ 123
G+ +Y TSP+RRY D++VH+ L A + K A +
Sbjct: 329 GMGLDLYAQATSPMRRYLDLVVHQQLRAFLAGRDPL----SSKVMAAHIAESQMNADATR 384
Query: 124 YAGRASVALHTHLFFRSRVQDE-DGYVLYVRKNALQILIP 162
A R S HT F ++ + D V+ R +LIP
Sbjct: 385 QAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIP 424
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR
family, hydrolase; 2.35A {Escherichia coli} SCOP:
b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A
Length = 644
Score = 83.0 bits (206), Expect = 4e-18
Identities = 37/202 (18%), Positives = 63/202 (31%), Gaps = 33/202 (16%)
Query: 7 RRHPVPPPANFEPLLHAARRQGFELSVG---TGKELATSLDAAA----VYFSSGML---Q 56
H PAN + L + G + T + S +
Sbjct: 414 NVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQS 473
Query: 57 QSDFH-----HYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTAL 111
++ H+GL Y +TSPIR+Y D+I HRLL A I + + +
Sbjct: 474 FAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGET------ATRPQDEI 527
Query: 112 CYNLNYRNRQAQYAGRASVALHTHLFFRSRVQDE---DGYV-------LYVR--KNALQI 159
+ R R + A R F + + + + + VR N
Sbjct: 528 TVQMAERRRLNRMAERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIA 587
Query: 160 LIPKSRVQDEDGYVLYVRKNAL 181
IP + ++ ++N
Sbjct: 588 FIPAPFLHAVRDELVCSQENGT 609
>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 = 55.8 bits (134), Expect = 6e-09
Identities = 56/315 (17%), Positives = 94/315 (29%), Gaps = 116/315 (36%)
Query: 8 RHPVPPPANFEPLLHAARR-----------QG-----F-EL-----------------SV 33
+ P +N L A QG F EL S
Sbjct: 134 KRPFDKKSN-SALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSA 192
Query: 34 GTGKELATSLDAAAVYFSSGM-----LQQSD----------------------FHHY--- 63
T EL + A F+ G+ L+ HY
Sbjct: 193 ETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVT 252
Query: 64 ----GLATP--IYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLD--KKASTALCYNL 115
G TP + ++ ++ A I ++ S +KA T L + +
Sbjct: 253 AKLLGF-TPGELRSYLKGATGHSQGLVT----AVAIAETDSWESFFVSVRKAITVLFF-I 306
Query: 116 NYRNRQAQYAGRASVALHTHLFFRSRVQD--EDG-----YVLYVR---KNALQILIPKSR 165
R +A S+ S ++D E+ +L + + +Q + K+
Sbjct: 307 GVRCYEA--YPNTSLPP-------SILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTN 357
Query: 166 VQDEDGYVLYV-RKNALQILI----PK--YGLEGTLFLRCDSPSVSWTYNEKEQSQSCGS 218
G + + N + L+ P+ YGL TL + +PS +QS+ S
Sbjct: 358 SHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTL-RKAKAPS------GLDQSRIPFS 410
Query: 219 ---VVF-HSFDPVTV 229
+ F + F PV
Sbjct: 411 ERKLKFSNRFLPVAS 425
Score = 52.7 bits (126), Expect = 5e-08
Identities = 46/284 (16%), Positives = 90/284 (31%), Gaps = 97/284 (34%)
Query: 27 QGFELSVGTGKELATSLDAAAVYFSSGMLQQSDFH---HYGLA---------TPIYTHFT 74
QG + G G +L + AA + ++D H YG + + HF
Sbjct: 1624 QGSQ-EQGMGMDLYKTSKAAQDVW-----NRADNHFKDTYGFSILDIVINNPVNLTIHFG 1677
Query: 75 SP----IR-RYADIIVHRLLAACIGADATYPSLLDKKASTALCYN-----LNYRNRQAQY 124
IR Y+ +I ++ + + + + + ST+ + L+ Q+
Sbjct: 1678 GEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEH--STSYTFRSEKGLLS----ATQF 1731
Query: 125 AGRA----SVALHTHLFFRSR-VQDEDGYV----------LYVRKNALQILIPKSRVQDE 169
A A L +S+ + D L + + I E
Sbjct: 1732 TQPALTLMEKAAFEDL--KSKGLIPADATFAGHSLGEYAALASLADVMSI---------E 1780
Query: 170 DG-YVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVT 228
V++ R +Q+ +P+ E +S ++ + +P
Sbjct: 1781 SLVEVVFYRGMTMQVAVPR----------------------DELGRSNYGMI--AINPGR 1816
Query: 229 VQLSLDRSNVQHEKLVLR-------LVRPV---IEGFSVSSAGE 262
V S + + + +V R LV V +E +AG+
Sbjct: 1817 VAASFSQEAL--QYVVERVGKRTGWLVEIVNYNVENQQYVAAGD 1858
Score = 42.7 bits (100), Expect = 1e-04
Identities = 40/228 (17%), Positives = 73/228 (32%), Gaps = 66/228 (28%)
Query: 12 PPPANF----EP-----LLHAARRQGF---ELSVGTGKELATSLDAAAVYFSSGMLQQSD 59
P F EP L+ + G+ + + L+ F + L+ +D
Sbjct: 43 EPTEGFAADDEPTTPAELV--GKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGND 100
Query: 60 FHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNLNYRN 119
H LA + + + + ++I + + A I A + KK+++AL
Sbjct: 101 IH--ALAAKLLQENDTTLVKTKELIKN-YITARIMAKRPFD----KKSNSAL-------F 146
Query: 120 RQAQYAGRASVAL------HTHLFFRSRVQDE-----DGYVLYVR---KNALQILIPKSR 165
R G A + +T +F +E Y + V K + + L R
Sbjct: 147 RAVG-EGNAQLVAIFGGQGNTDDYF-----EELRDLYQTYHVLVGDLIKFSAETLSELIR 200
Query: 166 VQDEDGYVLYVRKNALQIL--------IPKYGLEGTLFLRCDSPSVSW 205
D ++ + L IL P +L S +S
Sbjct: 201 -TTLDAEKVFTQ--GLNILEWLENPSNTP-----DKDYL--LSIPISC 238
Score = 38.1 bits (88), Expect = 0.003
Identities = 31/166 (18%), Positives = 55/166 (33%), Gaps = 32/166 (19%)
Query: 3 NAMLRRHPVPPPANFEPLLHAARRQGFE---LSVGTGKELA---TSL--DAAAVYFSSGM 54
N LR+ P + + + R+ F L V + + L A+ + +
Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVA-----SPFHSHLLVPASDLINKDLV 444
Query: 55 LQQSDFHHYGLATPIYTHFT-SPIRRYADIIVHRLLAACIGADATY-PSLLDKKASTALC 112
F+ + P+Y F S +R + I R + CI + KA+ L
Sbjct: 445 KNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISER-IVDCIIRLPVKWETTTQFKATHILD 503
Query: 113 Y---------NLNYRNRQAQYAGR-ASVALHTHLFFRSRVQDEDGY 148
+ L +RN+ G V + L D+ G+
Sbjct: 504 FGPGGASGLGVLTHRNKD----GTGVRVIVAGTL--DINPDDDYGF 543
>3d12_B Ephrin-B3; beta propeller, protein-receptor complex, envelope
protein, glycoprotein, hemagglutinin, hydrolase,
membrane, signal-AN transmembrane; HET: NAG BMA MAN BGC
LXZ NGA GL0 GLC LXB NGZ GXL; 3.00A {Mus musculus}
Length = 141
Score = 28.8 bits (64), Expect = 0.93
Identities = 24/84 (28%), Positives = 31/84 (36%), Gaps = 10/84 (11%)
Query: 140 SRVQDEDGYVLYVRKNA-LQILIPKSRVQDEDG------YVLY-VRKNALQILIPKYGLE 191
R Q E GYVLY + L +L P++R Y LY V +
Sbjct: 12 KRFQAEGGYVLYPQIGDRLDLLCPRARPPGPHSSPSYEFYKLYLVEGAQGRRCEAP--PA 69
Query: 192 GTLFLRCDSPSVSWTYNEKEQSQS 215
L L CD P + + K Q S
Sbjct: 70 PNLLLTCDRPDLDLRFTIKFQEYS 93
>2vsm_B Ephrin-B2; developmental protein, henipavirus, neurogenesis,
glycoprotein, paramyxovirus, envelope protein, cell
surface receptor, hendra, virion; HET: NAG; 1.80A {Homo
sapiens} PDB: 2wo2_B* 2i85_A 3gxu_B 2vsk_B 2hle_B 1kgy_E
Length = 140
Score = 28.4 bits (63), Expect = 1.5
Identities = 19/87 (21%), Positives = 28/87 (32%), Gaps = 19/87 (21%)
Query: 140 SRVQDEDGYVLYVRKNA-LQILIPKSRVQDEDG---YVLYVRKNALQILIPKYGLE---- 191
S+ G VLY + L I+ PK + Y +Y ++ K +
Sbjct: 13 SKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVY--------MVDKDQADRCTI 64
Query: 192 ---GTLFLRCDSPSVSWTYNEKEQSQS 215
T L C P + K Q S
Sbjct: 65 KKENTPLLNCAKPDQDIKFTIKFQEFS 91
>1iko_P Ephrin-B2; greek KEY, glycosylation, signaling protein; HET: NAG
MAN; 1.92A {Mus musculus} SCOP: b.6.1.5
Length = 178
Score = 28.6 bits (63), Expect = 1.8
Identities = 22/81 (27%), Positives = 29/81 (35%), Gaps = 7/81 (8%)
Query: 140 SRVQDEDGYVLYVRKNA-LQILIPKSRVQDEDG---YVLY-VRKNALQILIPKYGLEGTL 194
S+ G VLY + L I+ PK + Y +Y V K+ K E T
Sbjct: 14 SKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQADRCTIK--KENTP 71
Query: 195 FLRCDSPSVSWTYNEKEQSQS 215
L C P + K Q S
Sbjct: 72 LLNCARPDQDVKFTIKFQEFS 92
>2hqb_A Transcriptional activator of COMK gene; berkeley structure
genomics center target 1957B, structural genomics, PSI;
2.70A {Bacillus halodurans}
Length = 296
Score = 27.6 bits (62), Expect = 4.2
Identities = 6/38 (15%), Positives = 7/38 (18%)
Query: 10 PVPPPANFEPLLHAARRQGFELSVGTGKELATSLDAAA 47
V + G L G G A
Sbjct: 45 GVNSEQKAHRRIKELVDGGVNLIFGHGHAFAEYFSTIH 82
>3ebw_A PER A 4 allergen; beta barrel, cockroach; HET: PE4; 2.80A
{Periplaneta americana}
Length = 163
Score = 27.3 bits (60), Expect = 4.6
Identities = 2/27 (7%), Positives = 3/27 (11%)
Query: 6 LRRHPVPPPANFEPLLHAARRQGFELS 32
A + L
Sbjct: 124 ASHETSFDDATKAKVNEVLAPYNLSLD 150
>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD,
transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP:
c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*
Length = 252
Score = 26.7 bits (59), Expect = 7.9
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 68 PIYTHFTSPIRRYADIIVHR 87
P + F P ++YAD+I+ R
Sbjct: 193 PAFEEFCLPTKKYADVIIPR 212
>2p8r_A PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, translation; 2.10A
{Caenorhabditis elegans} PDB: 2p87_A
Length = 273
Score = 26.5 bits (58), Expect = 9.5
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 128 ASVALHT---HLFFRSRVQDEDGYVLYVRKNALQILIPKSRVQDEDGYVLY 175
+S LH H++ S + GY + KN L+ I S ++ + +Y
Sbjct: 16 SSTNLHLRTQHIYVNSDDVKDTGYTYILPKNILKKFITISDLRTQIAGFMY 66
>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding,
nucleoside kinase, nucleotide-binding; 2.50A {Homo
sapiens} PDB: 2uvq_A*
Length = 245
Score = 26.3 bits (58), Expect = 9.8
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 68 PIYTHFTSPIRRYADIIVHR 87
P + F P ++YAD+I+ R
Sbjct: 195 PAFEEFCLPTKKYADVIIPR 214
>2wo3_B Ephrin-A2; transferase-signaling protein complex, EFN, EPHA4, KINA
ephrin, complex, membrane, cell surface receptor,
tyrosine- kinase, glycoprotein; HET: NAG; 2.35A {Homo
sapiens}
Length = 157
Score = 26.2 bits (57), Expect = 9.8
Identities = 22/100 (22%), Positives = 26/100 (26%), Gaps = 16/100 (16%)
Query: 136 LFFRSRVQDEDGYVLYVRKNA-LQILIPK---SRVQDEDG--YVLY-VRKNALQILIPKY 188
F D GY + V N L I P E YVLY V +
Sbjct: 18 RFHAGAGDDGGGYTVEVSINDYLDIYCPHYGAPLPPAERMEHYVLYMVNGEGHASCDHR- 76
Query: 189 GLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVT 228
G C+ P S F F P +
Sbjct: 77 -QRGFKRWECNRP-------AAPGGPLKFSEKFQLFTPFS 108
>3alz_B CDW150; viral protein-receptor complex, six-bladed beta-propeller
FO immunoglobulin fold, beta-sandwich, viral
protein-membrane complex; HET: NAG; 4.51A {Saguinus
oedipus}
Length = 149
Score = 26.2 bits (57), Expect = 9.9
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 145 EDGYVLYVRKNALQILIPKSRVQDEDGYVLYVRKN 179
+D Y Y+ +L I +S +DE Y + + KN
Sbjct: 93 KDRYRFYLENLSLAIR--ESTKKDEGWYFMTLEKN 125
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 0.135 0.398
Gapped
Lambda K H
0.267 0.0564 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,273,883
Number of extensions: 250746
Number of successful extensions: 737
Number of sequences better than 10.0: 1
Number of HSP's gapped: 722
Number of HSP's successfully gapped: 28
Length of query: 279
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 187
Effective length of database: 4,133,061
Effective search space: 772882407
Effective search space used: 772882407
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: 57 (26.1 bits)