RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3755
(692 letters)
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 1106 bits (2864), Expect = 0.0
Identities = 378/690 (54%), Positives = 528/690 (76%), Gaps = 1/690 (0%)
Query: 1 MFRFILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 60
+ I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +FFPLT
Sbjct: 7 LLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 66
Query: 61 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
V+Y E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++ V+SV
Sbjct: 67 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 126
Query: 121 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 180
NPQ++PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LDL+VA
Sbjct: 127 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 186
Query: 181 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 240
GTE A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P ++
Sbjct: 187 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 246
Query: 241 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 300
L +++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++ IL+
Sbjct: 247 ALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLA-EDETLDENELGEILHA 305
Query: 301 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 360
+E ++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV ATLGT+
Sbjct: 306 IEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTA 365
Query: 361 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 420
RD Q +D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+P+ +
Sbjct: 366 RDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMD 425
Query: 421 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 480
KF Y++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+ V+LS
Sbjct: 426 KFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLS 485
Query: 481 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKT 540
DILGDED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL M+
Sbjct: 486 DILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQ 545
Query: 541 EVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIAS 600
+ + ++S+FAPR+ TIKI+P KI+DVIGKGGS IR LTEETGT I+I D+G + IA+
Sbjct: 546 AINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDDGTVKIAA 605
Query: 601 FNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV 660
+ + A RRIE++T +++G+VYTG V R+ DFGA + I GK+GL+HISQI+ KRV
Sbjct: 606 TDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRV 665
Query: 661 NIITDFLKENQKVRVKVLGIDDRGRIKLSM 690
+TD+L+ Q+V VKVL +D +GRI+LS+
Sbjct: 666 EKVTDYLQMGQEVPVKVLEVDRQGRIRLSI 695
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 1103 bits (2856), Expect = 0.0
Identities = 344/692 (49%), Positives = 484/692 (69%), Gaps = 3/692 (0%)
Query: 1 MFRFILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 60
MF K+ ++G + +E G IARQA +VL ++ +TV+LAT V K +FFPLT
Sbjct: 15 MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLT 74
Query: 61 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
V+Y EK +AAG+IPG FFKREG+PSE+ET++SRLIDRPIRPLF +G+ NE+Q+VV VL
Sbjct: 75 VNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQH 134
Query: 121 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 180
+ + DPDI ++ S AL +S PF+GP+G A+VG++DG Y+LNPT +++K+S +DL+VA
Sbjct: 135 DLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVA 194
Query: 181 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 240
GT A++ VESE ++L E+I+L + F H++M+ I+AI +L ++ ++ ++P D
Sbjct: 195 GTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTD- 253
Query: 241 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDN--ENLTIDINDINCIL 298
+ +K+ ++ I AY+I+ KQ R K ++L + D + I
Sbjct: 254 AIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIF 313
Query: 299 YDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLG 358
+LE+ ++R+ ILD GLRID R V +RPI GILPRTHGS+LFTRG+TQA+VVATLG
Sbjct: 314 KELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLG 373
Query: 359 TSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPN 418
T DEQ IDAL G + +SF+LHYN PP++ G+ GR+G P RREIGHG+LA RAL P+LP
Sbjct: 374 TGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPT 433
Query: 419 NNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVI 478
F Y+IRLVSEITESNGSSSMA+VCG LA++DAGVP+ V+GIAMGLI + + +
Sbjct: 434 KEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAV 493
Query: 479 LSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 538
LSDILGDED GDMDFKVAGT G+T+LQMDIKI GIT I++ AL +AK+G ++IL +M
Sbjct: 494 LSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEM 553
Query: 539 KTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITI 598
+ + ++ FAP++ TI I KIR+VIG GG IR + TG ++DIND+G++ +
Sbjct: 554 NKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKV 613
Query: 599 ASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK 658
++ + + A I+ +T+ ++GK+Y G V+++ DFGA + KDGL+H+SQIS++
Sbjct: 614 SASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNE 673
Query: 659 RVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 690
RV +D LKE Q V+VK+LG DDRG+ KLSM
Sbjct: 674 RVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSM 705
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide
transferase, ATP-GTP diphosphotransferase RNA
processing, RNA degradation; 2.5A {Streptomyces
antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4
d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
Length = 757
Score = 1045 bits (2705), Expect = 0.0
Identities = 268/719 (37%), Positives = 404/719 (56%), Gaps = 32/719 (4%)
Query: 1 MFRFILKSFKYGSYKISIEIGEIARQATSSVLVSI-EDTVILATVVSCKDPTSTYNFFPL 59
++ + +G+ I E G +ARQA S + + +DT++L+ + K+P +FFPL
Sbjct: 24 YAEAVIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPL 83
Query: 60 TVDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLS 119
TVD E+ YAAG+IPGSFF+REG+PSE + RLIDRP+RP F +G NEIQ+V +++
Sbjct: 84 TVDVEERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMA 143
Query: 120 VNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLV 179
+NP D+ +I S + ++ LPF GP+G +V I G+++ PT +L+ + D++V
Sbjct: 144 LNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVV 203
Query: 180 AGT-----EKAIITVESESKQL------------PEDIILNAIIFGHEKMKIAINAINEL 222
AG + AI+ VE+E+ + E+++ + +K+ A +L
Sbjct: 204 AGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADL 263
Query: 223 VQNVGQKKVNWDPIVK-DKTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSL 281
+ + + ++ + ++ A I KQ R+ + L
Sbjct: 264 AAKAAKPTGEFPVFLDYQDDVLEALSAAVRPELSAALTIAGKQDREAELDRVKALAAEKL 323
Query: 282 IDNENLTIDINDINCILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGS 341
+ +I+ L ++R++++ + RID RGV DIR ++ +PR HGS
Sbjct: 324 L--PEFEGREKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGS 381
Query: 342 SLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRRE 401
+LF RG+TQ L V TL R EQ++D L +M +YN PP++ G+ GR+G PKRRE
Sbjct: 382 ALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRRE 441
Query: 402 IGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEH 461
IGHG LA+RA++PVLP +F Y+IR VSE SNGS+SM SVC ++LL+AGVP+
Sbjct: 442 IGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAP 501
Query: 462 VAGIAMGLIKD----GEKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITY 517
VAGIAMGLI V L+DILG ED GDMDFKVAGT +TALQ+D K+ GI
Sbjct: 502 VAGIAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPA 561
Query: 518 DIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTI 577
++ AL +A+ +IL+ M + +E+S APR+IT+KI KI +VIG I
Sbjct: 562 SVLAAALKQARDARLHILDVMMEAIDT-PDEMSPNAPRIITVKIPVDKIGEVIGPKRQMI 620
Query: 578 RTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTES--VQIGKVYTGIVLRLFD 635
+ E+TG +I I D+G I I + + + + A+ I + ++G+ G V++
Sbjct: 621 NQIQEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTT 680
Query: 636 FGAIIRILSGKDGLLHISQIS----SKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 690
FGA + +L GKDGLLHISQI KRV + D L QKV+V++ ID RG++ L
Sbjct: 681 FGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSLIP 739
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 945 bits (2446), Expect = 0.0
Identities = 228/626 (36%), Positives = 349/626 (55%), Gaps = 19/626 (3%)
Query: 7 KSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEK 66
+ G+ K+ I G++AR A S +V DT ++ T VS P S F PL VDY +K
Sbjct: 8 VAVDLGNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKP-SPSQFMPLVVDYRQK 66
Query: 67 AYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDP 126
A AAGRIP ++ +RE S++E + SR+IDR IRPLFP GY + Q++ +L+V+ +P
Sbjct: 67 AAAAGRIPTNYLRREVGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNEP 126
Query: 127 DIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEK-A 185
D+ +I G S ALS+S++P+ GP+G ++G IDG+Y++NPT +++ S L+L+VAG K
Sbjct: 127 DVLAINGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKSQ 186
Query: 186 IITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNW-DPIVKDKTLIS 244
I+ +E+ ++ + + +AI G + + I I +LV+ G K ++
Sbjct: 187 IVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVK 246
Query: 245 KIINISEHKIRKAYQI--KNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDLE 302
++ ++ + +K RD I D L + + D +I +
Sbjct: 247 YTHKLAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKE-KFPEADPYEIIESFNVVA 305
Query: 303 SKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGT--- 359
++ R +L++ R D R + +R +S + HGS+LF RG TQ L T +
Sbjct: 306 KEVFRSIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLES 365
Query: 360 -SRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPN 418
+ +Q I A+ G +FMLHY PP+AT +IG++ RRE+GHG LA++AL PV+P
Sbjct: 366 GIKSDQVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIP- 424
Query: 419 NNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDG----- 473
F ++IR+ SE+ ESNGSSSMAS CGG LAL+D+GVPIS VAG+A+GL+
Sbjct: 425 -RDFPFTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKG 483
Query: 474 --EKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGL 531
E +L+DILG ED GDMDFK+AGT GITALQ DIK+ GI I+ A+ +A
Sbjct: 484 EIEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAK 543
Query: 532 SYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN 591
IL+ M + K + + P + T+++ SK +G GG ++ L ETG I
Sbjct: 544 KEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV 603
Query: 592 DEGIITIASFNSVSGQEAKRRIEKLT 617
DE ++ + + EA+ I ++
Sbjct: 604 DEETFSVFAPTPSAMHEARDFITEIC 629
>3gme_A Polyribonucleotide nucleotidyltransferase; protein-RNA complex,
cytoplasm, nucleotidyltransferase, RNA- binding,
transferase, hydrolase; 2.40A {Escherichia coli E24377A}
PDB: 3gll_A 3gcm_A 3h1c_A 3cdj_A
Length = 549
Score = 886 bits (2293), Expect = 0.0
Identities = 300/550 (54%), Positives = 420/550 (76%), Gaps = 1/550 (0%)
Query: 1 MFRFILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 60
M I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +FFPLT
Sbjct: 1 MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 60
Query: 61 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
V+Y E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++ V+SV
Sbjct: 61 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 120
Query: 121 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 180
NPQ++PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LDL+VA
Sbjct: 121 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 180
Query: 181 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 240
GTE A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P ++
Sbjct: 181 GTEAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 240
Query: 241 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 300
L +++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++ IL+
Sbjct: 241 ALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLA-EDETLDENELGEILHA 299
Query: 301 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 360
+E ++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV ATLGT+
Sbjct: 300 IEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTA 359
Query: 361 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 420
RD Q +D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+P+ +
Sbjct: 360 RDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMD 419
Query: 421 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 480
KF Y++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+ V+LS
Sbjct: 420 KFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLS 479
Query: 481 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKT 540
DILGDED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL M+
Sbjct: 480 DILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQ 539
Query: 541 EVPKCKNELS 550
+ + ++S
Sbjct: 540 AINAPRGDIS 549
>3m7n_D Probable exosome complex exonuclease 1; exosome, RNA, exonuclease,
hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus
fulgidus} PDB: 3m85_D 2ba0_F 2ba1_E
Length = 258
Score = 380 bits (978), Expect = e-128
Identities = 67/266 (25%), Positives = 115/266 (43%), Gaps = 16/266 (6%)
Query: 302 ESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSR 361
E ++++ GLR+D R +++RPI I +L R GS G + +
Sbjct: 3 EFNEKPEKLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGP--- 59
Query: 362 DEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNK 421
E + L YNM PF+ + R G P RR I +++K A V+
Sbjct: 60 REVHPEHLQDPSKAIIRYRYNMAPFSVEERKRPG-PDRRSIEISKVSKEAFEAVIMKELF 118
Query: 422 FNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSD 481
+I + E+ +++ S A + +AL+DAGVP+ + +A+G ++ D
Sbjct: 119 PRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADG----QLVLD 174
Query: 482 ILGDEDRCGDMDFKVA-----GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILE 536
+ +ED G+ D A G + I LQMD + +T D ++ A+ AKKG I E
Sbjct: 175 PMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGR---MTRDEVKQAIELAKKGALQIYE 231
Query: 537 KMKTEVPKCKNELSKFAPRLITIKID 562
+ + + E+ + + D
Sbjct: 232 MQREAILRRYIEVGEEMDEITEGGED 257
>2je6_B RRP41, exosome complex exonuclease 1; nuclease, hydrolase,
exonuclease, phosphorolytic, exoribonuclease, RNA
degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus}
SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_B* 2jeb_B* 2br2_B
2c37_B* 2c38_B* 2c39_B* 3l7z_B
Length = 250
Score = 370 bits (953), Expect = e-125
Identities = 67/258 (25%), Positives = 117/258 (45%), Gaps = 13/258 (5%)
Query: 298 LYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATL 357
+ ++ K ILD G R D R +++R I I G+L GS++F G+T+A+
Sbjct: 3 MREMLQVERPKLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYG 62
Query: 358 GTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLP 417
E L + Y+M PF+T + P RREI ++ + AL +
Sbjct: 63 P---KEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPA-PSRREIELSKVIREALESAVL 118
Query: 418 NNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVV 477
+I + +EI +++ S + S+ LAL DAG+P+ + +AG+A+G V
Sbjct: 119 VELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADG----V 174
Query: 478 ILSDILGDEDRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYIL 535
I+ D+ E G+ D +A ++N +T Q++ +T D + A A KG++ I
Sbjct: 175 IILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNG---SMTPDEFRQAFDLAVKGINIIY 231
Query: 536 EKMKTEVPKCKNELSKFA 553
+ + E +
Sbjct: 232 NLEREALKSKYVEFKEEG 249
>2po1_A Probable exosome complex exonuclease 1; RNAse PH,
hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus
abyssi} PDB: 2po0_A* 2pnz_A 2po2_A*
Length = 249
Score = 365 bits (938), Expect = e-123
Identities = 70/257 (27%), Positives = 114/257 (44%), Gaps = 13/257 (5%)
Query: 301 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 360
+E K I + G RID R ++RPI + G+L +GS+ G + +
Sbjct: 2 MEKPEGLKLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGP-- 59
Query: 361 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 420
E L + YNM PF+ + + G P RR I ++ K AL P L
Sbjct: 60 -RELHPKHLQRPDRAILRVRYNMAPFSVEERKKPG-PDRRSIEISKVIKGALEPALILEM 117
Query: 421 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 480
+I + E+ +++ + +A + LAL DAG+P+ + VA A G I+ I+
Sbjct: 118 FPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEG----EIVL 173
Query: 481 DILGDEDRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 538
D+ +ED G+ D VA N IT LQMD +T D A+ A KG + +K
Sbjct: 174 DLNKEEDNYGEADVPVAIMPLKNDITLLQMDGY---LTKDEFIEAVKLAIKGAKAVYQKQ 230
Query: 539 KTEVPKCKNELSKFAPR 555
+ + + ++++
Sbjct: 231 REALKEKYLKIAQEVEG 247
Score = 29.9 bits (68), Expect = 2.5
Identities = 42/209 (20%), Positives = 74/209 (35%), Gaps = 38/209 (18%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATV-------VSCKDPTST------YNFFPLTV 61
I +E+G + A S + I+A V YN P +V
Sbjct: 28 PIKMEVGVLKN-ANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFSV 86
Query: 62 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYL--NEIQIVVYVLS 119
+ K+ G P R IS++I + P I + + VL
Sbjct: 87 EER--------------KKPG-PDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQ 131
Query: 120 VNPQIDPDIASIIGVSTALSISELPFLGPL-GVAKVGYIDGKYILNPTTEQLKKSHLDLL 178
+ +A I S AL+ + +P + A G I+G+ +L+ E+ D+
Sbjct: 132 ADAGT--RVAGITAASLALADAGIPMRDLVAACA-AGKIEGEIVLDLNKEEDNYGEADVP 188
Query: 179 VA--GTEKAIITVESESKQLPEDIILNAI 205
VA + I ++ + L +D + A+
Sbjct: 189 VAIMPLKNDITLLQMDGY-LTKDEFIEAV 216
>2nn6_B Exosome complex exonuclease RRP41; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 249
Score = 342 bits (879), Expect = e-114
Identities = 53/246 (21%), Positives = 99/246 (40%), Gaps = 11/246 (4%)
Query: 307 RKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKI 366
+ + D+G R+D R ++R I R G+ + GS+ +G+T+AL V +
Sbjct: 8 LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRA 67
Query: 367 DALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSI 426
AL Y+ F+TG+ R R+ G ++ + I
Sbjct: 68 RALPDR--ALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 125
Query: 427 RLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDE 486
+ ++ +++G + A V LA+LDAG+P+ + V + G + L+D+ E
Sbjct: 126 DIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDG----TALADLSHVE 181
Query: 487 DRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPK 544
+ G +A I L+MD + + D ++ L A + + + V +
Sbjct: 182 EAAGGPQLALALLPASGQIALLEMDAR---LHEDHLERVLEAAAQAARDVHTLLDRVVRQ 238
Query: 545 CKNELS 550
E S
Sbjct: 239 HVREAS 244
Score = 29.9 bits (68), Expect = 2.1
Identities = 22/166 (13%), Positives = 53/166 (31%), Gaps = 25/166 (15%)
Query: 79 KREGKPSERETIISRLIDRPIRPLFPE----GYLNEIQIVVYVLSVNPQIDPDIASIIGV 134
KR + + + + +I I V VL + A +
Sbjct: 91 KRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRS--QIDIYVQVLQADGGTYA--ACVNAA 146
Query: 135 STALSISELPFLGPL-GVAKVGYIDGKYILNPTTEQLKKSHL---DLLVA--GTEKAIIT 188
+ A+ + +P + + G++DG + + + + L +A I
Sbjct: 147 TLAVLDAGIPMRDFVCACS-AGFVDGTALADLSHVE---EAAGGPQLALALLPASGQIAL 202
Query: 189 VESESK--QLPEDIILNAIIFG----HEKMKIAI-NAINELVQNVG 227
+E +++ + + +L A H + + + E +G
Sbjct: 203 LEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVREASILLG 248
>2wnr_B Probable exosome complex exonuclease 1; phosphate binding, 3'-5'
exoribonuclease, hydrolase; 2.65A {Methanothermobacter
thermautotrophicusorganism_taxid}
Length = 240
Score = 313 bits (804), Expect = e-103
Identities = 73/249 (29%), Positives = 106/249 (42%), Gaps = 15/249 (6%)
Query: 304 KIIRKQIL--DKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSR 361
II + L +R D R +++RP+ I GIL R GSS G + LV
Sbjct: 3 TIITQDQLKTSPSVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVY---GP 59
Query: 362 DEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNK 421
E +I L YNM PF+ + R G P RR + ++ AL P L
Sbjct: 60 REAQIRKLQRPDRAVIRCRYNMAPFSVEERKRPG-PDRRSVEISKITAEALRPALILEKF 118
Query: 422 FNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSD 481
I + E+ E+ G + A + +AL DAG+P+ + V A G + D ++ D
Sbjct: 119 PRSVIDVFIEVLEAEGGTRCAGITAASVALADAGIPMRDMVVACAAGKVGD----QVVLD 174
Query: 482 ILGDEDRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMK 539
+ +ED+ G D VA IT LQ D +T + + AL A +G I E K
Sbjct: 175 LSEEEDKEGQADVPVAILPRTREITLLQSDG---NLTPEEFERALDLAVEGCLRIHEVQK 231
Query: 540 TEVPKCKNE 548
+ K E
Sbjct: 232 EALRKRYGE 240
Score = 46.0 bits (110), Expect = 1e-05
Identities = 41/234 (17%), Positives = 77/234 (32%), Gaps = 59/234 (25%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDP-------------TSTYNFFPLTV 61
+ IE G I +A S + IL V ++ YN P
Sbjct: 28 PLKIEAG-ILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMAP--- 83
Query: 62 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVN 121
++ ++ P R IS++ +RP I V++
Sbjct: 84 ------FSVEE------RKRPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFI---- 127
Query: 122 PQIDPDI---------ASIIGVSTALSISELPFLGPL-GVAKVGYIDGKYILNPTTEQLK 171
++ A I S AL+ + +P + A G + + +L+ + E+ K
Sbjct: 128 -----EVLEAEGGTRCAGITAASVALADAGIPMRDMVVACA-AGKVGDQVVLDLSEEEDK 181
Query: 172 KSHLDLLVA--GTEKAIITVESESKQLPEDII-------LNAIIFGHEKMKIAI 216
+ D+ VA + I ++S+ L + + + HE K A+
Sbjct: 182 EGQADVPVAILPRTREITLLQSDGN-LTPEEFERALDLAVEGCLRIHEVQKEAL 234
>3hkm_A OS03G0854200 protein; RNAse PH domain, phosphorylase, hydrolase;
1.98A {Oryza sativa japonica group}
Length = 246
Score = 299 bits (767), Expect = 2e-97
Identities = 52/245 (21%), Positives = 91/245 (37%), Gaps = 29/245 (11%)
Query: 314 GLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEF 373
R D R N +RP S L R HGS+ + +GDT L A G +K GE
Sbjct: 3 ESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLA-AVYGPKPGTRK-----GEN 56
Query: 374 TDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEIT 433
+ + P G ++E + KR L + N + ++ ++
Sbjct: 57 PEKASIEVVWKPMT-------GQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVV 109
Query: 434 ESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCG-DM 492
++GS ++ C AL+ AG+P+ I G+++DGE VIL +E +
Sbjct: 110 GNDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGE--VILDTNKAEEQQLKSFA 167
Query: 493 DFKVAGTVNGITALQMDIKIFGITYDIIQI-------------ALYKAKKGLSYILEKMK 539
+ ++ + + K +I + + S I + M+
Sbjct: 168 HLVFPNSRKSASSKEPNQKEEDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMR 227
Query: 540 TEVPK 544
T + K
Sbjct: 228 TTLQK 232
Score = 42.8 bits (101), Expect = 2e-04
Identities = 41/213 (19%), Positives = 78/213 (36%), Gaps = 22/213 (10%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAGRIP 74
S + R A S + DT++LA V K + EKA I
Sbjct: 16 PFSCTRNPLDR-AHGSARWAQGDTIVLAAVYGPKPG-------TRKGENPEKAS----IE 63
Query: 75 GSFFKREGKPSERETIISRLIDRPIRPLFP-EGYLN-EIQIVVYVLSVNPQIDPDIASII 132
+ G+ ++E + R ++ + + N +++ V+ + + P +I
Sbjct: 64 VVWKPMTGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLP--CAIN 121
Query: 133 GVSTALSISELPFLGPL-GVAKVGYI-DGKYILNPTT--EQLKKSHLDLLVAGTEKAIIT 188
AL + +P + G + DG+ IL+ EQ KS L+ + K+ +
Sbjct: 122 ACCAALVFAGIPLKHLAVAIG-CGVLEDGEVILDTNKAEEQQLKSFAHLVFPNSRKSASS 180
Query: 189 VESESK-QLPEDIILNAIIFGHEKMKIAINAIN 220
E K + E ++ +I G + + I
Sbjct: 181 KEPNQKEEDSERGLITSITHGVMSEEDYFSCIE 213
>1oys_A Ribonuclease PH; transferase, tRNA processing; 2.40A {Bacillus
subtilis} SCOP: d.14.1.4 d.101.1.1 PDB: 1oyp_A 1oyr_A
Length = 245
Score = 287 bits (736), Expect = 9e-93
Identities = 61/251 (24%), Positives = 110/251 (43%), Gaps = 23/251 (9%)
Query: 315 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 374
+R D R +++RPI+ + GS L T G+T+ + A++ +++ L G
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASV----EDRVPPFLRGGGK 56
Query: 375 DSFMLHYNMPPFATGDIGRI----GVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVS 430
Y+M P AT G R + RL RAL V+ +I +
Sbjct: 57 GWITAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 431 EITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKVVIL 479
++ +++G + AS+ G LA+ A PI++ +A I++G+ K+ IL
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQG---IL 173
Query: 480 SDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 538
D+ +ED ++D V T +G LQ + + + + L A+KG+ +++K
Sbjct: 174 LDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQ 233
Query: 539 KTEVPKCKNEL 549
K + EL
Sbjct: 234 KEVLGDSLPEL 244
Score = 49.2 bits (118), Expect = 1e-06
Identities = 43/217 (19%), Positives = 62/217 (28%), Gaps = 75/217 (34%)
Query: 16 ISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVDY 63
I+ ++ SVL++ +T ++ V + P T+ Y+ P +
Sbjct: 14 ITFDLD-FISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPQATNQ 72
Query: 64 IEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQ 123
+GK S R I RLI R +R + L E I
Sbjct: 73 Q----------TIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTI---------W 113
Query: 124 IDPDI---------ASIIGVSTAL-----------SISELPFLGPLGVAKVGYIDGKYIL 163
ID D+ ASI G A+ +I P L VG + IL
Sbjct: 114 IDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGIL 173
Query: 164 NPTTEQLKKSHLDLL------------VAGTEKAIIT 188
LDL V T
Sbjct: 174 -----------LDLNYEEDSSAEVDMNVIMTGSGRFV 199
>2nn6_F MTR3, exosome component 6; RNA, exosome, PM/SCL, phosphorolytic,
hydrolase/transferase complex; 3.35A {Homo sapiens}
SCOP: d.14.1.4 d.101.1.1
Length = 272
Score = 273 bits (700), Expect = 3e-87
Identities = 47/263 (17%), Positives = 84/263 (31%), Gaps = 14/263 (5%)
Query: 302 ESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVAT----- 356
ES+ + D+ R +RP+ R G+L + GS+ G T+ L +
Sbjct: 13 ESQPPQLYAADEEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQA 72
Query: 357 ---LGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALL 413
+ + PFA R E + AL
Sbjct: 73 EGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRR-RRAPPGGCEERELALALQEALE 131
Query: 414 PVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDG 473
P + + + + + E GS+ A++ LAL DAGV + + V G + L
Sbjct: 132 PAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGP 191
Query: 474 EKVVILSDILGDEDRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGL 531
+L D E+ VA +N + L + G + A+ +G
Sbjct: 192 APTWLL-DPTRLEEERAAAGLTVALMPVLNQVAGLLGSGE--GGLTESWAEAVRLGLEGC 248
Query: 532 SYILEKMKTEVPKCKNELSKFAP 554
+ ++ + + A
Sbjct: 249 QRLYPVLQQSLVRAARRRGAAAQ 271
Score = 56.8 bits (137), Expect = 6e-09
Identities = 28/239 (11%), Positives = 73/239 (30%), Gaps = 31/239 (12%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATV---------------VSCKDPTSTYNFFPL 59
+ G +++ A S + T +L V L
Sbjct: 38 PVYARAGLLSQ-AKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRL 96
Query: 60 TVDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFP-EGYLN-EIQIVVYV 117
D+ +A R +R E ++ + + P Y ++++ +
Sbjct: 97 LCDFRRAPFAGRR------RRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALL 150
Query: 118 LSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGK---YILNPTTEQLKKSH 174
L A++ + AL+ + + + + G ++L+PT + +++
Sbjct: 151 LEDGGSALA--AALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAA 208
Query: 175 LDLLVA--GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKV 231
L VA + + + + A+ G E + + + + +++
Sbjct: 209 AGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVLQQSLVRAARRRG 267
>3dd6_A Ribonuclease PH; exoribonuclease, tRNA maturation, RNAse PH.,
transferase; 1.70A {Bacillus anthracis}
Length = 255
Score = 270 bits (692), Expect = 4e-86
Identities = 53/251 (21%), Positives = 105/251 (41%), Gaps = 23/251 (9%)
Query: 305 IIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQ 364
+ +R+D R ++R I I T L GS L GDT+ + AT+ +E+
Sbjct: 1 MGSSHHHHHHMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATI----EER 56
Query: 365 KIDALMGEFTDSFMLHYNMPPFATGDIGRI----GVPKRREIGHGRLAKRALLPVLPNNN 420
+ GE Y M P AT G R + RL RAL V+
Sbjct: 57 VPPFMRGEGKGWVTAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEA 116
Query: 421 KFNYSIRLVSEITESNGSSSMASVCGGCLALLD-----------AGVPISEHVAGIAMGL 469
++ + ++ +++G + AS+ G +A++ + +P+ +++A ++G+
Sbjct: 117 LGERTVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGI 176
Query: 470 IKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAK 528
+++ ++ D+ ED D+D V T G +Q + + + L A+
Sbjct: 177 VEEQG---VVLDLNYAEDSKADVDMNVIMTGKGQFVEVQGTGEEATFSRAQLNELLDAAE 233
Query: 529 KGLSYILEKMK 539
+G+ +++ K
Sbjct: 234 QGIFQLIDIQK 244
Score = 45.8 bits (109), Expect = 2e-05
Identities = 34/181 (18%), Positives = 60/181 (33%), Gaps = 52/181 (28%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVD 62
I I + SVL+ + DT ++ + + + P T+ Y P +
Sbjct: 23 HIHIHTN-YLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVTAEYAMIPRATE 81
Query: 63 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNP 122
S +GK + R I RLI R +R + L E + +
Sbjct: 82 ------QRTIRESS----KGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDC----- 126
Query: 123 QIDPDI---------ASIIGVSTAL-----------SISELPFLGPLGVAKVGYIDGKYI 162
D+ ASI G A+ +S++P L VG ++ + +
Sbjct: 127 ----DVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGV 182
Query: 163 L 163
+
Sbjct: 183 V 183
>2nn6_D Exosome complex exonuclease RRP46; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 237
Score = 253 bits (647), Expect = 7e-80
Identities = 50/250 (20%), Positives = 89/250 (35%), Gaps = 22/250 (8%)
Query: 298 LYDLESKIIRKQILDKGLRIDNRGVN-DIRPISIRTGILPRTHGSSLFTRGDTQALVVAT 356
L + E+ K + G RG +R + +L R GS+ F +GDT L
Sbjct: 2 LMEEETHTDAKIRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVY 61
Query: 357 LGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVL 416
G + E K+ +N +IG+P E RL + V+
Sbjct: 62 -GPA--EVKV----------SKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVV 108
Query: 417 PNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKV 476
SI +V ++ GS + C+AL+DAGVP+ G+A L DG
Sbjct: 109 LGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGT-- 166
Query: 477 VILSDILGDEDR--CGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYI 534
++ D +++ + F + + + +Q L A+ ++
Sbjct: 167 -LVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKG---LYSDTELQQCLAAAQAASQHV 222
Query: 535 LEKMKTEVPK 544
+ + +
Sbjct: 223 FRFYRESLQR 232
>2wp8_B Exosome complex component SKI6; nucleus, hydrolase, RNA-binding,
exonucle binding, mitochondrion, rRNA processing; 3.00A
{Saccharomyces cerevisiae}
Length = 246
Score = 252 bits (646), Expect = 2e-79
Identities = 47/247 (19%), Positives = 94/247 (38%), Gaps = 11/247 (4%)
Query: 310 ILDKGLRIDNRGVNDIRPISIRTGILPRT-HGSSLFTRGDTQALVVATLGTSRDEQKIDA 368
+GLR+D R N++R P GSS +G+ + + + E ++ +
Sbjct: 7 YSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVK---GPKEPRLKS 63
Query: 369 LMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHG-RLAKRALLPVLPNNNKFNYSIR 427
M + N+ F+ + + R + R + N I
Sbjct: 64 QMDTSKALLNVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVID 123
Query: 428 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 487
+ + E +G + + G LAL+DAG+ + ++++GI++GL +L +E+
Sbjct: 124 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDT---TPLLDTNSLEEN 180
Query: 488 RCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKN 547
+ V G ++ L ++ K I D ++ L G + + M E+ K
Sbjct: 181 AMSTVTLGVVGKSEKLSLLLVEDK---IPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQ 237
Query: 548 ELSKFAP 554
+ A
Sbjct: 238 KRVSNAS 244
Score = 60.8 bits (148), Expect = 2e-10
Identities = 39/221 (17%), Positives = 74/221 (33%), Gaps = 29/221 (13%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFP----LTVDYIEKAYAA 70
+ I A S + + I+ V K+P L V ++
Sbjct: 24 RFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNINKFSK 83
Query: 71 GRIPGSFFKREGKPSERETI-ISRLIDRPIRP-----LFPEGYLNEIQIVVYVLSVNPQI 124
+ +ER + I + R ++P I I ++VL + I
Sbjct: 84 FER-----SKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPR---TVIDIEIHVLEQDGGI 135
Query: 125 DPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTT-EQLKKSHLDLLVAGTE 183
+ I G++ AL + + + VG D +L+ + E+ S + L V G
Sbjct: 136 MG--SLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMSTVTLGVVGKS 193
Query: 184 KAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQ 224
+ + + E K +P D + N + I I + +
Sbjct: 194 EKLSLLLVEDK-IPLDRLENV-------LAIGIAGAHRVRD 226
>1udn_A Ribonuclease PH, RNAse PH; transferase, riken structural
genomics/proteomics initiative structural genomics;
2.30A {Aquifex aeolicus} SCOP: d.14.1.4 d.101.1.1 PDB:
1udq_A 1uds_A 1udo_A
Length = 255
Score = 233 bits (595), Expect = 5e-72
Identities = 57/261 (21%), Positives = 113/261 (43%), Gaps = 24/261 (9%)
Query: 315 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 374
+R D R + +RP+SI+ L GS L + G T+ + A++ E + L G+
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQ 56
Query: 375 DSFMLHYNMPPFATGDIGRIGVPK----RREIGHGRLAKRALLPVLPNNNKFNYSIRLVS 430
Y+M P AT + R R+ RA+ + +I +
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDC 116
Query: 431 EITESNGSSSMASVCGGCLALLDAGV-----------PISEHVAGIAMGLIKDGEKVVIL 479
++ +++G + A++ G +A+ DA + PI + VA +++G++ D IL
Sbjct: 117 DVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND----RIL 172
Query: 480 SDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 538
D+ +ED +D V GT +G ++ + + + T D + L A+KG++ ++E
Sbjct: 173 LDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQ 232
Query: 539 KTEVPKCKNELSKFAPRLITI 559
K + + + ++
Sbjct: 233 KKLYVIQDGKWERSELKEVSS 253
Score = 52.8 bits (127), Expect = 9e-08
Identities = 47/246 (19%), Positives = 85/246 (34%), Gaps = 52/246 (21%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVD 62
+SI+ S L+S T ++ T V P T+ Y+ P
Sbjct: 13 PVSIQRD-FLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPRAT- 70
Query: 63 YIEKAYAAGRIPGSFFKRE---GKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLS 119
RE G+ R I R+I R +R + E I V
Sbjct: 71 ------------QQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDV 118
Query: 120 VNPQIDPDIASIIGVSTALSISELPFLGPLGVAK-----------VGYIDGKYILNPTTE 168
+ A+I G A++ + + + + VG ++ + +L+ E
Sbjct: 119 IQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFE 178
Query: 169 QLKKSHLDLLVAGTEK-AIITVES--ESKQLPEDIILNAIIFGHEKMKIAINAINELVQN 225
+ + +D+ V GT + V + E +D ++ + +A INEL++
Sbjct: 179 EDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKM-------LDLAQKGINELIEL 231
Query: 226 VGQKKV 231
QKK+
Sbjct: 232 --QKKL 235
>1r6l_A Ribonuclease PH; beta-alpha-beta-alpha fold, hexamer, phosphate
bound, transf; HET: NHE; 1.90A {Pseudomonas aeruginosa}
SCOP: d.14.1.4 d.101.1.1 PDB: 1r6m_A
Length = 239
Score = 203 bits (518), Expect = 6e-61
Identities = 52/240 (21%), Positives = 95/240 (39%), Gaps = 24/240 (10%)
Query: 316 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTD 375
R R + +RPI I GS L GDT+ + + + L G+
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSA----ESGVPRFLKGQGQG 58
Query: 376 SFMLHYNMPPFATGDIGRI----GVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSE 431
Y M P +TG+ + G R + RL R+L L + ++ + +
Sbjct: 59 WLTAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCD 118
Query: 432 ITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKVVILS 480
+ +++G + AS+ G +AL+DA G P+ + VA +++G+ + V +
Sbjct: 119 VIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQG----VPVL 174
Query: 481 DILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMK 539
D+ ED + D V T G +Q + + L A++G+ + E +
Sbjct: 175 DLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQR 234
Score = 52.8 bits (127), Expect = 8e-08
Identities = 51/246 (20%), Positives = 79/246 (32%), Gaps = 52/246 (21%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVD 62
I I + A SVLV DT ++ TV P T+ Y P +
Sbjct: 14 PIRITRH-YTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPRST- 71
Query: 63 YIEKAYAAGRIPGSFFKRE---GKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLS 119
G +RE GK R I RLI R +R L E + +
Sbjct: 72 ------------GERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDV 119
Query: 120 VNPQIDPDIASIIGVSTAL-----------SISELPFLGPLGVAKVGYIDGKYILNPTTE 168
+ ASI G + AL ++ P + VG G +L+
Sbjct: 120 IQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVPVLDLDYL 179
Query: 169 QLKKSHLDLLVAGTEK-AIITVE--SESKQLPEDIILNAIIFGHEKMKIAINAINELVQN 225
+ + DL V T+ I V+ +E + +++A + EL +
Sbjct: 180 EDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAM-------LELAQQGMQELFEL 232
Query: 226 VGQKKV 231
Q+
Sbjct: 233 --QRAA 236
>3b4t_A Ribonuclease PH; RNAse, tRNA nucleotidyltransferase, RPHA, STRU
genomics, TBSGC; 2.10A {Mycobacterium tuberculosis}
Length = 262
Score = 165 bits (420), Expect = 9e-47
Identities = 46/253 (18%), Positives = 91/253 (35%), Gaps = 17/253 (6%)
Query: 316 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTD 375
R D R +++RP+ I G GS L G T+ L A++ + +G T
Sbjct: 7 REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTA 66
Query: 376 SFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITES 435
+ + + + G R RL R+L + +I + ++ ++
Sbjct: 67 EYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQA 126
Query: 436 NGSSSMASVCGGCLALLDAGV------------PISEHVAGIAMGLIKDGEKVVILSDIL 483
+G + A++ G +AL DA P+S +A +++G++ I D+
Sbjct: 127 DGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDG----RIRVDLP 182
Query: 484 GDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 542
+ED ++D V T G + +Q + + L A + + +
Sbjct: 183 YEEDSRAEVDMNVVATDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFAAQRDAL 242
Query: 543 PKCKNELSKFAPR 555
+ P
Sbjct: 243 ALPYPGVLPQGPP 255
Score = 39.0 bits (91), Expect = 0.003
Identities = 49/248 (19%), Positives = 80/248 (32%), Gaps = 55/248 (22%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVD 62
+ I G SVL+ T +L T V+ P T+ Y P
Sbjct: 18 PVIITRG-FTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTAEYAMLP---- 72
Query: 63 YIEKAYAAGRIPGSFFKRE---GKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLS 119
S RE G+ S R ISRLI R +R L E I +
Sbjct: 73 ---------SATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDV 123
Query: 120 VNPQIDPDIASIIGVSTALSISELPFLGPLGVAK------------VGYIDGKYILNPTT 167
+ A+I G AL+ + ++ VG +DG+ ++
Sbjct: 124 LQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDGRIRVDLPY 183
Query: 168 EQLKKSHLDLLVAGTEKAIITVE----SESKQLPEDIILNAIIFGHEKMKIAINAINELV 223
E+ ++ +D+ V T+ + VE E + + +A+ A + L
Sbjct: 184 EEDSRAEVDMNVVATDTGTL-VEIQGTGEGATFARSTLDKL-------LDMALGACDTLF 235
Query: 224 QNVGQKKV 231
Q+
Sbjct: 236 AA--QRDA 241
>3krn_A Protein C14A4.5, confirmed by transcript evidence; RNAse PH domain,
homodimer, exosome, cell-death-related DNAS hydrolase;
3.92A {Caenorhabditis elegans}
Length = 222
Score = 123 bits (311), Expect = 3e-32
Identities = 38/222 (17%), Positives = 74/222 (33%), Gaps = 21/222 (9%)
Query: 323 NDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYN 382
+R + L GS+ F++G T + G ++ L +
Sbjct: 3 GRLREMRCELSFLKNADGSACFSQGATCIWASCS-GPGDVHAS-----KASDEAMTLDIS 56
Query: 383 MPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMA 442
G K + + L + + +I + + +GS
Sbjct: 57 YRANC-------GDNKFNVLN--NIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAV 107
Query: 443 SVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDR--CGDMDFKVAGTV 500
++ G C ALLD G+P G+ + +KD ++ D ++ G + F V
Sbjct: 108 AINGACFALLDNGMPFETVFCGVLIVRVKD----ELIIDPTAKQEAASTGRVLFSVCKGS 163
Query: 501 NGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 542
+G + I + ++ A A+ S I + KT +
Sbjct: 164 DGHPEVCAMDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVM 205
Score = 69.4 bits (170), Expect = 2e-13
Identities = 34/233 (14%), Positives = 78/233 (33%), Gaps = 40/233 (17%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATV---VSCKDPTSTYNFFPLTVDYIEKAYAAG 71
++ E+ + A S S T I A+ ++ L + Y
Sbjct: 7 EMRCELS-FLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISY-------- 57
Query: 72 RIPGSFFKREGKPSERETIISRLIDRPIRP-----LFPEGYLNEIQIVVYVLSVNPQIDP 126
R + +++ +I + LFP I + V+ + + +
Sbjct: 58 --------RANCGDNKFNVLNNIIHSTLSNAINLELFPH---TTISVTVHGIQDDGSMGA 106
Query: 127 DIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA-----G 181
+I G AL + +PF + + + I++PT +Q S +L +
Sbjct: 107 --VAINGACFALLDNGMPFETVFCGVLIVRVKDELIIDPTAKQEAASTGRVLFSVCKGSD 164
Query: 182 TEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWD 234
+ +++ + A + + +AI + + V ++K++ D
Sbjct: 165 GHPEVCAMDAIGH-WDFIQLEAAW----SLAQPSASAIFDFYKTVMKRKLSVD 212
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA
binding protein; NMR {Bacillus subtilis}
Length = 130
Score = 102 bits (255), Expect = 8e-26
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 616 LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRV 675
+ ++G VYTG V L +GA + + GL+HIS+++ V I + L +V+V
Sbjct: 1 MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60
Query: 676 KVLGID-DRGRIKLSM 690
KVL +D ++G+I LS+
Sbjct: 61 KVLAVDEEKGKISLSI 76
>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 119
Score = 97.9 bits (244), Expect = 2e-24
Identities = 29/93 (31%), Positives = 49/93 (52%), Gaps = 4/93 (4%)
Query: 602 NSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRIL-SGKDGLLHISQISSKRV 660
+S S R E + + ++ G V + D+GA I+I K GL+H + +SS RV
Sbjct: 2 SSGSSGMNSGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRV 61
Query: 661 NIITDFLKENQKVRVKVLGID---DRGRIKLSM 690
+ ++ + KV VK++G + DR ++ LSM
Sbjct: 62 DKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSM 94
>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 103
Score = 94.3 bits (235), Expect = 2e-23
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 616 LTESVQIGKVYTGIVLRLFDFGAIIRILSGK---DGLLHISQISS-KRVNIITDFLKENQ 671
E IG +Y G V + FG +++ + +GL+HIS++ RV + D + + Q
Sbjct: 6 SGEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQ 65
Query: 672 KVRVKVLGIDDRGRIKLSM 690
+V+VKVL + LSM
Sbjct: 66 RVKVKVLSF-TGTKTSLSM 83
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger,
structural genomics, PSI-2, protein structure
initiative; NMR {Methanocaldococcus jannaschii}
Length = 80
Score = 84.2 bits (209), Expect = 3e-20
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 620 VQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLG 679
V+ GK Y G+V R+ +GA I + GLL + S R+ L ++ V+ +
Sbjct: 3 VEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLEN----LNVGDEIIVQAID 58
Query: 680 ID-DRGRIKLSMI 691
+ ++ I I
Sbjct: 59 VRPEKREIDFKYI 71
>2wnr_A Probable exosome complex exonuclease 2; phosphate binding, 3'-5'
exoribonuclease, hydrolase; 2.65A {Methanothermobacter
thermautotrophicusorganism_taxid}
Length = 271
Score = 84.7 bits (210), Expect = 2e-18
Identities = 54/278 (19%), Positives = 101/278 (36%), Gaps = 47/278 (16%)
Query: 299 YDLESKIIRKQI---LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVA 355
D+ +I RK I ++ RID R +++ R ISI TG++ + GSS G+TQ +V
Sbjct: 5 MDIIPEITRKSITDLINNKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGV 64
Query: 356 TLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL--- 412
+ + + + P A+ G P R + R+ R +
Sbjct: 65 KP-----QIGEPFPDTPEMGVILTNSELLPMASPTFEP-GPPDERSVELSRVVDRCIRES 118
Query: 413 -------LPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP-------- 457
L ++ + + L I + +G+ A+V ALLD +P
Sbjct: 119 RMIDLEKLCIIE--GSKVWMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGE 176
Query: 458 ------------ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-IT 504
++ I + I+ D +E+ + T G I
Sbjct: 177 VVINREKMQPLPVNRKALMCTFAKIGN----EIVLDPSLEEEDILTARISIGVTEEGSIC 232
Query: 505 ALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 542
A+Q + +T D + A+ A + + ++E + +
Sbjct: 233 AMQKGGEG-PLTRDDVLKAVSIAVEKVPQLIEYLDKSM 269
Score = 42.7 bits (101), Expect = 2e-04
Identities = 40/215 (18%), Positives = 73/215 (33%), Gaps = 67/215 (31%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATVVSC-------KDP-----TSTYNFFPLTVD 62
ISIE G I+ +A S V + +T I+ V P + P+
Sbjct: 36 DISIETGVIS-KAEGSSRVKLGNTQIIVGV-KPQIGEPFPDTPEMGVILTNSELLPMASP 93
Query: 63 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRP----------LFPEGYLNEIQ 112
E G P ER +SR++DR IR + + +
Sbjct: 94 TFEP---------------GPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLF 138
Query: 113 IVVYVLSVNPQID---PDIASIIGVSTALSISELPF--------------LGPLGVAK-- 153
+ ++++ D D A+++ AL + +P + PL V +
Sbjct: 139 LDLHII----DYDGNLFD-AAVLATVAALLDTRIPAAEVEDGEVVINREKMQPLPVNRKA 193
Query: 154 ----VGYIDGKYILNPTTEQLKKSHLDLLVAGTEK 184
I + +L+P+ E+ + + TE+
Sbjct: 194 LMCTFAKIGNEIVLDPSLEEEDILTARISIGVTEE 228
>3m7n_G Probable exosome complex exonuclease 2; exosome, RNA, exonuclease,
hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus
fulgidus} PDB: 2ba1_H 2ba0_I 3m85_G
Length = 259
Score = 82.8 bits (205), Expect = 9e-18
Identities = 45/267 (16%), Positives = 89/267 (33%), Gaps = 40/267 (14%)
Query: 300 DLESKIIRKQI---LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVAT 356
D+ I R + L RID RG ++ R + I ++ + GS+L GDTQ +V
Sbjct: 4 DILVDIKRDYVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVK 63
Query: 357 LGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL---- 412
+ + +++ + P A+ G P I R+ R +
Sbjct: 64 M-----QPGEPYPDTPDRGVIIVNAELVPLASPTFEP-GPPDENSIELARVVDRGIRESE 117
Query: 413 ------LPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP--------- 457
L + + + + + + +G+ AS AL++ VP
Sbjct: 118 AVDLSKLVIEE--GEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGED 175
Query: 458 ----ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKI 512
+ + + ++ + L D +E GD + + + A+Q
Sbjct: 176 YLLPVRDLPVSVTSLIVGN----KYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGY 231
Query: 513 FGITYDIIQIALYKAKKGLSYILEKMK 539
+ + L + + EK K
Sbjct: 232 -LLDEKLFDELLDVSINCARKLREKFK 257
Score = 43.5 bits (103), Expect = 1e-04
Identities = 43/250 (17%), Positives = 92/250 (36%), Gaps = 57/250 (22%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP---TSTYNFFPLTVDYIEKAYAA 70
K+ I I +A S LV + DT ++ V + +P T + + +
Sbjct: 34 KVEIIPNVI-EKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELV------ 86
Query: 71 GRIPGSFFKRE-GKPSERETIISRLIDRPIRP----------LFPEGYLNEIQIVVYVLS 119
P + E G P E ++R++DR IR + + + + ++ L
Sbjct: 87 ---PLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHAL- 142
Query: 120 VNPQIDPDI--ASIIGVSTALSISELPFLG--------------PLGVAKVGYIDGKYIL 163
D ++ AS + AL +++P P+ V + KY++
Sbjct: 143 ---DDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVT-SLIVGNKYLV 198
Query: 164 NPTTEQLKKSHLDLLVAGTEK-AIITVE-SESKQLPEDIILNAIIFGHEKMKIAINAINE 221
+P+ E++ L + + ++ ++ S L E + + ++IN +
Sbjct: 199 DPSREEMSVGDTTLTITTDKDDNVVAMQKSGGYLLDEKLFDELL-------DVSINCARK 251
Query: 222 LVQNVGQKKV 231
L + K++
Sbjct: 252 LREK--FKEI 259
>2po1_B Probable exosome complex exonuclease 2; RNAse PH,
hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus
abyssi} PDB: 2po0_B* 2pnz_B 2po2_B*
Length = 277
Score = 82.4 bits (204), Expect = 1e-17
Identities = 55/273 (20%), Positives = 92/273 (33%), Gaps = 44/273 (16%)
Query: 303 SKIIRKQI---LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGT 359
+ I+R I L +G RID+RG D RPI I G++ + GS+L G TQ LV
Sbjct: 11 AGIMRDHIINLLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKT-- 68
Query: 360 SRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNN 419
+ + P A+ G P R I R+ R + N
Sbjct: 69 ---SLGEPFPDTPNMGVMTTNVELVPLASPTFEP-GPPDERAIELARVIDRGIRESKALN 124
Query: 420 --------NKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAG---------------- 455
K + + + + +G+ A ALL+A
Sbjct: 125 LEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETL 184
Query: 456 -----VPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMD 509
+P+ + + I + +++ D DE+ D + G I+A+Q
Sbjct: 185 DETEPLPVEKIPVPVTFAKIGN----ILVVDPSLDEELVMDGKITITTDETGHISAVQKS 240
Query: 510 IKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 542
+ + A+ A K I + + V
Sbjct: 241 EGG-AFKLEEVMYAVETAFKKAEEIRKLILEAV 272
Score = 45.1 bits (107), Expect = 4e-05
Identities = 51/257 (19%), Positives = 85/257 (33%), Gaps = 75/257 (29%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATVVSC-------KDP-----TSTYNFFPLTVD 62
I IE+G I +A S LV + T +L + P T+ PL
Sbjct: 38 PIEIEVGVIE-KAEGSALVKLGSTQVLVGI-KTSLGEPFPDTPNMGVMTTNVELVPLASP 95
Query: 63 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRP----------LFPEGYLNEIQ 112
E G P ER ++R+IDR IR + P + +
Sbjct: 96 TFEP---------------GPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVF 140
Query: 113 IVVYVLSVNPQIDPDI--ASIIGVSTALSISELPFL---------------GPLGVAK-- 153
I V+VL D ++ A I AL + +P + PL V K
Sbjct: 141 IDVHVL----DHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIP 196
Query: 154 ----VGYIDGKYILNPTTEQLKKSHLDLLVAGTEK-AIITVE-SESKQLPEDIILNAIIF 207
I +++P+ ++ + + E I V+ SE + ++ A+
Sbjct: 197 VPVTFAKIGNILVVDPSLDEELVMDGKITITTDETGHISAVQKSEGGAFKLEEVMYAV-- 254
Query: 208 GHEKMKIAINAINELVQ 224
+ A E+ +
Sbjct: 255 -----ETAFKKAEEIRK 266
>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA
complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus
horikoshii} PDB: 1yz6_A
Length = 275
Score = 80.8 bits (199), Expect = 5e-17
Identities = 29/82 (35%), Positives = 46/82 (56%), Gaps = 3/82 (3%)
Query: 613 IEKLTESVQIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKEN 670
K E + G+ V R+ ++GA + + GK+ +HIS+++S V I D+LKE
Sbjct: 2 PRKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEG 61
Query: 671 QKVRVKVLGID-DRGRIKLSMI 691
QKV KV+ +D +G I LS+
Sbjct: 62 QKVVAKVIRVDPRKGHIDLSLR 83
>2nn6_C Exosome complex exonuclease RRP43; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 278
Score = 80.0 bits (197), Expect = 1e-16
Identities = 38/268 (14%), Positives = 81/268 (30%), Gaps = 45/268 (16%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 367
++ L + R D R + + R ++ G + GS+L G+T + E
Sbjct: 17 RRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKA-----EFAAP 71
Query: 368 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL----------LPVLP 417
+ + + ++PP + R G P + + L + P
Sbjct: 72 STDAPDKGYVVPNVDLPPLCSSRF-RSGPPGEEAQVASQFIADVIENSQIIQKEDLCISP 130
Query: 418 NNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP-------------------- 457
K + + + +G+ A AL + +P
Sbjct: 131 --GKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSY 188
Query: 458 --ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFG 514
I H + + D +++ D G+E+ + G + L G
Sbjct: 189 LNIRTHPVATSFAVFDDT---LLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKP-GGSG 244
Query: 515 ITYDIIQIALYKAKKGLSYILEKMKTEV 542
+T +Q + +A + + M +
Sbjct: 245 LTGAKLQDCMSRAVTRHKEVKKLMDEVI 272
Score = 38.0 bits (88), Expect = 0.007
Identities = 38/251 (15%), Positives = 79/251 (31%), Gaps = 44/251 (17%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDPTSTYNFFPLTVD--YIEKAYAAG 71
++ IG I+ A S LV + +T ++ V P D Y+
Sbjct: 36 TTTVNIGSIS-TADGSALVKLGNTTVICGVKAEFAAP------STDAPDKGYVVPNVDLP 88
Query: 72 RIPGSFFKREGKPSERETIISRLIDRPIRP--------LFPEGYLNEIQIVVYVLSVNPQ 123
+ S F R G P E + S+ I I L + ++ ++
Sbjct: 89 PLCSSRF-RSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYD 147
Query: 124 IDPDIASIIGVSTALSISELPFL----------------GPLGVAK------VGYIDGKY 161
+ A + AL +LP + L + D
Sbjct: 148 GNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDDTL 207
Query: 162 IL-NPTTEQLKKSHLDLLVAGTEKAIITV--ESESKQLPEDIILNAIIFGHEKMKIAINA 218
++ +PT E+ + L + E+ + + L + + + + K
Sbjct: 208 LIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEVKKL 267
Query: 219 INELVQNVGQK 229
++E+++++ K
Sbjct: 268 MDEVIKSMKPK 278
>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha;
transferase, protein biosynthesis, protein synthesis
transferase complex; HET: TPO ANP; 2.50A {Saccharomyces
cerevisiae} PDB: 2a1a_A* 1q46_A
Length = 175
Score = 76.0 bits (187), Expect = 3e-16
Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 678
+I + V ++ + GA +++L +G++ +S++S +R+ I ++ + VL
Sbjct: 14 EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVL 73
Query: 679 GID-DRGRIKLSM 690
+D ++G I LS
Sbjct: 74 RVDKEKGYIDLSK 86
>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical
domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5
Length = 182
Score = 75.6 bits (186), Expect = 6e-16
Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 678
++ V V + + GA + +L +G++ +S++S +R+ I ++ + V V+
Sbjct: 14 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVI 73
Query: 679 GID-DRGRIKLSM 690
+D ++G I LS
Sbjct: 74 RVDKEKGYIDLSK 86
>2je6_A RRP42, exosome complex exonuclease 2; nuclease, hydrolase,
exonuclease, phosphorolytic, exoribonuclease, RNA
degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus}
SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_A* 2jeb_A* 2br2_A
2c37_A* 2c38_A* 2c39_A* 3l7z_A
Length = 277
Score = 77.4 bits (191), Expect = 7e-16
Identities = 53/275 (19%), Positives = 97/275 (35%), Gaps = 46/275 (16%)
Query: 297 ILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVAT 356
I+ ++ + I + +KG+R D R + D RP+SI + GS+L G T L
Sbjct: 12 IIPIIKKESIVS-LFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTK 70
Query: 357 LGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL---- 412
L E + +++ + P A G P I R+ R+L
Sbjct: 71 L-----EIDKPYEDTPNQGNLIVNVELLPLAYETFEP-GPPDENAIELARVVDRSLRDSK 124
Query: 413 ------LPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAG----------- 455
L + P K +++ L + + G+ A AL +
Sbjct: 125 ALDLTKLVIEP--GKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGI 182
Query: 456 ----------VPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-IT 504
+P++ V I++ + ++ D DE+ D + T + I
Sbjct: 183 SVNKNEVVGKLPLNYPVVTISVAKVDK----YLVVDPDLDEESIMDAKISFSYTPDLKIV 238
Query: 505 ALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMK 539
+Q K ++ I A A+ +LE++K
Sbjct: 239 GIQKSGKG-SMSLQDIDQAENTARSTAVKLLEELK 272
Score = 43.1 bits (102), Expect = 2e-04
Identities = 34/212 (16%), Positives = 67/212 (31%), Gaps = 60/212 (28%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATVVSC-------KDPTSTYNFFPLTVDYIEKA 67
+SI + ++A S LV + T++LA P L V+
Sbjct: 41 PLSITLDYA-KKADGSALVKLGTTMVLAGT-KLEIDKPYEDTPNQGN----LIVNV---- 90
Query: 68 YAAGRIPGSFFKRE-GKPSERETIISRLIDRPIRP----------LFPEGYLNEIQIVVY 116
+P ++ E G P E ++R++DR +R + P + + + VY
Sbjct: 91 ---ELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVY 147
Query: 117 VLSVNPQID---PDIASIIGVSTALSISELPFLGPLGVAK-------------------- 153
VL D A + AL +++ +
Sbjct: 148 VL----DYGGNVLD-ACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTI 202
Query: 154 -VGYIDGKYILNPTTEQLKKSHLDLLVAGTEK 184
V +D +++P ++ + + T
Sbjct: 203 SVAKVDKYLVVDPDLDEESIMDAKISFSYTPD 234
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein,
ribonucleoprotein, RNA-binding; NMR {Escherichia coli}
Length = 109
Score = 71.8 bits (177), Expect = 2e-15
Identities = 22/78 (28%), Positives = 32/78 (41%), Gaps = 1/78 (1%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 673
+ G + TG V + GA + + G +G L S+ S RV T L +V
Sbjct: 23 NNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEV 82
Query: 674 RVKVLGID-DRGRIKLSM 690
K G+D I LS+
Sbjct: 83 EAKFTGVDRKNRAISLSV 100
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein,
ribonucleoprotein, RNA-binding; NMR {Escherichia coli}
Length = 115
Score = 70.7 bits (174), Expect = 5e-15
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 2/79 (2%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 672
+ + G TG V L D+G + I G +GL+H+S++ + + + +
Sbjct: 22 VAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDV 81
Query: 673 VRVKVLGID-DRGRIKLSM 690
V V VL ID +R RI L +
Sbjct: 82 VEVMVLDIDEERRRISLGL 100
>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2,
initiation factor 2 alpha subunit, initiation factor 2
beta subunit; 2.80A {Sulfolobus solfataricus} PDB:
2aho_B 3v11_B*
Length = 266
Score = 74.3 bits (182), Expect = 7e-15
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 3/73 (4%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 678
G++ V ++FD+G+ + + G L S++SSK V I D LKEN+KV VKV+
Sbjct: 10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVI 69
Query: 679 GID-DRGRIKLSM 690
+D +G + +S+
Sbjct: 70 RVDRRKGTVDVSL 82
>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo
sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1
Length = 308
Score = 73.1 bits (179), Expect = 4e-14
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 3/73 (4%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 678
++ V V + + GA + +L +G++H+S++S +R+ I ++ + VKV+
Sbjct: 12 EVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVI 71
Query: 679 GID-DRGRIKLSM 690
+D ++G I LS
Sbjct: 72 RVDKEKGYIDLSK 84
>2nn6_A Polymyositis/scleroderma autoantigen 1; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 358
Score = 73.1 bits (179), Expect = 5e-14
Identities = 42/267 (15%), Positives = 79/267 (29%), Gaps = 48/267 (17%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 367
+ +++ R+D R D R I I G +G + G T+ L + E
Sbjct: 32 LRAIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSC-----ELVSP 83
Query: 368 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL----------LPVLP 417
L + + A G + RL +R L L V+
Sbjct: 84 KLNRATEGILFFNLELSQMAAPAFEP-GRQSDLLVKLNRLMERCLRNSKCIDTESLCVVA 142
Query: 418 NNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP-------------------- 457
+ + IR+ + +G+ A+ +AL P
Sbjct: 143 --GEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPV 200
Query: 458 ---ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIF 513
I ++ + G +++ D E+R D +A + I +Q
Sbjct: 201 PLSIHHMPICVSFAFFQQGTYLLV--DPNEREERVMDGLLVIAMNKHREICTIQSS-GGI 257
Query: 514 GITYDIIQIALYKAKKGLSYILEKMKT 540
+ D + A ++ I E +
Sbjct: 258 MLLKDQVLRCSKIAGVKVAEITELILK 284
Score = 37.3 bits (86), Expect = 0.015
Identities = 40/249 (16%), Positives = 76/249 (30%), Gaps = 58/249 (23%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP---TSTYNFFPLTVDYIEKAYAA 70
I I G +V + T +L V P +T ++
Sbjct: 51 NIRISFGT----DYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLEL------- 99
Query: 71 GRIPGSFFKREGKPSERETIISRLIDRPIRP--------LFPEGYLNEIQIVVYVLSVNP 122
+ G+ S+ ++RL++R +R L QI V + +N
Sbjct: 100 -SQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNH 158
Query: 123 QIDPDIASIIGVSTALSISELPFLG-----------------PLGVAK------VGY--I 157
+ A+ I AL P + PL + +
Sbjct: 159 DGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPICVSFAFFQQ 218
Query: 158 DGKYILNPTTEQLKKSHLDLLVAGTEKA-IITVE-SESKQLPEDIILNAIIFGHEKMKIA 215
+++P + + L++A + I T++ S L +D +L KIA
Sbjct: 219 GTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKDQVLRCS-------KIA 271
Query: 216 INAINELVQ 224
+ E+ +
Sbjct: 272 GVKVAEITE 280
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces
cerevisiae}
Length = 1030
Score = 73.4 bits (180), Expect = 2e-13
Identities = 10/75 (13%), Positives = 29/75 (38%), Gaps = 2/75 (2%)
Query: 618 ESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNI-ITDFLKENQKVRVK 676
++ G + V R + I S + +++ + + ++ + + + K
Sbjct: 901 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAK 960
Query: 677 VLGID-DRGRIKLSM 690
V+ ID ++S+
Sbjct: 961 VIYIDYANITAEVSL 975
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces
cerevisiae}
Length = 1219
Score = 73.0 bits (179), Expect = 2e-13
Identities = 13/94 (13%), Positives = 37/94 (39%), Gaps = 3/94 (3%)
Query: 600 SFNSVSGQEAKRRIEKLT-ESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK 658
F+ + G E + + + ++ G + V R + I S + +++ + +
Sbjct: 879 DFHPLQGDEIFQSLTGESEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGA 938
Query: 659 RVNI-ITDFLKENQKVRVKVLGID-DRGRIKLSM 690
++ + + + KV+ ID ++S+
Sbjct: 939 QLRRPANEIYEIGKTYPAKVIYIDYANITAEVSL 972
>2nn6_E Exosome complex exonuclease RRP42; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 305
Score = 69.3 bits (169), Expect = 5e-13
Identities = 37/268 (13%), Positives = 74/268 (27%), Gaps = 47/268 (17%)
Query: 311 LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALM 370
+ + LR+D RG D R + + T ++ T GS+ G T LV E L
Sbjct: 32 VQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKA-----EMGTPKLE 86
Query: 371 GEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLP--------NNNKF 422
+ AT + R + +
Sbjct: 87 KPNEGYLEFFVDCSASATPEF-EGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREH 145
Query: 423 NYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP------------------------- 457
+ + + + E G+ A AL + +P
Sbjct: 146 CWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIR 205
Query: 458 --ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFG 514
+ + + I + D E+ C V+ T G +T ++ +
Sbjct: 206 LSVENVPCIVTLCKIGY----RHVVDATLQEEACSLASLLVSVTSKGVVTCMRK-VGKGS 260
Query: 515 ITYDIIQIALYKAKKGLSYILEKMKTEV 542
+ + I + K+ + +++ V
Sbjct: 261 LDPESIFEMMETGKRVGKVLHASLQSVV 288
Score = 38.1 bits (88), Expect = 0.007
Identities = 36/249 (14%), Positives = 77/249 (30%), Gaps = 44/249 (17%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAGRIP 74
+ +E ++ + S V + T IL V + + +
Sbjct: 48 CVEVETDVVS-NTSGSARVKLGHTDILVGVKAEMGTP-----KLEKPNEGYLEFFVDCSA 101
Query: 75 GSFFKRE-GKPSERETIISRLIDRPIRP---LFPEGYL-----NEIQIVVYVLSVNPQID 125
+ + E + T I+ + R + + + + V VL + +
Sbjct: 102 SATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGN 161
Query: 126 PDIASIIGVSTALSISELPFLG---------------------PLGVAK------VGYID 158
A I V AL + +P + L V + I
Sbjct: 162 LFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIG 221
Query: 159 GKYILNPTTEQLKKSHLDLLVAGTEKAIITV--ESESKQLPEDIILNAIIFGHEKMKIAI 216
+++++ T ++ S LLV+ T K ++T + L + I + G K+
Sbjct: 222 YRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKRVGKVLH 281
Query: 217 NAINELVQN 225
++ +V
Sbjct: 282 ASLQSVVHK 290
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain,
transcription, RNA binding protein; 2.27A {Pseudomonas
aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5
c.55.3.13 PDB: 3bzk_A 2oce_A
Length = 785
Score = 68.4 bits (168), Expect = 4e-12
Identities = 30/83 (36%), Positives = 48/83 (57%), Gaps = 2/83 (2%)
Query: 610 KRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKE 669
+ +E L + ++ G V G+V + +FGA + I +DGL+HIS +S K V + +K
Sbjct: 643 QEGVESL-KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKA 701
Query: 670 NQKVRVKVLGID-DRGRIKLSMI 691
V+VKV+ +D R R+ LSM
Sbjct: 702 GDIVKVKVMEVDIPRNRVGLSMR 724
>3h36_A Polyribonucleotide nucleotidyltransferase; polyribonucleotide
nucleotidyltransfer structural genomics, PSI-2, protein
structure initiative; 1.80A {Streptococcus mutans}
Length = 93
Score = 60.5 bits (147), Expect = 1e-11
Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 239 DKTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLI----DNENLTIDINDI 294
D L ++I+ ++KA QI+ K+ ++ + + + + + ++E + D+
Sbjct: 10 DADLQAEIVGKYNADLQKAVQIEEKKASEIATEAVKEHVTAEYEERYAEHEEHDRIMRDV 69
Query: 295 NCILYDLESKIIRKQILDKGLRID 318
IL +E +R+ I + +R D
Sbjct: 70 AEILEQMEHAEVRRLITEDKVRPD 93
>1whu_A Polynucleotide phosphorylase; 3'-5' RNA exonuclease; pnpase,
alpha-helical domain, structural genomics; NMR {Mus
musculus} SCOP: a.4.9.1
Length = 104
Score = 60.1 bits (146), Expect = 2e-11
Identities = 16/95 (16%), Positives = 31/95 (32%), Gaps = 3/95 (3%)
Query: 228 QKKVNWDPIVKDKTLISKIINISEHKIRKAYQI--KNKQIRDLTFKNISKDIYSSLIDNE 285
++ I+ K+ + +K RD I D L + +
Sbjct: 4 GSSGPQKIFTPSAEIVKYTKIIAMEKLYAVFTDYEHDKVSRDEAVNKIRLDTEEHLKE-K 62
Query: 286 NLTIDINDINCILYDLESKIIRKQILDKGLRIDNR 320
+D +I + ++ R IL++ R D R
Sbjct: 63 FPEVDQFEIIESFNIVAKEVFRSIILNEYKRCDGR 97
>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains,
type I domains, fragIle X mental retardation protein,
RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A
Length = 144
Score = 60.0 bits (145), Expect = 7e-11
Identities = 22/129 (17%), Positives = 53/129 (41%), Gaps = 8/129 (6%)
Query: 553 APRLITIKIDPSKIRDVIGKGGSTIRTLTEETG-TQIDINDE-GIITIASFNSVSGQEAK 610
+ + + IG G+ I+ + G T ID++++ I + + ++A+
Sbjct: 2 SRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKAR 61
Query: 611 RRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKEN 670
+E + +Q+ + G V + G +I+ + K G++ + + N+ +E
Sbjct: 62 SFLEFAEDVIQVPRNLVGKV--IGKNGKLIQEIVDKSGVVRVRIEAENEKNVP----QEE 115
Query: 671 QKVRVKVLG 679
V +G
Sbjct: 116 GMVPFVFVG 124
Score = 40.8 bits (95), Expect = 3e-04
Identities = 24/159 (15%), Positives = 55/159 (34%), Gaps = 31/159 (19%)
Query: 474 EKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSY 533
E+ ++ D++G + + A V G+TA+ +D
Sbjct: 6 EQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFH----------------- 48
Query: 534 ILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETG-TQIDIND 592
I + + V K ++ L I++ + + VIGK G I+ + +++G ++ I
Sbjct: 49 IYGEDQDAVKKARSFLE---FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEA 105
Query: 593 EGIITIASFNSVSG----------QEAKRRIEKLTESVQ 621
E + + A ++ ++
Sbjct: 106 ENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNYLK 144
>2wp8_A Exosome complex component RRP45; nucleus, hydrolase, RNA-binding,
exonucle binding, mitochondrion, rRNA processing; 3.00A
{Saccharomyces cerevisiae}
Length = 305
Score = 61.6 bits (149), Expect = 2e-10
Identities = 34/293 (11%), Positives = 82/293 (27%), Gaps = 55/293 (18%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 367
+ L + R+D R + R + I G + G G+T+ + +
Sbjct: 16 LEALRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISC-----QIAQP 67
Query: 368 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL----------LPVLP 417
F F++ + P A + E+ R+ ++++ L ++
Sbjct: 68 YEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVA 127
Query: 418 NNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP-------------------- 457
+++R + +G AS L+ P
Sbjct: 128 --GSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPV 185
Query: 458 ---ISEHVAGIAMGLIKDGEKV----------VILSDILGDEDRCGDMDFKVAGTVNG-I 503
I + + + + D E+ D V N +
Sbjct: 186 PLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKNREV 245
Query: 504 TALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRL 556
+ + + ++A + I +++ + + + +K+A L
Sbjct: 246 VQVSKAGG-LPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRNKYAAML 297
>1we8_A Tudor and KH domain containing protein; structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Mus musculus} SCOP: d.51.1.1
Length = 104
Score = 57.1 bits (138), Expect = 2e-10
Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 9/82 (10%)
Query: 548 ELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG--------IITIA 599
L++ P + + + +IG+GG TIR++ + +G +I + E +I I+
Sbjct: 8 ILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKIS 67
Query: 600 SFNSVSGQEAKRRIEKLTESVQ 621
AK I + +
Sbjct: 68 G-TQKEVAAAKHLILEKVSEDE 88
>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 = 61.2 bits (148), Expect = 8e-10
Identities = 115/762 (15%), Positives = 197/762 (25%), Gaps = 325/762 (42%)
Query: 16 ISIEIGEIARQATSSVLVSIEDTVILATVVSCKD------PTSTYNF---------FPLT 60
+++ G + +LV + +A+ + ++ P T F L
Sbjct: 9 LTLSHGSL----EHVLLVP-TASFFIASQL--QEQFNKILPEPTEGFAADDEPTTPAELV 61
Query: 61 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
++ Y + + K + + +++ + F YL
Sbjct: 62 GKFL--GYVSSLV------EPSKVGQFDQVLNLCLTE-----FENCYLEG---------- 98
Query: 121 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 180
N DI ++ + L ++ + + K YI + + ++ S L
Sbjct: 99 N-----DIHAL--AAKLLQENDTTLVKTKELIKN-YITARIMAKRPFDKKSNSAL-FRAV 149
Query: 181 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVN--WDPIVK 238
G A + IFG GQ + ++
Sbjct: 150 GEGNAQLVA----------------IFG------------------GQGNTDDYFE---- 171
Query: 239 DKTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCIL 298
E +R Y Y L+ +L I L
Sbjct: 172 ------------E--LRDLY-----------------QTYHVLV--GDL---IKFSAETL 195
Query: 299 YDL-ESKIIRKQILDKGLRIDN--RGVNDIR--------PISI----------------R 331
+L + + +++ +GL I ++ PIS
Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKL 255
Query: 332 TGILP---RTHGSSLFTRGDTQALVVAT-LGTSRDEQKIDALMGEFTDSF--MLHYNMPP 385
G P R++ Q LV A + + + F S +
Sbjct: 256 LGFTPGELRSYLKGATGHS--QGLVTAVAIAETDSWE-------SFFVSVRKAITV---L 303
Query: 386 FATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNG---SSSMA 442
F IGV R + +L P + E + N S M
Sbjct: 304 F------FIGV---R--CYEAYPNTSLPP-------------SILEDSLENNEGVPSPML 339
Query: 443 SVCGGCLALLDAGV-------PISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFK 495
S+ + V P + V I+ L+ G +
Sbjct: 340 SISNLTQEQVQDYVNKTNSHLPAGKQVE-IS--LV------------------NGAKNLV 378
Query: 496 VAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPR 555
V+G +LY GL+ L K K AP
Sbjct: 379 VSGPP---------------------QSLY----GLNLTLRKAK-------------APS 400
Query: 556 LITIKIDPSKI----RDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKR 611
+D S+I R + + R L + + F+S A
Sbjct: 401 ----GLDQSRIPFSERKLKF----SNRFLP--------------VA-SPFHSHLLVPASD 437
Query: 612 RIEK--LTESVQIGKVYTGI-VLRLFDFGAIIRILSGKDGLLHISQISSKRVN------- 661
I K + +V I V FD G+ +R+LSG + I V
Sbjct: 438 LINKDLVKNNVSFNAKDIQIPVYDTFD-GSDLRVLSGSISERIVDCIIRLPVKWETTTQF 496
Query: 662 ----IITDF--------------LKENQKVRVKVLGIDDRGR 685
I+ DF K+ VRV V G D
Sbjct: 497 KATHIL-DFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINP 537
Score = 50.4 bits (120), Expect = 2e-06
Identities = 102/628 (16%), Positives = 178/628 (28%), Gaps = 228/628 (36%)
Query: 4 FILKSFKYGSYKISIEI-------GEIAR--------QATSSVLVSIEDTVI-------L 41
L +GS + + + + + T E T L
Sbjct: 9 LTLS---HGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFL 65
Query: 42 ATVVSCKDPTSTYNFFP---LTVDYIEKAY--------AAGRIPGSFFKREGKPSERETI 90
V S +P+ F L + E Y A ++ + + + +
Sbjct: 66 GYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQE---NDTTLVKTKEL 122
Query: 91 I------SRLIDRPIRP-----LF-------------------PEGYLNEIQIV--VYVL 118
I + RP LF + Y E++ + Y +
Sbjct: 123 IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHV 182
Query: 119 SVNPQIDP-----------------------DIAS-IIGVSTALSISEL---PFLGPL-G 150
V I +I + S L P PL G
Sbjct: 183 LVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIG 242
Query: 151 VAKVG-YIDGKYILNPTTEQLKKS------HLDLLVAGTEKAIITVESESKQLPEDIILN 203
V ++ Y+ +L T +L+ H LV A+ E++S + +
Sbjct: 243 VIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVT----AVAIAETDSWESFFVSVRK 298
Query: 204 AI--IF-----GHE---KMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKIINISEHK 253
AI +F +E + + + + ++N + P + + I N+++ +
Sbjct: 299 AITVLFFIGVRCYEAYPNTSLPPSILEDSLEN-NEGV----P-----SPMLSISNLTQEQ 348
Query: 254 IRKAYQIKNKQIRDLTFKNISKDIYSSLI---DNENLT---IDINDINCILYDLESKIIR 307
++ N + K + SL+ N ++ LY L +R
Sbjct: 349 VQDYVNKTNSHLPA------GKQVEISLVNGAKNLVVSGPPQS-------LYGLNLT-LR 394
Query: 308 KQILDKGL---RIDNRGVNDIRPISIRTGILPRT---HGSSLFTRGDTQALVVATLGTSR 361
K GL RI R + LP H S L L +
Sbjct: 395 KAKAPSGLDQSRIPFSE----RKLKFSNRFLPVASPFH-SHL-------------LVPAS 436
Query: 362 DEQKIDALMGEFT-DSFMLHYNMPPFATGDIGRIGVPKRREIGHG-RLAKRALLPVLPNN 419
D D + + ++ + +P + T D G R+ ++
Sbjct: 437 DLINKDLVKNNVSFNAKDIQ--IPVYDTFD------------GSDLRVLSGSISE----- 477
Query: 420 NKFNYSIRLVSEITES-----NGSSSMASVCGGCLALLDAGVPISEHVAGIAMGL----- 469
R+V I + A+ +LD G P G A GL
Sbjct: 478 -------RIVDCIIRLPVKWETTTQFKAT------HILDFG-P------GGASGLGVLTH 517
Query: 470 -IKDGEKV-VILSDILGDEDRCGDMDFK 495
KDG V VI++ L D + D FK
Sbjct: 518 RNKDGTGVRVIVAGTL-DINPDDDYGFK 544
Score = 42.3 bits (99), Expect = 6e-04
Identities = 48/319 (15%), Positives = 97/319 (30%), Gaps = 121/319 (37%)
Query: 370 MGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLV 429
MG M Y A +++ RA + + +SI
Sbjct: 1631 MG------MDLYKTSKAA------------QDV-----WNRADNHFK---DTYGFSI--- 1661
Query: 430 SEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDG----EKVV-----ILS 480
+I +N + + GG + G I E+ + + I DG EK+ +
Sbjct: 1662 LDIVINNPVN-LTIHFGG-----EKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHST 1715
Query: 481 DIL--GDEDRCGDMDFKVAGTVN---GITALQM----DIKIFGITYDIIQIALYKAKKGL 531
++ T +T ++ D+K G+ I A G
Sbjct: 1716 SYTFRSEKGLLSA-------TQFTQPALTLMEKAAFEDLKSKGL----IPADATFA--GH 1762
Query: 532 S---Y-----------------ILEK----MKTEVPKCKNELSKFAPRLITIKIDPSKIR 567
S Y ++ M+ VP+ + S + I I+P ++
Sbjct: 1763 SLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYG----MIAINPGRV- 1817
Query: 568 DVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNS------VSGQ-EA----------- 609
++ + E G + ++ I ++N +G A
Sbjct: 1818 -AASFSQEALQYVVERVGKRTG----WLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFI 1872
Query: 610 -KRRIE--KLTESVQIGKV 625
++I+ +L +S+ + +V
Sbjct: 1873 KLQKIDIIELQKSLSLEEV 1891
Score = 42.3 bits (99), Expect = 6e-04
Identities = 43/276 (15%), Positives = 87/276 (31%), Gaps = 78/276 (28%)
Query: 11 YGSYKISIEIGEIARQATSSVL-VSIEDTVILATVVSCKDPTS-TYNFFPLTVDYIEKAY 68
Y + K + ++ A SI D VI +P + T +F I + Y
Sbjct: 1636 YKTSKAAQDVWNRADNHFKDTYGFSILDIVI-------NNPVNLTIHFGGEKGKRIRENY 1688
Query: 69 AAGRIPGSFFKREGKPSER---ETIISRLIDRPIRPLF--PEGYLN--EI-QIVVYVLSV 120
+A E + E I + + F +G L+ + Q + ++
Sbjct: 1689 SA-------MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEK 1741
Query: 121 -------NPQIDPDIASIIGVS----TAL-SISE-LPF-------------------LGP 148
+ + P A+ G S AL S+++ +
Sbjct: 1742 AAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDE 1801
Query: 149 LGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKAIITVESESKQLPEDII-LNA--- 204
LG + G I +NP + + + V + L E I+ N
Sbjct: 1802 LGRSNYGMIA----INPG-----RVAASFSQEALQYVVERVGKRTGWLVE-IVNYNVENQ 1851
Query: 205 --IIFGHEKMKIAINAINELVQNVGQKKVNWDPIVK 238
+ G + A++ + ++ + +K+ I++
Sbjct: 1852 QYVAAGDLR---ALDTVTNVLNFIKLQKI---DIIE 1881
Score = 31.9 bits (72), Expect = 0.79
Identities = 48/299 (16%), Positives = 80/299 (26%), Gaps = 129/299 (43%)
Query: 224 QNVG-----------QKKVNWD---------------PIVKD--KTLISKIINISEHKIR 255
Q G + V W+ IV + L +IR
Sbjct: 1627 QEQGMGMDLYKTSKAAQDV-WNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIR 1685
Query: 256 KAY-----------QIKNKQIRDLTFKNISKDIYSSLIDNE--NLTIDINDIN---CILY 299
+ Y ++K ++I ++ + + S + + T +
Sbjct: 1686 ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRS--EKGLLSATQ-----FTQPALT- 1737
Query: 300 DLESKIIRKQILDKGLRIDNR-----------------GVNDIRPISIRTGI-LPRTHGS 341
L K + + KGL + V +SI + + +
Sbjct: 1738 -LMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADV-----MSIESLVEV------ 1785
Query: 342 SLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRRE 401
+F RG T + V RDE +Y M + GR+ +E
Sbjct: 1786 -VFYRGMTMQVAVP-----RDELG------------RSNYGM---IAINPGRVAASFSQE 1824
Query: 402 IGHG---RLAKRA--LL-PVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDA 454
R+ KR L+ V NY N + V G L LD
Sbjct: 1825 ALQYVVERVGKRTGWLVEIV-------NY-----------N-VENQQYVAAGDLRALDT 1864
>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 94
Score = 53.6 bits (129), Expect = 3e-09
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI----NDEGIITIASFNSVSGQEAKRR 612
T+ I R VIGK G ++ L +T T+I I + I I ++A+
Sbjct: 19 ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITG-TKEGIEKARHE 77
Query: 613 IEKLTE 618
+ ++
Sbjct: 78 VLLISA 83
>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 104
Score = 52.9 bits (127), Expect = 6e-09
Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 5/80 (6%)
Query: 546 KNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG----IITIASF 601
K L P I +++ R VIG+ GS IR + +E I + II I
Sbjct: 8 KEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITG- 66
Query: 602 NSVSGQEAKRRIEKLTESVQ 621
+ + AK + + + +Q
Sbjct: 67 LAANLDRAKAGLLERVKELQ 86
>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA,
exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A
{Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A
Length = 179
Score = 53.5 bits (128), Expect = 2e-08
Identities = 25/126 (19%), Positives = 52/126 (41%), Gaps = 12/126 (9%)
Query: 574 GSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTE--SVQIGKVYTGIVL 631
G I + E + + G + A + ++ ++E ++ + G V G V+
Sbjct: 7 GDRIGSAEEYVKGEGVYEEGGELFAAVAGKLIIKDRVAKVESISPIPEIVKGDVVLGRVV 66
Query: 632 RLFDFGAIIRILSGKD----------GLLHISQISSKRVNIITDFLKENQKVRVKVLGID 681
L + A+I + S K G+LH+S + V I++ + ++ +V+G +
Sbjct: 67 DLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIGDN 126
Query: 682 DRGRIK 687
R K
Sbjct: 127 LRLSTK 132
>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 97
Score = 50.2 bits (120), Expect = 6e-08
Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 8/72 (11%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG-------IITIASFNSVSGQEA 609
+++ +DP +IG+ G+ I + E I D+ ITI + + A
Sbjct: 19 LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITG-YEKNTEAA 77
Query: 610 KRRIEKLTESVQ 621
+ I ++ ++
Sbjct: 78 RDAILRIVGELE 89
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 106
Score = 48.6 bits (116), Expect = 2e-07
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 9/72 (12%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI------NDEGIITIA-SFNSVSGQEA 609
I + + + VIG+ G I+ + + G +I E I I + + A
Sbjct: 13 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRC--EHA 70
Query: 610 KRRIEKLTESVQ 621
R I L +S++
Sbjct: 71 ARIINDLLQSLR 82
>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA
binding protein, KH domain, KSRP, posttranscriptional
regulation, mRNA decay; NMR {Homo sapiens}
Length = 164
Score = 49.4 bits (118), Expect = 4e-07
Identities = 22/108 (20%), Positives = 41/108 (37%), Gaps = 9/108 (8%)
Query: 523 ALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTE 582
+ +A + + IL + +NE I + + + VIG+ G I+ +
Sbjct: 59 KVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQN 118
Query: 583 ETGTQIDI------NDEGIITIA-SFNSVSGQEAKRRIEKLTESVQIG 623
+ G +I E I I + + A R I L +S++ G
Sbjct: 119 DAGVRIQFKQDDGTGPEKIAHIMGPPDRC--EHAARIINDLLQSLRSG 164
Score = 40.9 bits (96), Expect = 3e-04
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG 594
I I K VIGKGG TI+ L E G ++ + +G
Sbjct: 4 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG 41
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens}
SCOP: d.51.1.1 PDB: 1vih_A
Length = 71
Score = 46.2 bits (110), Expect = 7e-07
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG----IITIASFNSVSGQEAKRR 612
+ I ID R +IGK G+ I + ++ + I + +I I + Q+AKR
Sbjct: 7 VEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEG-DPQGVQQAKRE 65
Query: 613 IEKL 616
+ +L
Sbjct: 66 LLEL 69
>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 95
Score = 46.7 bits (111), Expect = 8e-07
Identities = 16/71 (22%), Positives = 25/71 (35%), Gaps = 8/71 (11%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI-----NDEGIITIA-SFNSVSGQEAK 610
+ +D +IG G IR + +E I D +T+ +V +EA
Sbjct: 19 EDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENV--EEAI 76
Query: 611 RRIEKLTESVQ 621
I L E
Sbjct: 77 DHILNLEEEYL 87
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo
sapiens}
Length = 85
Score = 46.2 bits (110), Expect = 1e-06
Identities = 19/69 (27%), Positives = 28/69 (40%), Gaps = 11/69 (15%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI--------NDEGIITIA-SFNSVSGQ 607
I I K VIGKGG TI+ L E G ++ + N + + I V Q
Sbjct: 16 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKV--Q 73
Query: 608 EAKRRIEKL 616
+A + +
Sbjct: 74 QACEMVMDI 82
>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase,
transcription; 1.75A {Methanococcus jannaschii} SCOP:
b.40.4.5 d.230.1.1
Length = 187
Score = 48.0 bits (114), Expect = 2e-06
Identities = 28/159 (17%), Positives = 58/159 (36%), Gaps = 29/159 (18%)
Query: 558 TIKIDPSKI-RDVIGKGGSTIRTLTEETGTQ--------IDINDEGIITIASFNSVSGQE 608
+K+ P + +D+ + E + +D+ D G + + +
Sbjct: 10 VVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHP 69
Query: 609 AKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNII----- 663
++ ++ G V+ + +FG+ +R L DGL+H+SQI V+
Sbjct: 70 VVFETLVY--IPEMYELIEGEVVDVVEFGSFVR-LGPLDGLIHVSQIMDDYVSYDPKREA 126
Query: 664 ------TDFLKENQKVRVKVLGIDDRGR------IKLSM 690
L+ VR +++ I + I L+M
Sbjct: 127 IIGKETGKVLEIGDYVRARIVAISLKAERKRGSKIALTM 165
>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein,
cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum
pernix} SCOP: b.40.4.5 d.51.1.1
Length = 235
Score = 47.4 bits (112), Expect = 5e-06
Identities = 21/91 (23%), Positives = 39/91 (42%)
Query: 533 YILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND 592
+K ++ + + E R ++I P+K+ VIG+ S ++TL E+T +I +
Sbjct: 126 VAFDKTRSPLLTVQGEGLGRIVRGKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR 185
Query: 593 EGIITIASFNSVSGQEAKRRIEKLTESVQIG 623
G I + N A I+ + E
Sbjct: 186 NGRIHLECPNEDLEAIAVMAIKIIDEEAYTS 216
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 107
Score = 44.9 bits (106), Expect = 6e-06
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 13/78 (16%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG---------IITIA-SFNSVSG 606
+T I K VIG+GG ++ + ++TG ++I+ + + I S +
Sbjct: 9 MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQI-- 66
Query: 607 QEAKRRI-EKLTESVQIG 623
AK+ I EK+ +
Sbjct: 67 DHAKQLIEEKIEGPLCPV 84
>1x4m_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.51.1.1
Length = 94
Score = 43.9 bits (104), Expect = 9e-06
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG 594
I I SK VIGKGG TI+ L E G ++ + +G
Sbjct: 17 QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG 54
>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain,
cell projection, cytoplasm, nucleus, phosphoprotein,
translation regulation; 2.75A {Homo sapiens}
Length = 163
Score = 44.8 bits (106), Expect = 1e-05
Identities = 26/136 (19%), Positives = 51/136 (37%), Gaps = 15/136 (11%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG-------IITI-ASFNSVSGQE 608
+ + I + +IGK G I+ L+ I I ++ I + +
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQ--FK 62
Query: 609 AKRRIEKL--TESVQIGKVYTGIVLRLFDFGAIIRILSGKDG--LLHISQISSKRVNIIT 664
A+ RI E+ K + + + + GK G + + +++ V +
Sbjct: 63 AQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 122
Query: 665 DFL-KENQKVRVKVLG 679
D EN +V VK++G
Sbjct: 123 DQTPDENDQVIVKIIG 138
>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding,
DNA-binding, nucleus, phosph ribonucleoprotein,
RNA-binding, RNA binding protein; NMR {Homo sapiens}
Length = 160
Score = 44.8 bits (106), Expect = 1e-05
Identities = 29/135 (21%), Positives = 58/135 (42%), Gaps = 16/135 (11%)
Query: 559 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND----EGIITI-ASFNSVSGQEAKRRI 613
+ + ++ +IGK G +++ + EE+G +I+I++ E IIT+ N++ +A I
Sbjct: 9 LLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAI--FKAFAMI 66
Query: 614 EKLTESVQIGKVYTG-------IVLRLFDFGAIIRILSGKDGLL--HISQISSKRVNIIT 664
E + + LRL + L GK G I + + +V +
Sbjct: 67 IDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG 126
Query: 665 DFLKENQKVRVKVLG 679
D L + + + + G
Sbjct: 127 DMLPNSTERAITIAG 141
Score = 42.1 bits (99), Expect = 1e-04
Identities = 24/104 (23%), Positives = 49/104 (47%), Gaps = 13/104 (12%)
Query: 527 AKKGLSYILEKMKTEVPKCKNELSKFAPRLITIK--IDPSKIRDVIGKGGSTIRTLTEET 584
K + I++K++ ++ + + +T++ + S+ +IGKGG I+ + E T
Sbjct: 59 IFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIREST 118
Query: 585 GTQIDI-------NDEGIITIA-SFNSVSGQEAKRRI-EKLTES 619
G Q+ + + E ITIA S+ E ++I + E+
Sbjct: 119 GAQVQVAGDMLPNSTERAITIAGIPQSI--IECVKQICVVMLET 160
>1x4n_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.51.1.1 PDB: 2opu_A
Length = 92
Score = 42.8 bits (101), Expect = 2e-05
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG------IITIA-SFNSVSGQEA 609
K+ + +IG+GG I + +E+G +I I + + + SV Q A
Sbjct: 17 EEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESV--QSA 74
Query: 610 KRRIEKLTESVQIG 623
KR ++++ E + G
Sbjct: 75 KRLLDQIVEKGRSG 88
>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA
binding protein, transcription factor, hnRNP K, CT
element, C-MYC oncogene; NMR {Homo sapiens} SCOP:
d.51.1.1 PDB: 1khm_A
Length = 89
Score = 42.3 bits (100), Expect = 2e-05
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND------EGIITIA-SFNSVSGQEA 609
+ I +IGKGG I+ + E+G I I++ + IITI + + + Q A
Sbjct: 16 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQI--QNA 73
Query: 610 KRRIEKL 616
+ ++
Sbjct: 74 QYLLQNS 80
>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta
fold, DNA binding protein; 0.95A {Homo sapiens} SCOP:
d.51.1.1 PDB: 1zzj_A 1zzi_A
Length = 82
Score = 40.7 bits (96), Expect = 7e-05
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND------EGIITIA-SFNSVSGQEA 609
+ I +IGKGG I+ + E+G I I++ + IITI + + + Q A
Sbjct: 9 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQI--QNA 66
Query: 610 KRRIEKL 616
+ ++
Sbjct: 67 QYLLQNS 73
>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding
motif, protein/RNA structure, RNA binding protein/RNA
complex; 2.40A {Homo sapiens} SCOP: d.51.1.1
Length = 87
Score = 40.8 bits (96), Expect = 9e-05
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 12/75 (16%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG---------IITIA-SFNSVSG 606
+ I + + + ++GKGG T+ E TG +I I+ +G +TI S +
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT-- 62
Query: 607 QEAKRRIEKLTESVQ 621
Q A+ I + Q
Sbjct: 63 QAAQYLISQRVTYEQ 77
>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain,
alpha-beta fold RNA-binding motif, immune system; 2.00A
{Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A
Length = 76
Score = 40.3 bits (95), Expect = 1e-04
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG 594
+ + + + + ++GKGG T+ E TG +I I+ +G
Sbjct: 5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKG 42
>2dgr_A Ring finger and KH domain-containing protein 1; structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 83
Score = 40.3 bits (94), Expect = 1e-04
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI---NDEGIITIASFNSVSGQEAKRRI 613
I +++ + V+G G+TI+ + + T T I + E + + + + A+ I
Sbjct: 12 IQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAV-TGMPENVDRAREEI 70
Query: 614 E 614
E
Sbjct: 71 E 71
>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding
protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1
PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*
Length = 73
Score = 39.6 bits (93), Expect = 2e-04
Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 10/70 (14%)
Query: 557 ITIKI--DPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG----IITI-ASFNSVSGQEA 609
+TI++ ++ +IGK G +++ + EE+G +I+I++ IIT+ N++ +A
Sbjct: 5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAI--FKA 62
Query: 610 KRRI-EKLTE 618
I +KL E
Sbjct: 63 FAMIIDKLEE 72
>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA
binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1
Length = 82
Score = 39.6 bits (93), Expect = 2e-04
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG------IITIA-SFNSVSGQEA 609
+ I + I +IG+ G+ I + + +G QI I + +TI S S+ A
Sbjct: 8 HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASI--SLA 65
Query: 610 KRRIE 614
+ I
Sbjct: 66 QYLIN 70
>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 = 43.7 bits (102), Expect = 2e-04
Identities = 40/331 (12%), Positives = 88/331 (26%), Gaps = 103/331 (31%)
Query: 401 EIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISE 460
E G + + +L V + N+ + V ++ +S L + +
Sbjct: 10 ETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKS--------------ILSKEEI---D 52
Query: 461 HVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDII 520
H+ + + L L + F V L+++ Y +
Sbjct: 53 HI----IMSKDAVSGTLRLFWTLLSKQEEMVQKF-----VE--EVLRIN-------YKFL 94
Query: 521 QIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVI---------- 570
+ ++ S + + + N+ FA ++ K+R +
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL 154
Query: 571 --GKGGSTIRTLTEETGTQIDI---NDEGI--ITIASFNS-------------------V 604
G GS + + + D I + + + NS
Sbjct: 155 IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214
Query: 605 SGQEAKRRIEKLTESVQIGK------------------VYTGIVLRLFDFGAIIRILSGK 646
S + I+ S+Q V F+ +IL
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC--KIL--- 269
Query: 647 DGLLHISQISSKRVNIITDFLKENQKVRVKV 677
++++ +TDFL + +
Sbjct: 270 --------LTTRFKQ-VTDFLSAATTTHISL 291
Score = 43.3 bits (101), Expect = 2e-04
Identities = 67/550 (12%), Positives = 163/550 (29%), Gaps = 162/550 (29%)
Query: 156 YIDGKYILNPTTEQLKKSHLDLLVAGTEKAIITVESESKQL-PEDIILNAIIFGHEKMK- 213
YI+ + L + K ++ + + + +L P + +I G +
Sbjct: 112 YIEQRDRLYNDNQVFAKYNVS-----RLQPYLKLRQALLELRPAKNV---LIDG---VLG 160
Query: 214 -----IAINAI-NELVQNVGQKKVNWDPIVKDKTLISKIINISEHKIRKAYQIKNKQIRD 267
+A++ + VQ K+ W +N+ + ++ Q
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFW-------------LNLKNCNSPET-VLEMLQ--K 204
Query: 268 LTFKNISKDIYSSLIDN-ENLTIDINDINCILYDLESKIIRKQILDKGLRI-DNRGVNDI 325
L ++ I + ++S D+ N+ + I+ I L ++++ + + L + N V +
Sbjct: 205 LLYQ-IDPN-WTSRSDHSSNIKLRIHSIQAEL----RRLLKSKPYENCLLVLLN--VQNA 256
Query: 326 RPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPP 385
+ + F + L T+R +Q D L T L ++
Sbjct: 257 KAWN-------------AF---NLSC---KILLTTRFKQVTDFLSAATTTHISLDHHSMT 297
Query: 386 FATGDIGRIGVPKRREIGHGRLAKRALLPV--LPNNNKFNYSIRLVSEITES-------- 435
+ + + L K LP + R +S I ES
Sbjct: 298 LTP--------DEVKSL----LLKYLDCRPQDLPREVL-TTNPRRLSIIAESIRDGLATW 344
Query: 436 -----NGSSSMASVCGGCLALLDA---------------GVPISEHVAGIAMGLIKDGEK 475
+ ++ L +L+ I + + + +
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDV 404
Query: 476 VVILSDI----LGDEDRCG------DMDFKVAGTVNGITALQMDIKIFGIT-YDIIQ--- 521
+V+++ + L ++ + ++ + AL I + Y+I +
Sbjct: 405 MVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI----VDHYNIPKTFD 460
Query: 522 ----------------IA--LYKAKKG------------LSYILEKMKTEVPKCKNELSK 551
I L + ++ +K++ + N
Sbjct: 461 SDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAW-NASGS 519
Query: 552 FAPRLITIKIDPSKIRDVIGKGGSTIRTLTE---ETGTQIDINDE-GIITIASFNSVSG- 606
L +K I D K + + + + + + ++ IA
Sbjct: 520 ILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAI 579
Query: 607 -QEAKRRIEK 615
+EA +++++
Sbjct: 580 FEEAHKQVQR 589
Score = 30.2 bits (67), Expect = 3.2
Identities = 28/213 (13%), Positives = 64/213 (30%), Gaps = 59/213 (27%)
Query: 72 RIPGSFFKREGKPSERETIISRLIDR--PIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIA 129
IP + + + K + ++D + + + P +D
Sbjct: 427 SIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLI------------PPYLDQYFY 474
Query: 130 SIIG-----VSTALSISELP--FLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGT 182
S IG + ++ FL +++ K + T S L+ L
Sbjct: 475 SHIGHHLKNIEHPERMTLFRMVFL------DFRFLEQKIRHDSTAWNASGSILNTL---- 524
Query: 183 EKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTL 242
++ I N K + +NAI + + + + +
Sbjct: 525 ----QQLKFYKPY----ICDN-----DPKYERLVNAILDFLPKIEE-----------NLI 560
Query: 243 ISKIINISEHKIRKAYQIKNKQIRDLTFKNISK 275
SK ++ +R A +++ I + K + +
Sbjct: 561 CSKYTDL----LRIALMAEDEAIFEEAHKQVQR 589
>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E
4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E
Length = 180
Score = 41.4 bits (97), Expect = 2e-04
Identities = 31/158 (19%), Positives = 63/158 (39%), Gaps = 28/158 (17%)
Query: 558 TIKIDPSKIRDVIGK------GGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEA-- 609
++I P++ + + + ++ G + I + + T V G A
Sbjct: 10 IVRIPPNEFGKPLNEIALNELRQQYQEKILKDLGLVLAILN--VKTSEEGMLVFGDGATY 67
Query: 610 -KRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIIT---- 664
+ + +T + +V G VL++ ++G + L DGL+HISQI+ +
Sbjct: 68 HEVEFDMITYVPVVQEVVEGEVLQVDNYGVFVN-LGPMDGLVHISQITDDTLKYDNVRGI 126
Query: 665 -------DFLKENQKVRVKVLGIDD-----RGRIKLSM 690
+++ KVR +V+ + RI L+M
Sbjct: 127 IFGEKSKKVIQKGDKVRARVISVASTVTGRLPRIALTM 164
>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing
factor, RNA binding protein; 2.30A {Pyrococcus
horikoshii} PDB: 3aev_B
Length = 219
Score = 42.0 bits (98), Expect = 3e-04
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 563 PSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQI 622
P +IG+ G T + + E +G + + + + I + + + AK IEKL
Sbjct: 137 PRVRGRIIGRKGRTRQIIEEMSGASVSVYGKTVAIIGNPIQI--EIAKTAIEKLARGSPH 194
Query: 623 GKVY 626
G VY
Sbjct: 195 GSVY 198
Score = 40.1 bits (93), Expect = 0.001
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 541 EVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITI 598
E+ + ++E +F + +KI +I +IGK G T + + + T T+I I+ + G + I
Sbjct: 20 EIVEDEDEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWI 78
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA
binding protein/DNA complex; 1.60A {Homo sapiens}
Length = 76
Score = 37.7 bits (88), Expect = 7e-04
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 9/70 (12%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND------EGIITIA-SFNSVSGQEA 609
+ I I +IG+ G+ I + + +G QI I + + +TI S S+ A
Sbjct: 7 HELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASI--SLA 64
Query: 610 KRRIEKLTES 619
+ I S
Sbjct: 65 QYLINVRLSS 74
>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET:
DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1
Length = 174
Score = 39.8 bits (93), Expect = 0.001
Identities = 19/72 (26%), Positives = 27/72 (37%), Gaps = 9/72 (12%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI------NDEGIITI-ASFNSVSGQEA 609
I + I + VIG+ G I+ + + G +I E I I + Q A
Sbjct: 5 IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRA--QHA 62
Query: 610 KRRIEKLTESVQ 621
I L SVQ
Sbjct: 63 AEIITDLLRSVQ 74
Score = 35.6 bits (82), Expect = 0.021
Identities = 10/38 (26%), Positives = 22/38 (57%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG 594
+ K +IGKGG TI+++++++G +I++
Sbjct: 106 FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP 143
>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH
domain, hairpin, RNA-binding protein complex; HET: 5BU;
1.94A {Homo sapiens} PDB: 2ann_A*
Length = 178
Score = 39.8 bits (93), Expect = 0.001
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG 594
+ + I +IGKGG TI L +ETG I ++
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSK 45
Score = 38.7 bits (90), Expect = 0.002
Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 12/75 (16%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI--------NDEGIITIA-SFNSVSGQ 607
+ I + S +IGKGG+T++ + E++G + + ++T++ +
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQN--R 163
Query: 608 EAKRRI-EKLTESVQ 621
+A I +K+ E Q
Sbjct: 164 KAVELIIQKIQEDPQ 178
>1tua_A Hypothetical protein APE0754; structural genomics, protein
structure initiative, MCSG, four layers alpha-beta
sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1
d.51.1.1
Length = 191
Score = 39.6 bits (92), Expect = 0.001
Identities = 10/43 (23%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 559 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITIAS 600
+K+ P ++ VIG G + TGT I ++ + ++ +
Sbjct: 8 VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEP 50
Score = 39.6 bits (92), Expect = 0.001
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 569 VIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 626
+IG+GG RT+ E T T I++ + + I + AK+ IE L E VY
Sbjct: 112 IIGEGGRARRTIEEMTDTYINVGEYEVAIIGDYERA--MAAKQAIEMLAEGRMHSTVY 167
>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 95
Score = 37.1 bits (86), Expect = 0.002
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEE-TGTQIDINDEG----IITIA-SFNSVSGQEAK 610
+ + I +IG G IR++ EE G I EG + I + V ++AK
Sbjct: 19 VEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDV--EKAK 76
Query: 611 RRIEKLTESVQ 621
+++ L E Q
Sbjct: 77 KQLLHLAEEKQ 87
>3go5_A Multidomain protein with S1 RNA-binding domains; structural
genomics, joint center for structural genomics, JCSG;
HET: MSE; 1.40A {Streptococcus pneumoniae}
Length = 285
Score = 39.9 bits (93), Expect = 0.002
Identities = 16/92 (17%), Positives = 37/92 (40%), Gaps = 10/92 (10%)
Query: 601 FNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGK-DGLLHISQISSKR 659
+ ++ QE +R+ + + + + IV RL G + + G +H S+ ++
Sbjct: 131 WGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERYAE- 189
Query: 660 VNIITDFLKENQKVRVKVLGID-DRGRIKLSM 690
+ Q + +V+G + LS+
Sbjct: 190 -------PRLGQVLDARVIGFREVDRTLNLSL 214
Score = 34.9 bits (80), Expect = 0.061
Identities = 14/88 (15%), Positives = 36/88 (40%), Gaps = 7/88 (7%)
Query: 607 QEAKRRIEKLTESVQIGKVYTGIVLRLF-DFGAIIRI-LSGKDGLLHISQISSKRVNIIT 664
+ K R+ L + + G V + D G + L K+ ++ + + +
Sbjct: 54 MKQKLRLTTLEVTATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKEL--- 110
Query: 665 DFLKENQKVRVKVLGIDDRGRIKLSMIY 692
+ K+ ++ +++ +D + RI + Y
Sbjct: 111 -WPKKGDQLYIRLE-VDKKDRIWGLLAY 136
Score = 31.8 bits (72), Expect = 0.68
Identities = 7/72 (9%), Positives = 22/72 (30%), Gaps = 12/72 (16%)
Query: 619 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 678
+ + G+++ D ++ G+ L + V+
Sbjct: 3 NTNLASFIVGLIIDENDRFYFVQK-DGQTYALAKEEGQ----------HTVGDTVKGFAY 51
Query: 679 GIDDRGRIKLSM 690
D + +++L+
Sbjct: 52 -TDMKQKLRLTT 62
>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 = 39.6 bits (93), Expect = 0.003
Identities = 14/105 (13%), Positives = 35/105 (33%), Gaps = 19/105 (18%)
Query: 593 EGIITIASFNSVSGQEAKRRIEKLTESV----QIGKVYTGIVLRLFDFGAIIRILS-GKD 647
I + N+ + ++A+R + Q +V+ +V+ A + I D
Sbjct: 370 AAHIAESQMNADATRQAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFD 429
Query: 648 GLLHISQISSKRVNIITDFLKENQKVRVKVLGID-DRGRIKLSMI 691
++ ++V+ ID + R++ +
Sbjct: 430 VQVNTP-------------AAPGTALQVQFADIDLPQMRVRARSV 461
>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 102
Score = 36.4 bits (84), Expect = 0.004
Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 5/68 (7%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEE-TGTQIDIND-EGIITIA-SFNSVSGQEAKRRI 613
++ R +IGK G + +T++ I+ + E IT+ V A+ +I
Sbjct: 29 SSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKITLEGPTEDV--SVAQEQI 86
Query: 614 EKLTESVQ 621
E + + +
Sbjct: 87 EGMVKDLI 94
>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform
B'; KH domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.51.1.1
Length = 91
Score = 35.8 bits (82), Expect = 0.005
Identities = 13/66 (19%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 559 IKIDPSKIRDVIGKGGSTIRTLTEETG-TQIDINDE-GIITIASFNSVSGQEAKRRIEKL 616
+ + IG GS I+ + G T I+++++ G I ++ + ++A+ +E +
Sbjct: 19 FVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLEFV 78
Query: 617 TESVQI 622
+ +Q+
Sbjct: 79 EDFIQV 84
>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics,
riken structural genomics/proteomics initiative, RSGI,
unknown function; NMR {Homo sapiens} SCOP: b.40.4.5
Length = 119
Score = 35.4 bits (81), Expect = 0.015
Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 3/76 (3%)
Query: 618 ESVQIGKVYTGIVLRLFDFGAIIRI-LSGKDGLLHISQISS-KRVNIITDFLKENQKVRV 675
E+++ G + TG V L D G ++ I + G L + + R LK Q +
Sbjct: 17 EALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNC 76
Query: 676 KVLGID-DRGRIKLSM 690
V + + G + LS+
Sbjct: 77 IVEKVKGNGGVVSLSV 92
>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA
binding, cell cycle; 2.79A {Caenorhabditis elegans}
Length = 376
Score = 33.8 bits (76), Expect = 0.19
Identities = 12/103 (11%), Positives = 35/103 (33%), Gaps = 15/103 (14%)
Query: 530 GLSYILEKMKTEVP-KCKNELSKFAPRLITIKIDPSKI--RDVIGKGG--STIRTLTEET 584
+++I + +P + + P +T+ ++ + G + ++ ET
Sbjct: 2 AMAHIHQLKAQGLPLPSNIPMIEINPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAET 61
Query: 585 GTQIDINDEGIITIASFN-----SVSG-----QEAKRRIEKLT 617
T I + D + +++G A+ + +
Sbjct: 62 NTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNC 104
>3aqq_A Calcium-regulated heat stable protein 1; compact beta-barrel, cold
shock domain, ssDNA binding, DNA B protein; 2.80A {Homo
sapiens}
Length = 147
Score = 32.3 bits (73), Expect = 0.24
Identities = 20/78 (25%), Positives = 27/78 (34%), Gaps = 11/78 (14%)
Query: 612 RIEKLTESVQIGKVYTGIVLRLFD----FGAIIRILSGKDGLLHISQISSKRVNIITDFL 667
R T G VY G+ + F G I G D LHIS + + V
Sbjct: 49 RTFSATVRASQGPVYKGVC-KCFCRSKGHGFITPADGGPDIFLHISDVEGEYV------P 101
Query: 668 KENQKVRVKVLGIDDRGR 685
E +V K+ I +
Sbjct: 102 VEGDEVTYKMCSIPPKNE 119
>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 119
Score = 31.4 bits (71), Expect = 0.34
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 16/72 (22%)
Query: 566 IRDVIGKGGSTIRTLTEETGTQIDINDEGI----------------ITIASFNSVSGQEA 609
V G G S ++ + ETG ++ + +G I I+ A
Sbjct: 30 KEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA 89
Query: 610 KRRIEKLTESVQ 621
K+ E L ++V
Sbjct: 90 KKLCENLLQTVH 101
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.7 bits (68), Expect = 0.83
Identities = 7/35 (20%), Positives = 13/35 (37%), Gaps = 10/35 (28%)
Query: 539 KTEVPKCKNELSKFAPRLITIKID--PS-KIRDVI 570
K + K + L +A D P+ I+ +
Sbjct: 19 KQALKKLQASLKLYAD-------DSAPALAIKATM 46
Score = 29.9 bits (66), Expect = 1.6
Identities = 6/17 (35%), Positives = 11/17 (64%), Gaps = 3/17 (17%)
Query: 610 KRRIEKLTESVQIGKVY 626
K+ ++KL S+ K+Y
Sbjct: 19 KQALKKLQASL---KLY 32
>3u5c_D RP13, YS3, 40S ribosomal protein S3; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_B 3o30_C 3o2z_C 3u5g_D 1s1h_C
3jyv_C*
Length = 240
Score = 29.3 bits (66), Expect = 3.1
Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 7/50 (14%)
Query: 553 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE-------TGTQIDINDEGI 595
P + I ++ +DV+G+ G I LT I + E +
Sbjct: 42 TPTKTEVIIRATRTQDVLGENGRRINELTLLVQKRFKYAPGTIVLYAERV 91
>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide;
multiprotein complex, nucleotidyltransferase, nuclear
protein, hypothetical protein; 3.2A {Saccharomyces
cerevisiae}
Length = 218
Score = 29.3 bits (65), Expect = 3.1
Identities = 9/73 (12%), Positives = 25/73 (34%), Gaps = 14/73 (19%)
Query: 622 IGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITD--------------FL 667
+G++ TG + + G + +L D + + + + +
Sbjct: 81 LGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYF 140
Query: 668 KENQKVRVKVLGI 680
N+K+R ++
Sbjct: 141 DVNEKIRFRIERE 153
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase,
phosphoprotein, transfe two-component regulatory system;
3.80A {Thermotoga maritima}
Length = 349
Score = 29.5 bits (67), Expect = 3.8
Identities = 8/57 (14%), Positives = 22/57 (38%), Gaps = 12/57 (21%)
Query: 551 KFAPRLITIKIDPSKIRDVI-----------GKGGS-TIRTLTEETGTQIDINDEGI 595
+ + ++ D ++I+ V+ G+ G I + T ++ + + G
Sbjct: 230 ETDNEDLRVEADRTRIKQVLINLVQNAIEATGENGKIKITSEDMYTKVRVSVWNSGP 286
>3rh7_A Hypothetical oxidoreductase; FMN-binding split barrel, nudix,
structural genomics, joint for structural genomics,
JCSG; HET: FMN; 3.00A {Sinorhizobium meliloti}
Length = 321
Score = 29.3 bits (66), Expect = 3.9
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 561 IDPSKIRDVIGK--GGSTIRTLTEETGTQIDINDEGIITIASFNSVS 605
DP +RD G G T+ T ++ G I G T SF SVS
Sbjct: 16 FDPRALRDAFGAFATGVTVVTASDAAGKPI-----GF-TANSFTSVS 56
>3a0y_A Sensor protein; ATP-LID, kinase, phosphoprotein, transferase,
two-component regulatory system; 1.57A {Thermotoga
maritima} PDB: 3a0t_A* 3a0x_A 3a0w_A 3a0z_A
Length = 152
Score = 28.3 bits (64), Expect = 4.8
Identities = 8/57 (14%), Positives = 22/57 (38%), Gaps = 12/57 (21%)
Query: 551 KFAPRLITIKIDPSKIRDVI-----------GKGGS-TIRTLTEETGTQIDINDEGI 595
+ + ++ D ++I+ V+ G+ G I + T ++ + + G
Sbjct: 33 ETDNEDLRVEADRTRIKQVLINLVQNAIEATGENGKIKITSEDMYTKVRVSVWNSGP 89
>2bh8_A 1B11; transcription, molecular evolution, unique architecture,
transcription regulation, phosphorylation; 1.9A
{Escherichia coli}
Length = 101
Score = 27.4 bits (61), Expect = 4.9
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 635 DFGAIIRILSGKDGLLHISQISSKRVN 661
DFG I + G DGL+H+S IS +
Sbjct: 74 DFGIFIGLDGGIDGLVHLSDISWAQAE 100
>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA
binding; NMR {Xenopus laevis} SCOP: d.51.1.1
Length = 140
Score = 28.0 bits (62), Expect = 5.5
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 569 VIGKGGSTIRTLTEETGTQIDINDEG 594
++G G T + L ETG +I + +G
Sbjct: 22 ILGPRGLTAKQLEAETGCKIMVRGKG 47
>2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C*
1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F*
1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C
1xmo_C* 1xmq_C* 1xnq_C* ...
Length = 239
Score = 28.4 bits (64), Expect = 6.7
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 553 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE----TGTQIDIN 591
A + + + +K VIG+GG IR L EE TG + +N
Sbjct: 60 AADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALN 102
>3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C
3i1q_C 3i1s_C 3i1z_C 3i21_C 3izv_G* 3izw_G* 3kc4_C
3or9_C 3ora_C 3sfs_C* 3uoq_C* 2qal_C* 1p6g_C 1p87_C
2aw7_C ...
Length = 233
Score = 28.3 bits (64), Expect = 8.1
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 553 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE----TGTQIDIN 591
+ I + I ++ VIGK G + L + G IN
Sbjct: 60 PAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQIN 102
>3r8n_C 30S ribosomal protein S3; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2gyb_C 2gy9_C* 2ykr_C 3fih_C* 2wwl_C 3oar_C
3oaq_C 3ofb_C 3ofa_C 3ofp_C 3ofx_C 3ofy_C 3ofo_C 3r8o_C
4a2i_C
Length = 206
Score = 27.9 bits (63), Expect = 8.5
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 553 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE----TGTQIDIN 591
+ I + I ++ VIGK G + L + G IN
Sbjct: 59 PAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQIN 101
>3iz6_B 40S ribosomal protein S3 (S3P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
1s1h_C 3jyv_C*
Length = 227
Score = 28.2 bits (63), Expect = 8.6
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 7/46 (15%)
Query: 553 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE-------TGTQIDIN 591
P I I ++ ++V+G+ G IR LT +++
Sbjct: 42 TPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFNFLENGVELY 87
>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA
recognition, complex E, KH domain, QUA2 homology; NMR
{Homo sapiens} SCOP: d.51.1.1
Length = 131
Score = 27.5 bits (61), Expect = 8.7
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 569 VIGKGGSTIRTLTEETGTQIDINDEGIIT 597
+IG G+T++ + +E +I I +G +
Sbjct: 27 LIGPRGNTLKNIEKECNAKIMIRGKGSVK 55
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 243
Score = 28.2 bits (63), Expect = 9.3
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 553 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE 583
P I I ++ ++V+G+ G IR LT
Sbjct: 42 TPTRTEIIILATRTQNVLGEKGRRIRELTAV 72
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
0.319 0.139 0.387
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 10,701,729
Number of extensions: 700107
Number of successful extensions: 1950
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1782
Number of HSP's successfully gapped: 171
Length of query: 692
Length of database: 6,701,793
Length adjustment: 100
Effective length of query: 592
Effective length of database: 3,909,693
Effective search space: 2314538256
Effective search space used: 2314538256
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 (21.7 bits)
S2: 61 (27.3 bits)