RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3754
(755 letters)
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 1115 bits (2886), Expect = 0.0
Identities = 381/694 (54%), Positives = 530/694 (76%), Gaps = 1/694 (0%)
Query: 60 KGNFLFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNF 119
K L N I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +F
Sbjct: 3 KDITLLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDF 62
Query: 120 FPLTVDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVY 179
FPLTV+Y E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++
Sbjct: 63 FPLTVNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIAT 122
Query: 180 VLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLD 239
V+SVNPQ++PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LD
Sbjct: 123 VVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLD 182
Query: 240 LLVAGTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPI 299
L+VAGTE A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P
Sbjct: 183 LVVAGTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPE 242
Query: 300 VKDKTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINC 359
++ L +++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++
Sbjct: 243 PVNEALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLA-EDETLDENELGE 301
Query: 360 ILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVAT 419
IL+ +E ++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV AT
Sbjct: 302 ILHAIEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTAT 361
Query: 420 LGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVL 479
LGT+RD Q +D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+
Sbjct: 362 LGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVM 421
Query: 480 PNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKV 539
P+ +KF Y++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+
Sbjct: 422 PDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNY 481
Query: 540 VILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILE 599
V+LSDILGDED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL
Sbjct: 482 VVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILG 541
Query: 600 KMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGII 659
M+ + + ++S+FAPR+ TIKI+P KI+DVIGKGGS IR LTEETGT I+I D+G +
Sbjct: 542 VMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDDGTV 601
Query: 660 TIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS 719
IA+ + + A RRIE++T +++G+VYTG V R+ DFGA + I GK+GL+HISQI+
Sbjct: 602 KIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIA 661
Query: 720 SKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 753
KRV +TD+L+ Q+V VKVL +D +GRI+LS+
Sbjct: 662 DKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSI 695
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 1110 bits (2873), Expect = 0.0
Identities = 346/708 (48%), Positives = 487/708 (68%), Gaps = 9/708 (1%)
Query: 48 KDHHSRRGLIMMKGNFLFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATV 107
HH M F+ K+ ++G + +E G IARQA +VL ++ +TV+LAT
Sbjct: 5 HHHHHHSQDPM------FDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATA 58
Query: 108 VSCKDPTSTYNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFP 167
V K +FFPLTV+Y EK +AAG+IPG FFKREG+PSE+ET++SRLIDRPIRPLF
Sbjct: 59 VFAKSQKPGQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFV 118
Query: 168 EGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILN 227
+G+ NE+Q+VV VL + + DPDI ++ S AL +S PF+GP+G A+VG++DG Y+LN
Sbjct: 119 KGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLN 178
Query: 228 PTTEQLKKSHLDLLVAGTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQ 287
PT +++K+S +DL+VAGT A++ VESE ++L E+I+L + F H++M+ I+AI +L +
Sbjct: 179 PTLDEMKESKMDLVVAGTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAE 238
Query: 288 NVGQKKVNWDPIVKDKTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDN 347
+ ++ ++P D + +K+ ++ I AY+I+ KQ R K ++L +
Sbjct: 239 HAAKEPFAFEPEDTD-AIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLS 297
Query: 348 --ENLTIDINDINCILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSS 405
D + I +LE+ ++R+ ILD GLRID R V +RPI GILPRTHGS+
Sbjct: 298 DENPTGYDPLKLGAIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSA 357
Query: 406 LFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREI 465
LFTRG+TQA+VVATLGT DEQ IDAL G + +SF+LHYN PP++ G+ GR+G P RREI
Sbjct: 358 LFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREI 417
Query: 466 GHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHV 525
GHG+LA RAL P+LP F Y+IRLVSEITESNGSSSMA+VCG LA++DAGVP+ V
Sbjct: 418 GHGKLAWRALRPMLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPV 477
Query: 526 AGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQI 585
+GIAMGLI + + +LSDILGDED GDMDFKVAGT G+T+LQMDIKI GIT I++
Sbjct: 478 SGIAMGLILEQDGFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQ 537
Query: 586 ALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTE 645
AL +AK+G ++IL +M + + ++ FAP++ TI I KIR+VIG GG IR +
Sbjct: 538 ALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVA 597
Query: 646 ETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRI 705
TG ++DIND+G++ +++ + + A I+ +T+ ++GK+Y G V+++ DFGA +
Sbjct: 598 TTGAKVDINDDGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNF 657
Query: 706 LSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 753
KDGL+H+SQIS++RV +D LKE Q V+VK+LG DDRG+ KLSM
Sbjct: 658 FGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSM 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 = 1058 bits (2739), Expect = 0.0
Identities = 270/732 (36%), Positives = 405/732 (55%), Gaps = 32/732 (4%)
Query: 51 HSRRGLIMMKGNFLFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSI-EDTVILATVVS 109
M +I + +G+ I E G +ARQA S + + +DT++L+ +
Sbjct: 11 RGSGSEFMENETHYAEAVIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTA 70
Query: 110 CKDPTSTYNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEG 169
K+P +FFPLTVD E+ YAAG+IPGSFF+REG+PSE + RLIDRP+RP F +G
Sbjct: 71 SKNPKDQLDFFPLTVDVEERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKG 130
Query: 170 YLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPT 229
NEIQ+V ++++NP D+ +I S + ++ LPF GP+G +V I G+++ PT
Sbjct: 131 LRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPT 190
Query: 230 TEQLKKSHLDLLVAGT-----EKAIITVESESKQL------------PEDIILNAIIFGH 272
+L+ + D++VAG + AI+ VE+E+ + E+++ +
Sbjct: 191 HTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAK 250
Query: 273 EKMKIAINAINELVQNVGQKKVNWDPIVK-DKTLISKIINISEHKIRKAYQIKNKQIRDL 331
+K+ A +L + + + ++ + ++ A I KQ R+
Sbjct: 251 PFIKVLCKAQADLAAKAAKPTGEFPVFLDYQDDVLEALSAAVRPELSAALTIAGKQDREA 310
Query: 332 TFKNISKDIYSSLIDNENLTIDINDINCILYDLESKIIRKQILDKGLRIDNRGVNDIRPI 391
+ L+ +I+ L ++R++++ + RID RGV DIR +
Sbjct: 311 ELDRVKALAAEKLL--PEFEGREKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTL 368
Query: 392 SIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFAT 451
+ +PR HGS+LF RG+TQ L V TL R EQ++D L +M +YN PP++
Sbjct: 369 AAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSV 428
Query: 452 GDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGC 511
G+ GR+G PKRREIGHG LA+RA++PVLP +F Y+IR VSE SNGS+SM SVC
Sbjct: 429 GETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCAST 488
Query: 512 LALLDAGVPISEHVAGIAMGLIKD----GEKVVILSDILGDEDRCGDMDFKVAGTVNGIT 567
++LL+AGVP+ VAGIAMGLI V L+DILG ED GDMDFKVAGT +T
Sbjct: 489 MSLLNAGVPLKAPVAGIAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVT 548
Query: 568 ALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPS 627
ALQ+D K+ GI ++ AL +A+ +IL+ M + +E+S APR+IT+KI
Sbjct: 549 ALQLDTKLDGIPASVLAAALKQARDARLHILDVMMEAIDT-PDEMSPNAPRIITVKIPVD 607
Query: 628 KIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTES--VQI 685
KI +VIG I + E+TG +I I D+G I I + + + + A+ I + ++
Sbjct: 608 KIGEVIGPKRQMINQIQEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEV 667
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS----SKRVNIITDFLKENQKVRVKVL 741
G+ G V++ FGA + +L GKDGLLHISQI KRV + D L QKV+V++
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIA 727
Query: 742 GIDDRGRIKLSM 753
ID RG++ L
Sbjct: 728 EIDSRGKLSLIP 739
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 948 bits (2454), Expect = 0.0
Identities = 228/627 (36%), Positives = 349/627 (55%), Gaps = 19/627 (3%)
Query: 69 IKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIE 128
+ G+ K+ I G++AR A S +V DT ++ T VS P S F PL VDY +
Sbjct: 7 AVAVDLGNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKP-SPSQFMPLVVDYRQ 65
Query: 129 KAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQID 188
KA AAGRIP ++ +RE S++E + SR+IDR IRPLFP GY + Q++ +L+V+ +
Sbjct: 66 KAAAAGRIPTNYLRREVGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNE 125
Query: 189 PDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEK- 247
PD+ +I G S ALS+S++P+ GP+G ++G IDG+Y++NPT +++ S L+L+VAG K
Sbjct: 126 PDVLAINGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKS 185
Query: 248 AIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNW-DPIVKDKTLI 306
I+ +E+ ++ + + +AI G + + I I +LV+ G K ++
Sbjct: 186 QIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIV 245
Query: 307 SKIINISEHKIRKAYQI--KNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDL 364
++ ++ + +K RD I D L + + D +I +
Sbjct: 246 KYTHKLAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKE-KFPEADPYEIIESFNVV 304
Query: 365 ESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGT-- 422
++ R +L++ R D R + +R +S + HGS+LF RG TQ L T +
Sbjct: 305 AKEVFRSIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLE 364
Query: 423 --SRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLP 480
+ +Q I A+ G +FMLHY PP+AT +IG++ RRE+GHG LA++AL PV+P
Sbjct: 365 SGIKSDQVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIP 424
Query: 481 NNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDG---- 536
F ++IR+ SE+ ESNGSSSMAS CGG LAL+D+GVPIS VAG+A+GL+
Sbjct: 425 --RDFPFTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEK 482
Query: 537 ---EKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKG 593
E +L+DILG ED GDMDFK+AGT GITALQ DIK+ GI I+ A+ +A
Sbjct: 483 GEIEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVA 542
Query: 594 LSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI 653
IL+ M + K + + P + T+++ SK +G GG ++ L ETG I
Sbjct: 543 KKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQ 602
Query: 654 NDEGIITIASFNSVSGQEAKRRIEKLT 680
DE ++ + + EA+ I ++
Sbjct: 603 VDEETFSVFAPTPSAMHEARDFITEIC 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 = 892 bits (2307), Expect = 0.0
Identities = 300/550 (54%), Positives = 421/550 (76%), Gaps = 1/550 (0%)
Query: 64 LFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 123
+ N I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +FFPLT
Sbjct: 1 MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 60
Query: 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 183
V+Y E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++ V+SV
Sbjct: 61 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 120
Query: 184 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 243
NPQ++PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LDL+VA
Sbjct: 121 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 180
Query: 244 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 303
GTE A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P ++
Sbjct: 181 GTEAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 240
Query: 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 363
L +++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++ IL+
Sbjct: 241 ALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLA-EDETLDENELGEILHA 299
Query: 364 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 423
+E ++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV ATLGT+
Sbjct: 300 IEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTA 359
Query: 424 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 483
RD Q +D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+P+ +
Sbjct: 360 RDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMD 419
Query: 484 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 543
KF Y++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+ V+LS
Sbjct: 420 KFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLS 479
Query: 544 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKT 603
DILGDED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL M+
Sbjct: 480 DILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQ 539
Query: 604 EVPKCKNELS 613
+ + ++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 = 381 bits (980), Expect = e-128
Identities = 67/266 (25%), Positives = 115/266 (43%), Gaps = 16/266 (6%)
Query: 365 ESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSR 424
E ++++ GLR+D R +++RPI I +L R GS G + +
Sbjct: 3 EFNEKPEKLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGP--- 59
Query: 425 DEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNK 484
E + L YNM PF+ + R G P RR I +++K A V+
Sbjct: 60 REVHPEHLQDPSKAIIRYRYNMAPFSVEERKRPG-PDRRSIEISKVSKEAFEAVIMKELF 118
Query: 485 FNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSD 544
+I + E+ +++ S A + +AL+DAGVP+ + +A+G ++ D
Sbjct: 119 PRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADG----QLVLD 174
Query: 545 ILGDEDRCGDMDFKVA-----GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILE 599
+ +ED G+ D A G + I LQMD + +T D ++ A+ AKKG I E
Sbjct: 175 PMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGR---MTRDEVKQAIELAKKGALQIYE 231
Query: 600 KMKTEVPKCKNELSKFAPRLITIKID 625
+ + + 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 = 371 bits (956), Expect = e-125
Identities = 67/258 (25%), Positives = 117/258 (45%), Gaps = 13/258 (5%)
Query: 361 LYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATL 420
+ ++ K ILD G R D R +++R I I G+L GS++F G+T+A+
Sbjct: 3 MREMLQVERPKLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYG 62
Query: 421 GTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLP 480
E L + Y+M PF+T + P RREI ++ + AL +
Sbjct: 63 P---KEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPA-PSRREIELSKVIREALESAVL 118
Query: 481 NNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVV 540
+I + +EI +++ S + S+ LAL DAG+P+ + +AG+A+G V
Sbjct: 119 VELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADG----V 174
Query: 541 ILSDILGDEDRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYIL 598
I+ D+ E G+ D +A ++N +T Q++ +T D + A A KG++ I
Sbjct: 175 IILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNG---SMTPDEFRQAFDLAVKGINIIY 231
Query: 599 EKMKTEVPKCKNELSKFA 616
+ + 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 (940), Expect = e-122
Identities = 70/257 (27%), Positives = 114/257 (44%), Gaps = 13/257 (5%)
Query: 364 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 423
+E K I + G RID R ++RPI + G+L +GS+ G + +
Sbjct: 2 MEKPEGLKLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGP-- 59
Query: 424 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 483
E L + YNM PF+ + + G P RR I ++ K AL P L
Sbjct: 60 -RELHPKHLQRPDRAILRVRYNMAPFSVEERKKPG-PDRRSIEISKVIKGALEPALILEM 117
Query: 484 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 543
+I + E+ +++ + +A + LAL DAG+P+ + VA A G I+ I+
Sbjct: 118 FPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEG----EIVL 173
Query: 544 DILGDEDRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 601
D+ +ED G+ D VA N IT LQMD +T D A+ A KG + +K
Sbjct: 174 DLNKEEDNYGEADVPVAIMPLKNDITLLQMDGY---LTKDEFIEAVKLAIKGAKAVYQKQ 230
Query: 602 KTEVPKCKNELSKFAPR 618
+ + + ++++
Sbjct: 231 REALKEKYLKIAQEVEG 247
Score = 29.9 bits (68), Expect = 2.4
Identities = 42/209 (20%), Positives = 74/209 (35%), Gaps = 38/209 (18%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATV-------VSCKDPTST------YNFFPLTV 124
I +E+G + A S + I+A V YN P +V
Sbjct: 28 PIKMEVGVLKN-ANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFSV 86
Query: 125 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYL--NEIQIVVYVLS 182
+ K+ G P R IS++I + P I + + VL
Sbjct: 87 EER--------------KKPG-PDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQ 131
Query: 183 VNPQIDPDIASIIGVSTALSISELPFLGPL-GVAKVGYIDGKYILNPTTEQLKKSHLDLL 241
+ +A I S AL+ + +P + A G I+G+ +L+ E+ D+
Sbjct: 132 ADAGT--RVAGITAASLALADAGIPMRDLVAACA-AGKIEGEIVLDLNKEEDNYGEADVP 188
Query: 242 VA--GTEKAIITVESESKQLPEDIILNAI 268
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 = 343 bits (881), Expect = e-113
Identities = 53/246 (21%), Positives = 99/246 (40%), Gaps = 11/246 (4%)
Query: 370 RKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKI 429
+ + D+G R+D R ++R I R G+ + GS+ +G+T+AL V +
Sbjct: 8 LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRA 67
Query: 430 DALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSI 489
AL Y+ F+TG+ R R+ G ++ + I
Sbjct: 68 RALPDR--ALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 125
Query: 490 RLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDE 549
+ ++ +++G + A V LA+LDAG+P+ + V + G + L+D+ E
Sbjct: 126 DIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDG----TALADLSHVE 181
Query: 550 DRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPK 607
+ G +A I L+MD + + D ++ L A + + + V +
Sbjct: 182 EAAGGPQLALALLPASGQIALLEMDAR---LHEDHLERVLEAAAQAARDVHTLLDRVVRQ 238
Query: 608 CKNELS 613
E S
Sbjct: 239 HVREAS 244
Score = 30.3 bits (69), Expect = 2.1
Identities = 22/166 (13%), Positives = 53/166 (31%), Gaps = 25/166 (15%)
Query: 142 KREGKPSERETIISRLIDRPIRPLFPE----GYLNEIQIVVYVLSVNPQIDPDIASIIGV 197
KR + + + + +I I V VL + A +
Sbjct: 91 KRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRS--QIDIYVQVLQADGGTYA--ACVNAA 146
Query: 198 STALSISELPFLGPL-GVAKVGYIDGKYILNPTTEQLKKSHL---DLLVA--GTEKAIIT 251
+ A+ + +P + + G++DG + + + + L +A I
Sbjct: 147 TLAVLDAGIPMRDFVCACS-AGFVDGTALADLSHVE---EAAGGPQLALALLPASGQIAL 202
Query: 252 VESESK--QLPEDIILNAIIFG----HEKMKIAI-NAINELVQNVG 290
+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 = 314 bits (807), Expect = e-102
Identities = 73/249 (29%), Positives = 106/249 (42%), Gaps = 15/249 (6%)
Query: 367 KIIRKQIL--DKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSR 424
II + L +R D R +++RP+ I GIL R GSS G + LV
Sbjct: 3 TIITQDQLKTSPSVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVY---GP 59
Query: 425 DEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNK 484
E +I L YNM PF+ + R G P RR + ++ AL P L
Sbjct: 60 REAQIRKLQRPDRAVIRCRYNMAPFSVEERKRPG-PDRRSVEISKITAEALRPALILEKF 118
Query: 485 FNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSD 544
I + E+ E+ G + A + +AL DAG+P+ + V A G + D ++ D
Sbjct: 119 PRSVIDVFIEVLEAEGGTRCAGITAASVALADAGIPMRDMVVACAAGKVGD----QVVLD 174
Query: 545 ILGDEDRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMK 602
+ +ED+ G D VA IT LQ D +T + + AL A +G I E K
Sbjct: 175 LSEEEDKEGQADVPVAILPRTREITLLQSDG---NLTPEEFERALDLAVEGCLRIHEVQK 231
Query: 603 TEVPKCKNE 611
+ K E
Sbjct: 232 EALRKRYGE 240
Score = 46.4 bits (111), Expect = 1e-05
Identities = 41/234 (17%), Positives = 77/234 (32%), Gaps = 59/234 (25%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDP-------------TSTYNFFPLTV 124
+ IE G I +A S + IL V ++ YN P
Sbjct: 28 PLKIEAG-ILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMAP--- 83
Query: 125 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVN 184
++ ++ P R IS++ +RP I V++
Sbjct: 84 ------FSVEE------RKRPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFI---- 127
Query: 185 PQIDPDI---------ASIIGVSTALSISELPFLGPL-GVAKVGYIDGKYILNPTTEQLK 234
++ A I S AL+ + +P + A G + + +L+ + E+ K
Sbjct: 128 -----EVLEAEGGTRCAGITAASVALADAGIPMRDMVVACA-AGKVGDQVVLDLSEEEDK 181
Query: 235 KSHLDLLVA--GTEKAIITVESESKQLPEDII-------LNAIIFGHEKMKIAI 279
+ 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 = 8e-97
Identities = 52/245 (21%), Positives = 91/245 (37%), Gaps = 29/245 (11%)
Query: 377 GLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEF 436
R D R N +RP S L R HGS+ + +GDT L A G +K GE
Sbjct: 3 ESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLA-AVYGPKPGTRK-----GEN 56
Query: 437 TDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEIT 496
+ + P G ++E + KR L + N + ++ ++
Sbjct: 57 PEKASIEVVWKPMT-------GQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVV 109
Query: 497 ESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCG-DM 555
++GS ++ C AL+ AG+P+ I G+++DGE VIL +E +
Sbjct: 110 GNDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGE--VILDTNKAEEQQLKSFA 167
Query: 556 DFKVAGTVNGITALQMDIKIFGITYDIIQI-------------ALYKAKKGLSYILEKMK 602
+ ++ + + K +I + + S I + M+
Sbjct: 168 HLVFPNSRKSASSKEPNQKEEDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMR 227
Query: 603 TEVPK 607
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: 78 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAGRIP 137
S + R A S + DT++LA V K + EKA I
Sbjct: 16 PFSCTRNPLDR-AHGSARWAQGDTIVLAAVYGPKPG-------TRKGENPEKAS----IE 63
Query: 138 GSFFKREGKPSERETIISRLIDRPIRPLFP-EGYLN-EIQIVVYVLSVNPQIDPDIASII 195
+ G+ ++E + R ++ + + N +++ V+ + + P +I
Sbjct: 64 VVWKPMTGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLP--CAIN 121
Query: 196 GVSTALSISELPFLGPL-GVAKVGYI-DGKYILNPTT--EQLKKSHLDLLVAGTEKAIIT 251
AL + +P + G + DG+ IL+ EQ KS L+ + K+ +
Sbjct: 122 ACCAALVFAGIPLKHLAVAIG-CGVLEDGEVILDTNKAEEQQLKSFAHLVFPNSRKSASS 180
Query: 252 VESESK-QLPEDIILNAIIFGHEKMKIAINAIN 283
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 = 288 bits (738), Expect = 1e-92
Identities = 61/251 (24%), Positives = 110/251 (43%), Gaps = 23/251 (9%)
Query: 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 437
+R D R +++RPI+ + GS L T G+T+ + A++ +++ L G
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASV----EDRVPPFLRGGGK 56
Query: 438 DSFMLHYNMPPFATGDIGRI----GVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVS 493
Y+M P AT G R + RL RAL V+ +I +
Sbjct: 57 GWITAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 494 EITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKVVIL 542
++ +++G + AS+ G LA+ A PI++ +A I++G+ K+ IL
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQG---IL 173
Query: 543 SDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 601
D+ +ED ++D V T +G LQ + + + + L A+KG+ +++K
Sbjct: 174 LDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQ 233
Query: 602 KTEVPKCKNEL 612
K + EL
Sbjct: 234 KEVLGDSLPEL 244
Score = 49.6 bits (119), Expect = 1e-06
Identities = 43/217 (19%), Positives = 62/217 (28%), Gaps = 75/217 (34%)
Query: 79 ISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVDY 126
I+ ++ SVL++ +T ++ V + P T+ Y+ P +
Sbjct: 14 ITFDLD-FISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPQATNQ 72
Query: 127 IEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQ 186
+GK S R I RLI R +R + L E I
Sbjct: 73 Q----------TIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTI---------W 113
Query: 187 IDPDI---------ASIIGVSTAL-----------SISELPFLGPLGVAKVGYIDGKYIL 226
ID D+ ASI G A+ +I P L VG + IL
Sbjct: 114 IDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGIL 173
Query: 227 NPTTEQLKKSHLDLL------------VAGTEKAIIT 251
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 = 274 bits (703), Expect = 5e-87
Identities = 47/263 (17%), Positives = 84/263 (31%), Gaps = 14/263 (5%)
Query: 365 ESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVAT----- 419
ES+ + D+ R +RP+ R G+L + GS+ G T+ L +
Sbjct: 13 ESQPPQLYAADEEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQA 72
Query: 420 ---LGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALL 476
+ + PFA R E + AL
Sbjct: 73 EGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRR-RRAPPGGCEERELALALQEALE 131
Query: 477 PVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDG 536
P + + + + + E GS+ A++ LAL DAGV + + V G + L
Sbjct: 132 PAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGP 191
Query: 537 EKVVILSDILGDEDRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGL 594
+L D E+ VA +N + L + G + A+ +G
Sbjct: 192 APTWLL-DPTRLEEERAAAGLTVALMPVLNQVAGLLGSGE--GGLTESWAEAVRLGLEGC 248
Query: 595 SYILEKMKTEVPKCKNELSKFAP 617
+ ++ + + A
Sbjct: 249 QRLYPVLQQSLVRAARRRGAAAQ 271
Score = 57.2 bits (138), Expect = 5e-09
Identities = 28/239 (11%), Positives = 73/239 (30%), Gaps = 31/239 (12%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATV---------------VSCKDPTSTYNFFPL 122
+ G +++ A S + T +L V L
Sbjct: 38 PVYARAGLLSQ-AKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRL 96
Query: 123 TVDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFP-EGYLN-EIQIVVYV 180
D+ +A R +R E ++ + + P Y ++++ +
Sbjct: 97 LCDFRRAPFAGRR------RRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALL 150
Query: 181 LSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGK---YILNPTTEQLKKSH 237
L A++ + AL+ + + + + G ++L+PT + +++
Sbjct: 151 LEDGGSALA--AALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAA 208
Query: 238 LDLLVA--GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKV 294
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 = 271 bits (694), Expect = 7e-86
Identities = 53/251 (21%), Positives = 105/251 (41%), Gaps = 23/251 (9%)
Query: 368 IIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQ 427
+ +R+D R ++R I I T L GS L GDT+ + AT+ +E+
Sbjct: 1 MGSSHHHHHHMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATI----EER 56
Query: 428 KIDALMGEFTDSFMLHYNMPPFATGDIGRI----GVPKRREIGHGRLAKRALLPVLPNNN 483
+ GE Y M P AT G R + RL RAL V+
Sbjct: 57 VPPFMRGEGKGWVTAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEA 116
Query: 484 KFNYSIRLVSEITESNGSSSMASVCGGCLALLD-----------AGVPISEHVAGIAMGL 532
++ + ++ +++G + AS+ G +A++ + +P+ +++A ++G+
Sbjct: 117 LGERTVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGI 176
Query: 533 IKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAK 591
+++ ++ D+ ED D+D V T G +Q + + + L A+
Sbjct: 177 VEEQG---VVLDLNYAEDSKADVDMNVIMTGKGQFVEVQGTGEEATFSRAQLNELLDAAE 233
Query: 592 KGLSYILEKMK 602
+G+ +++ K
Sbjct: 234 QGIFQLIDIQK 244
Score = 46.2 bits (110), Expect = 1e-05
Identities = 34/181 (18%), Positives = 60/181 (33%), Gaps = 52/181 (28%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVD 125
I I + SVL+ + DT ++ + + + P T+ Y P +
Sbjct: 23 HIHIHTN-YLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVTAEYAMIPRATE 81
Query: 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNP 185
S +GK + R I RLI R +R + L E + +
Sbjct: 82 ------QRTIRESS----KGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDC----- 126
Query: 186 QIDPDI---------ASIIGVSTAL-----------SISELPFLGPLGVAKVGYIDGKYI 225
D+ ASI G A+ +S++P L VG ++ + +
Sbjct: 127 ----DVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGV 182
Query: 226 L 226
+
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 = 254 bits (650), Expect = 1e-79
Identities = 50/250 (20%), Positives = 89/250 (35%), Gaps = 22/250 (8%)
Query: 361 LYDLESKIIRKQILDKGLRIDNRGVN-DIRPISIRTGILPRTHGSSLFTRGDTQALVVAT 419
L + E+ K + G RG +R + +L R GS+ F +GDT L
Sbjct: 2 LMEEETHTDAKIRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVY 61
Query: 420 LGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVL 479
G + E K+ +N +IG+P E RL + V+
Sbjct: 62 -GPA--EVKV----------SKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVV 108
Query: 480 PNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKV 539
SI +V ++ GS + C+AL+DAGVP+ G+A L DG
Sbjct: 109 LGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGT-- 166
Query: 540 VILSDILGDEDR--CGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYI 597
++ D +++ + F + + + +Q L A+ ++
Sbjct: 167 -LVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKG---LYSDTELQQCLAAAQAASQHV 222
Query: 598 LEKMKTEVPK 607
+ + +
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 = 253 bits (648), Expect = 3e-79
Identities = 47/247 (19%), Positives = 94/247 (38%), Gaps = 11/247 (4%)
Query: 373 ILDKGLRIDNRGVNDIRPISIRTGILPRT-HGSSLFTRGDTQALVVATLGTSRDEQKIDA 431
+GLR+D R N++R P GSS +G+ + + + E ++ +
Sbjct: 7 YSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVK---GPKEPRLKS 63
Query: 432 LMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHG-RLAKRALLPVLPNNNKFNYSIR 490
M + N+ F+ + + R + R + N I
Sbjct: 64 QMDTSKALLNVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVID 123
Query: 491 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 550
+ + E +G + + G LAL+DAG+ + ++++GI++GL +L +E+
Sbjct: 124 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDT---TPLLDTNSLEEN 180
Query: 551 RCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKN 610
+ V G ++ L ++ K I D ++ L G + + M E+ K
Sbjct: 181 AMSTVTLGVVGKSEKLSLLLVEDK---IPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQ 237
Query: 611 ELSKFAP 617
+ A
Sbjct: 238 KRVSNAS 244
Score = 61.2 bits (149), Expect = 2e-10
Identities = 39/221 (17%), Positives = 74/221 (33%), Gaps = 29/221 (13%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFP----LTVDYIEKAYAA 133
+ I A S + + I+ V K+P L V ++
Sbjct: 24 RFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNINKFSK 83
Query: 134 GRIPGSFFKREGKPSERETI-ISRLIDRPIRP-----LFPEGYLNEIQIVVYVLSVNPQI 187
+ +ER + I + R ++P I I ++VL + I
Sbjct: 84 FER-----SKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPR---TVIDIEIHVLEQDGGI 135
Query: 188 DPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTT-EQLKKSHLDLLVAGTE 246
+ I G++ AL + + + VG D +L+ + E+ S + L V G
Sbjct: 136 MG--SLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMSTVTLGVVGKS 193
Query: 247 KAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQ 287
+ + + 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 = 234 bits (598), Expect = 7e-72
Identities = 57/261 (21%), Positives = 113/261 (43%), Gaps = 24/261 (9%)
Query: 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 437
+R D R + +RP+SI+ L GS L + G T+ + A++ E + L G+
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQ 56
Query: 438 DSFMLHYNMPPFATGDIGRIGVPK----RREIGHGRLAKRALLPVLPNNNKFNYSIRLVS 493
Y+M P AT + R R+ RA+ + +I +
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDC 116
Query: 494 EITESNGSSSMASVCGGCLALLDAGV-----------PISEHVAGIAMGLIKDGEKVVIL 542
++ +++G + A++ G +A+ DA + PI + VA +++G++ D IL
Sbjct: 117 DVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND----RIL 172
Query: 543 SDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 601
D+ +ED +D V GT +G ++ + + + T D + L A+KG++ ++E
Sbjct: 173 LDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQ 232
Query: 602 KTEVPKCKNELSKFAPRLITI 622
K + + + ++
Sbjct: 233 KKLYVIQDGKWERSELKEVSS 253
Score = 53.2 bits (128), Expect = 8e-08
Identities = 47/248 (18%), Positives = 87/248 (35%), Gaps = 56/248 (22%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVD 125
+SI+ S L+S T ++ T V P T+ Y+ P
Sbjct: 13 PVSIQRD-FLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPRAT- 70
Query: 126 YIEKAYAAGRIPGSFFKRE---GKPSERETIISRLIDRPIRPLFPEGYLNE--IQIVVYV 180
RE G+ R I R+I R +R + E I + V
Sbjct: 71 ------------QQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDV 118
Query: 181 LSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAK-----------VGYIDGKYILNPT 229
+ + A+I G A++ + + + + VG ++ + +L+
Sbjct: 119 IQADGGTRT--AAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLN 176
Query: 230 TEQLKKSHLDLLVAGTEK-AIITVES--ESKQLPEDIILNAIIFGHEKMKIAINAINELV 286
E+ + +D+ V GT + V + E +D ++ + +A INEL+
Sbjct: 177 FEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKM-------LDLAQKGINELI 229
Query: 287 QNVGQKKV 294
+ QKK+
Sbjct: 230 EL--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 (519), Expect = 8e-61
Identities = 52/240 (21%), Positives = 95/240 (39%), Gaps = 24/240 (10%)
Query: 379 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTD 438
R R + +RPI I GS L GDT+ + + + L G+
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSA----ESGVPRFLKGQGQG 58
Query: 439 SFMLHYNMPPFATGDIGRI----GVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSE 494
Y M P +TG+ + G R + RL R+L L + ++ + +
Sbjct: 59 WLTAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCD 118
Query: 495 ITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKVVILS 543
+ +++G + AS+ G +AL+DA G P+ + VA +++G+ + V +
Sbjct: 119 VIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQG----VPVL 174
Query: 544 DILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMK 602
D+ ED + D V T G +Q + + L A++G+ + E +
Sbjct: 175 DLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQR 234
Score = 53.2 bits (128), Expect = 7e-08
Identities = 51/246 (20%), Positives = 79/246 (32%), Gaps = 52/246 (21%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVD 125
I I + A SVLV DT ++ TV P T+ Y P +
Sbjct: 14 PIRITRH-YTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPRST- 71
Query: 126 YIEKAYAAGRIPGSFFKRE---GKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLS 182
G +RE GK R I RLI R +R L E + +
Sbjct: 72 ------------GERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDV 119
Query: 183 VNPQIDPDIASIIGVSTAL-----------SISELPFLGPLGVAKVGYIDGKYILNPTTE 231
+ ASI G + AL ++ P + VG G +L+
Sbjct: 120 IQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVPVLDLDYL 179
Query: 232 QLKKSHLDLLVAGTEK-AIITVE--SESKQLPEDIILNAIIFGHEKMKIAINAINELVQN 288
+ + DL V T+ I V+ +E + +++A + EL +
Sbjct: 180 EDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAM-------LELAQQGMQELFEL 232
Query: 289 VGQKKV 294
Q+
Sbjct: 233 --QRAA 236
>3b4t_A Ribonuclease PH; RNAse, tRNA nucleotidyltransferase, RPHA, STRU
genomics, TBSGC; 2.10A {Mycobacterium tuberculosis}
Length = 262
Score = 166 bits (421), Expect = 1e-46
Identities = 46/253 (18%), Positives = 91/253 (35%), Gaps = 17/253 (6%)
Query: 379 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTD 438
R D R +++RP+ I G GS L G T+ L A++ + +G T
Sbjct: 7 REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTA 66
Query: 439 SFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITES 498
+ + + + G R RL R+L + +I + ++ ++
Sbjct: 67 EYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQA 126
Query: 499 NGSSSMASVCGGCLALLDAGV------------PISEHVAGIAMGLIKDGEKVVILSDIL 546
+G + A++ G +AL DA P+S +A +++G++ I D+
Sbjct: 127 DGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDG----RIRVDLP 182
Query: 547 GDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 605
+ED ++D V T G + +Q + + L A + + +
Sbjct: 183 YEEDSRAEVDMNVVATDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFAAQRDAL 242
Query: 606 PKCKNELSKFAPR 618
+ P
Sbjct: 243 ALPYPGVLPQGPP 255
Score = 39.4 bits (92), Expect = 0.003
Identities = 49/248 (19%), Positives = 80/248 (32%), Gaps = 55/248 (22%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVD 125
+ I G SVL+ T +L T V+ P T+ Y P
Sbjct: 18 PVIITRG-FTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTAEYAMLP---- 72
Query: 126 YIEKAYAAGRIPGSFFKRE---GKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLS 182
S RE G+ S R ISRLI R +R L E I +
Sbjct: 73 ---------SATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDV 123
Query: 183 VNPQIDPDIASIIGVSTALSISELPFLGPLGVAK------------VGYIDGKYILNPTT 230
+ A+I G AL+ + ++ VG +DG+ ++
Sbjct: 124 LQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDGRIRVDLPY 183
Query: 231 EQLKKSHLDLLVAGTEKAIITVE----SESKQLPEDIILNAIIFGHEKMKIAINAINELV 286
E+ ++ +D+ V T+ + VE E + + +A+ A + L
Sbjct: 184 EEDSRAEVDMNVVATDTGTL-VEIQGTGEGATFARSTLDKL-------LDMALGACDTLF 235
Query: 287 QNVGQKKV 294
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: 386 NDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYN 445
+R + L GS+ F++G T + G ++ L +
Sbjct: 3 GRLREMRCELSFLKNADGSACFSQGATCIWASCS-GPGDVHAS-----KASDEAMTLDIS 56
Query: 446 MPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMA 505
G K + + L + + +I + + +GS
Sbjct: 57 YRANC-------GDNKFNVLN--NIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAV 107
Query: 506 SVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDR--CGDMDFKVAGTV 563
++ G C ALLD G+P G+ + +KD ++ D ++ G + F V
Sbjct: 108 AINGACFALLDNGMPFETVFCGVLIVRVKD----ELIIDPTAKQEAASTGRVLFSVCKGS 163
Query: 564 NGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 605
+G + I + ++ A A+ S I + KT +
Sbjct: 164 DGHPEVCAMDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVM 205
Score = 69.8 bits (171), Expect = 2e-13
Identities = 34/233 (14%), Positives = 78/233 (33%), Gaps = 40/233 (17%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATV---VSCKDPTSTYNFFPLTVDYIEKAYAAG 134
++ E+ + A S S T I A+ ++ L + Y
Sbjct: 7 EMRCELS-FLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISY-------- 57
Query: 135 RIPGSFFKREGKPSERETIISRLIDRPIRP-----LFPEGYLNEIQIVVYVLSVNPQIDP 189
R + +++ +I + LFP I + V+ + + +
Sbjct: 58 --------RANCGDNKFNVLNNIIHSTLSNAINLELFPH---TTISVTVHGIQDDGSMGA 106
Query: 190 DIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA-----G 244
+I G AL + +PF + + + I++PT +Q S +L +
Sbjct: 107 --VAINGACFALLDNGMPFETVFCGVLIVRVKDELIIDPTAKQEAASTGRVLFSVCKGSD 164
Query: 245 TEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWD 297
+ +++ + A + + +AI + + V ++K++ D
Sbjct: 165 GHPEVCAMDAIGH-WDFIQLEAAW----SLAQPSASAIFDFYKTVMKRKLSVD 212
>2vqe_O 30S ribosomal protein S15; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: i.1.1.1 PDB: 1eg0_F*
1gix_R* 1hnw_O* 1hnx_O* 1hnz_O* 1hr0_O 1ibk_O* 1ibl_O*
1ibm_O 1jgo_R* 1jgp_R* 1jgq_R* 1ml5_R* 1xmo_O* 1xmq_O*
1xnq_O* 1xnr_O* 1yl4_R 2b64_O* 2b9m_O* ...
Length = 89
Score = 104 bits (262), Expect = 4e-27
Identities = 35/61 (57%), Positives = 41/61 (67%)
Query: 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMK 60
M I K +I + +R DTGS EVQVALLT RIN L+ H K+H KDHHS RGL+MM
Sbjct: 1 MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMV 60
Query: 61 G 61
G
Sbjct: 61 G 61
>3ulw_A 30S ribosomal protein S15; structural genomics, IDP90515, CE
structural genomics of infectious diseases, csgid, rRNA
BIN translation; 2.36A {Campylobacter jejuni}
Length = 93
Score = 103 bits (258), Expect = 1e-26
Identities = 28/61 (45%), Positives = 39/61 (63%)
Query: 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMK 60
M + + KA I+ ++ DTGS EVQVALLT+RI +L H K++ KD SR GL+ +
Sbjct: 4 MALDSAKKAEIVAKFAKKPGDTGSTEVQVALLTARIAELTEHLKIYKKDFSSRLGLLKLV 63
Query: 61 G 61
G
Sbjct: 64 G 64
>3r8n_O 30S ribosomal protein S15; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 1p6g_O 1p87_O 2ykr_O 3oar_O
3oaq_O 3ofb_O 3ofa_O 3ofp_O 3ofx_O 3ofy_O 3ofo_O 3r8o_O
3i1m_O 2qan_O* 2qb9_O* 2qbb_O* 2qbd_O 2qbf_O 2qbh_O*
2qbj_O* ...
Length = 88
Score = 101 bits (253), Expect = 5e-26
Identities = 32/54 (59%), Positives = 37/54 (68%)
Query: 8 KASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKG 61
A I+ + R NDTGS EVQVALLT++IN L HF H KDHHSRRGL+ M
Sbjct: 7 TAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVS 60
>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: 679 LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRV 738
+ ++G VYTG V L +GA + + GL+HIS+++ V I + L +V+V
Sbjct: 1 MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60
Query: 739 KVLGID-DRGRIKLSM 753
KVL +D ++G+I LS+
Sbjct: 61 KVLAVDEEKGKISLSI 76
>1a32_A Ribosomal protein S15; multiwavelength anomalous diffraction,
protein-RNA, ribosomal protein interactions, ribosome,
RNA-binding; 2.10A {Geobacillus stearothermophilus}
SCOP: a.16.1.2 PDB: 1qd7_H
Length = 88
Score = 100 bits (251), Expect = 1e-25
Identities = 32/54 (59%), Positives = 40/54 (74%)
Query: 8 KASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKG 61
K II +NDTGSPEVQ+A+LT +IN+LN H ++H KDHHSRRGL+ M G
Sbjct: 7 KREIIEQFKVHENDTGSPEVQIAILTEQINNLNEHLRVHKKDHHSRRGLLKMVG 60
>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 = 98.3 bits (245), Expect = 2e-24
Identities = 29/93 (31%), Positives = 49/93 (52%), Gaps = 4/93 (4%)
Query: 665 NSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRIL-SGKDGLLHISQISSKRV 723
+S S R E + + ++ G V + D+GA I+I K GL+H + +SS RV
Sbjct: 2 SSGSSGMNSGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRV 61
Query: 724 NIITDFLKENQKVRVKVLGID---DRGRIKLSM 753
+ ++ + 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 = 94.7 bits (236), Expect = 2e-23
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 679 LTESVQIGKVYTGIVLRLFDFGAIIRILSGK---DGLLHISQISS-KRVNIITDFLKENQ 734
E IG +Y G V + FG +++ + +GL+HIS++ RV + D + + Q
Sbjct: 6 SGEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQ 65
Query: 735 KVRVKVLGIDDRGRIKLSM 753
+V+VKVL + LSM
Sbjct: 66 RVKVKVLSF-TGTKTSLSM 83
>3bbn_O Ribosomal protein S15; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
Length = 90
Score = 87.3 bits (217), Expect = 4e-21
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 7 IKASII--LDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKG 61
K S I + + + + + GS E QV T++I L +H +LH KD+ S+RGL G
Sbjct: 2 KKNSFISVISDEKKEENKGSVEFQVFCFTNKIRRLTLHLELHKKDYSSQRGLRKTLG 58
>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: 683 VQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLG 742
V+ GK Y G+V R+ +GA I + GLL + S R+ L ++ V+ +
Sbjct: 3 VEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLEN----LNVGDEIIVQAID 58
Query: 743 ID-DRGRIKLSMI 754
+ ++ 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 = 85.1 bits (211), Expect = 2e-18
Identities = 54/278 (19%), Positives = 101/278 (36%), Gaps = 47/278 (16%)
Query: 362 YDLESKIIRKQI---LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVA 418
D+ +I RK I ++ RID R +++ R ISI TG++ + GSS G+TQ +V
Sbjct: 5 MDIIPEITRKSITDLINNKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGV 64
Query: 419 TLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL--- 475
+ + + + P A+ G P R + R+ R +
Sbjct: 65 KP-----QIGEPFPDTPEMGVILTNSELLPMASPTFEP-GPPDERSVELSRVVDRCIRES 118
Query: 476 -------LPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP-------- 520
L ++ + + L I + +G+ A+V ALLD +P
Sbjct: 119 RMIDLEKLCIIE--GSKVWMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGE 176
Query: 521 ------------ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-IT 567
++ I + I+ D +E+ + T G I
Sbjct: 177 VVINREKMQPLPVNRKALMCTFAKIGN----EIVLDPSLEEEDILTARISIGVTEEGSIC 232
Query: 568 ALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 605
A+Q + +T D + A+ A + + ++E + +
Sbjct: 233 AMQKGGEG-PLTRDDVLKAVSIAVEKVPQLIEYLDKSM 269
Score = 43.1 bits (102), Expect = 2e-04
Identities = 40/215 (18%), Positives = 73/215 (33%), Gaps = 67/215 (31%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATVVSC-------KDP-----TSTYNFFPLTVD 125
ISIE G I+ +A S V + +T I+ V P + P+
Sbjct: 36 DISIETGVIS-KAEGSSRVKLGNTQIIVGV-KPQIGEPFPDTPEMGVILTNSELLPMASP 93
Query: 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRP----------LFPEGYLNEIQ 175
E G P ER +SR++DR IR + + +
Sbjct: 94 TFEP---------------GPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLF 138
Query: 176 IVVYVLSVNPQID---PDIASIIGVSTALSISELPF--------------LGPLGVAK-- 216
+ ++++ D D A+++ AL + +P + PL V +
Sbjct: 139 LDLHII----DYDGNLFD-AAVLATVAALLDTRIPAAEVEDGEVVINREKMQPLPVNRKA 193
Query: 217 ----VGYIDGKYILNPTTEQLKKSHLDLLVAGTEK 247
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 = 83.2 bits (206), Expect = 7e-18
Identities = 45/267 (16%), Positives = 89/267 (33%), Gaps = 40/267 (14%)
Query: 363 DLESKIIRKQI---LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVAT 419
D+ I R + L RID RG ++ R + I ++ + GS+L GDTQ +V
Sbjct: 4 DILVDIKRDYVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVK 63
Query: 420 LGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL---- 475
+ + +++ + P A+ G P I R+ R +
Sbjct: 64 M-----QPGEPYPDTPDRGVIIVNAELVPLASPTFEP-GPPDENSIELARVVDRGIRESE 117
Query: 476 ------LPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP--------- 520
L + + + + + + +G+ AS AL++ VP
Sbjct: 118 AVDLSKLVIEE--GEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGED 175
Query: 521 ----ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKI 575
+ + + ++ + L D +E GD + + + A+Q
Sbjct: 176 YLLPVRDLPVSVTSLIVGN----KYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGY 231
Query: 576 FGITYDIIQIALYKAKKGLSYILEKMK 602
+ + L + + EK K
Sbjct: 232 -LLDEKLFDELLDVSINCARKLREKFK 257
Score = 43.9 bits (104), Expect = 9e-05
Identities = 43/250 (17%), Positives = 92/250 (36%), Gaps = 57/250 (22%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP---TSTYNFFPLTVDYIEKAYAA 133
K+ I I +A S LV + DT ++ V + +P T + + +
Sbjct: 34 KVEIIPNVI-EKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELV------ 86
Query: 134 GRIPGSFFKRE-GKPSERETIISRLIDRPIRP----------LFPEGYLNEIQIVVYVLS 182
P + E G P E ++R++DR IR + + + + ++ L
Sbjct: 87 ---PLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHAL- 142
Query: 183 VNPQIDPDI--ASIIGVSTALSISELPFLG--------------PLGVAKVGYIDGKYIL 226
D ++ AS + AL +++P P+ V + KY++
Sbjct: 143 ---DDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVT-SLIVGNKYLV 198
Query: 227 NPTTEQLKKSHLDLLVAGTEK-AIITVE-SESKQLPEDIILNAIIFGHEKMKIAINAINE 284
+P+ E++ L + + ++ ++ S L E + + ++IN +
Sbjct: 199 DPSREEMSVGDTTLTITTDKDDNVVAMQKSGGYLLDEKLFDELL-------DVSINCARK 251
Query: 285 LVQNVGQKKV 294
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 = 82.8 bits (205), Expect = 1e-17
Identities = 55/273 (20%), Positives = 92/273 (33%), Gaps = 44/273 (16%)
Query: 366 SKIIRKQI---LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGT 422
+ I+R I L +G RID+RG D RPI I G++ + GS+L G TQ LV
Sbjct: 11 AGIMRDHIINLLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKT-- 68
Query: 423 SRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNN 482
+ + P A+ G P R I R+ R + N
Sbjct: 69 ---SLGEPFPDTPNMGVMTTNVELVPLASPTFEP-GPPDERAIELARVIDRGIRESKALN 124
Query: 483 --------NKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAG---------------- 518
K + + + + +G+ A ALL+A
Sbjct: 125 LEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETL 184
Query: 519 -----VPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMD 572
+P+ + + I + +++ D DE+ D + G I+A+Q
Sbjct: 185 DETEPLPVEKIPVPVTFAKIGN----ILVVDPSLDEELVMDGKITITTDETGHISAVQKS 240
Query: 573 IKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 605
+ + A+ A K I + + V
Sbjct: 241 EGG-AFKLEEVMYAVETAFKKAEEIRKLILEAV 272
Score = 45.5 bits (108), Expect = 3e-05
Identities = 51/257 (19%), Positives = 85/257 (33%), Gaps = 75/257 (29%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATVVSC-------KDP-----TSTYNFFPLTVD 125
I IE+G I +A S LV + T +L + P T+ PL
Sbjct: 38 PIEIEVGVIE-KAEGSALVKLGSTQVLVGI-KTSLGEPFPDTPNMGVMTTNVELVPLASP 95
Query: 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRP----------LFPEGYLNEIQ 175
E G P ER ++R+IDR IR + P + +
Sbjct: 96 TFEP---------------GPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVF 140
Query: 176 IVVYVLSVNPQIDPDI--ASIIGVSTALSISELPFL---------------GPLGVAK-- 216
I V+VL D ++ A I AL + +P + PL V K
Sbjct: 141 IDVHVL----DHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIP 196
Query: 217 ----VGYIDGKYILNPTTEQLKKSHLDLLVAGTEK-AIITVE-SESKQLPEDIILNAIIF 270
I +++P+ ++ + + E I V+ SE + ++ A+
Sbjct: 197 VPVTFAKIGNILVVDPSLDEELVMDGKITITTDETGHISAVQKSEGGAFKLEEVMYAV-- 254
Query: 271 GHEKMKIAINAINELVQ 287
+ 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 = 81.2 bits (200), Expect = 5e-17
Identities = 29/82 (35%), Positives = 46/82 (56%), Gaps = 3/82 (3%)
Query: 676 IEKLTESVQIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKEN 733
K E + G+ V R+ ++GA + + GK+ +HIS+++S V I D+LKE
Sbjct: 2 PRKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEG 61
Query: 734 QKVRVKVLGID-DRGRIKLSMI 754
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 = 80.4 bits (198), Expect = 1e-16
Identities = 38/268 (14%), Positives = 81/268 (30%), Gaps = 45/268 (16%)
Query: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 430
++ L + R D R + + R ++ G + GS+L G+T + E
Sbjct: 17 RRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKA-----EFAAP 71
Query: 431 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL----------LPVLP 480
+ + + ++PP + R G P + + L + P
Sbjct: 72 STDAPDKGYVVPNVDLPPLCSSRF-RSGPPGEEAQVASQFIADVIENSQIIQKEDLCISP 130
Query: 481 NNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP-------------------- 520
K + + + +G+ A AL + +P
Sbjct: 131 --GKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSY 188
Query: 521 --ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFG 577
I H + + D +++ D G+E+ + G + L G
Sbjct: 189 LNIRTHPVATSFAVFDDT---LLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKP-GGSG 244
Query: 578 ITYDIIQIALYKAKKGLSYILEKMKTEV 605
+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: 78 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDPTSTYNFFPLTVD--YIEKAYAAG 134
++ IG I+ A S LV + +T ++ V P D Y+
Sbjct: 36 TTTVNIGSIS-TADGSALVKLGNTTVICGVKAEFAAP------STDAPDKGYVVPNVDLP 88
Query: 135 RIPGSFFKREGKPSERETIISRLIDRPIRP--------LFPEGYLNEIQIVVYVLSVNPQ 186
+ S F R G P E + S+ I I L + ++ ++
Sbjct: 89 PLCSSRF-RSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYD 147
Query: 187 IDPDIASIIGVSTALSISELPFL----------------GPLGVAK------VGYIDGKY 224
+ A + AL +LP + L + D
Sbjct: 148 GNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDDTL 207
Query: 225 IL-NPTTEQLKKSHLDLLVAGTEKAIITV--ESESKQLPEDIILNAIIFGHEKMKIAINA 281
++ +PT E+ + L + E+ + + L + + + + K
Sbjct: 208 LIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEVKKL 267
Query: 282 INELVQNVGQK 292
++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 = 76.3 bits (188), Expect = 3e-16
Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 684 QIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 741
+I + V ++ + GA +++L +G++ +S++S +R+ I ++ + VL
Sbjct: 14 EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVL 73
Query: 742 GID-DRGRIKLSM 753
+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 = 5e-16
Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 684 QIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 741
++ V V + + GA + +L +G++ +S++S +R+ I ++ + V V+
Sbjct: 14 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVI 73
Query: 742 GID-DRGRIKLSM 753
+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 = 77.8 bits (192), Expect = 6e-16
Identities = 53/275 (19%), Positives = 97/275 (35%), Gaps = 46/275 (16%)
Query: 360 ILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVAT 419
I+ ++ + I + +KG+R D R + D RP+SI + GS+L G T L
Sbjct: 12 IIPIIKKESIVS-LFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTK 70
Query: 420 LGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL---- 475
L E + +++ + P A G P I R+ R+L
Sbjct: 71 L-----EIDKPYEDTPNQGNLIVNVELLPLAYETFEP-GPPDENAIELARVVDRSLRDSK 124
Query: 476 ------LPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAG----------- 518
L + P K +++ L + + G+ A AL +
Sbjct: 125 ALDLTKLVIEP--GKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGI 182
Query: 519 ----------VPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-IT 567
+P++ V I++ + ++ D DE+ D + T + I
Sbjct: 183 SVNKNEVVGKLPLNYPVVTISVAKVDK----YLVVDPDLDEESIMDAKISFSYTPDLKIV 238
Query: 568 ALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMK 602
+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: 78 KISIEIGEIARQATSSVLVSIEDTVILATVVSC-------KDPTSTYNFFPLTVDYIEKA 130
+SI + ++A S LV + T++LA P L V+
Sbjct: 41 PLSITLDYA-KKADGSALVKLGTTMVLAGT-KLEIDKPYEDTPNQGN----LIVNV---- 90
Query: 131 YAAGRIPGSFFKRE-GKPSERETIISRLIDRPIRP----------LFPEGYLNEIQIVVY 179
+P ++ E G P E ++R++DR +R + P + + + VY
Sbjct: 91 ---ELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVY 147
Query: 180 VLSVNPQID---PDIASIIGVSTALSISELPFLGPLGVAK-------------------- 216
VL D A + AL +++ +
Sbjct: 148 VL----DYGGNVLD-ACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTI 202
Query: 217 -VGYIDGKYILNPTTEQLKKSHLDLLVAGTEK 247
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: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 736
+ G + TG V + GA + + G +G L S+ S RV T L +V
Sbjct: 23 NNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEV 82
Query: 737 RVKVLGID-DRGRIKLSM 753
K G+D I LS+
Sbjct: 83 EAKFTGVDRKNRAISLSV 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 = 74.6 bits (183), Expect = 7e-15
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 3/73 (4%)
Query: 684 QIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 741
G++ V ++FD+G+ + + G L S++SSK V I D LKEN+KV VKV+
Sbjct: 10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVI 69
Query: 742 GID-DRGRIKLSM 753
+D +G + +S+
Sbjct: 70 RVDRRKGTVDVSL 82
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein,
ribonucleoprotein, RNA-binding; NMR {Escherichia coli}
Length = 115
Score = 70.4 bits (173), Expect = 7e-15
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 2/79 (2%)
Query: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 735
+ + G TG V L D+G + I G +GL+H+S++ + + + +
Sbjct: 22 VAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDV 81
Query: 736 VRVKVLGID-DRGRIKLSM 753
V V VL ID +R RI L +
Sbjct: 82 VEVMVLDIDEERRRISLGL 100
>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: 684 QIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 741
++ V V + + GA + +L +G++H+S++S +R+ I ++ + VKV+
Sbjct: 12 EVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVI 71
Query: 742 GID-DRGRIKLSM 753
+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: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 430
+ +++ R+D R D R I I G +G + G T+ L + E
Sbjct: 32 LRAIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSC-----ELVSP 83
Query: 431 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL----------LPVLP 480
L + + A G + RL +R L L V+
Sbjct: 84 KLNRATEGILFFNLELSQMAAPAFEP-GRQSDLLVKLNRLMERCLRNSKCIDTESLCVVA 142
Query: 481 NNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP-------------------- 520
+ + IR+ + +G+ A+ +AL P
Sbjct: 143 --GEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPV 200
Query: 521 ---ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIF 576
I ++ + G +++ D E+R D +A + I +Q
Sbjct: 201 PLSIHHMPICVSFAFFQQGTYLLV--DPNEREERVMDGLLVIAMNKHREICTIQSS-GGI 257
Query: 577 GITYDIIQIALYKAKKGLSYILEKMKT 603
+ 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: 78 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP---TSTYNFFPLTVDYIEKAYAA 133
I I G +V + T +L V P +T ++
Sbjct: 51 NIRISFGT----DYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLEL------- 99
Query: 134 GRIPGSFFKREGKPSERETIISRLIDRPIRP--------LFPEGYLNEIQIVVYVLSVNP 185
+ G+ S+ ++RL++R +R L QI V + +N
Sbjct: 100 -SQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNH 158
Query: 186 QIDPDIASIIGVSTALSISELPFLG-----------------PLGVAK------VGY--I 220
+ A+ I AL P + PL + +
Sbjct: 159 DGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPICVSFAFFQQ 218
Query: 221 DGKYILNPTTEQLKKSHLDLLVAGTEKA-IITVE-SESKQLPEDIILNAIIFGHEKMKIA 278
+++P + + L++A + I T++ S L +D +L KIA
Sbjct: 219 GTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKDQVLRCS-------KIA 271
Query: 279 INAINELVQ 287
+ 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: 681 ESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNI-ITDFLKENQKVRVK 739
++ G + V R + I S + +++ + + ++ + + + K
Sbjct: 901 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAK 960
Query: 740 VLGID-DRGRIKLSM 753
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: 663 SFNSVSGQEAKRRIEKLT-ESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK 721
F+ + G E + + + ++ G + V R + I S + +++ + +
Sbjct: 879 DFHPLQGDEIFQSLTGESEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGA 938
Query: 722 RVNI-ITDFLKENQKVRVKVLGID-DRGRIKLSM 753
++ + + + 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 = 69.7 bits (170), Expect = 5e-13
Identities = 37/268 (13%), Positives = 74/268 (27%), Gaps = 47/268 (17%)
Query: 374 LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALM 433
+ + LR+D RG D R + + T ++ T GS+ G T LV E L
Sbjct: 32 VQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKA-----EMGTPKLE 86
Query: 434 GEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLP--------NNNKF 485
+ AT + R + +
Sbjct: 87 KPNEGYLEFFVDCSASATPEF-EGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREH 145
Query: 486 NYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP------------------------- 520
+ + + + E G+ A AL + +P
Sbjct: 146 CWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIR 205
Query: 521 --ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFG 577
+ + + I + D E+ C V+ T G +T ++ +
Sbjct: 206 LSVENVPCIVTLCKIGY----RHVVDATLQEEACSLASLLVSVTSKGVVTCMRK-VGKGS 260
Query: 578 ITYDIIQIALYKAKKGLSYILEKMKTEV 605
+ + I + K+ + +++ V
Sbjct: 261 LDPESIFEMMETGKRVGKVLHASLQSVV 288
Score = 38.1 bits (88), Expect = 0.008
Identities = 36/249 (14%), Positives = 77/249 (30%), Gaps = 44/249 (17%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAGRIP 137
+ +E ++ + S V + T IL V + + +
Sbjct: 48 CVEVETDVVS-NTSGSARVKLGHTDILVGVKAEMGTP-----KLEKPNEGYLEFFVDCSA 101
Query: 138 GSFFKRE-GKPSERETIISRLIDRPIRP---LFPEGYL-----NEIQIVVYVLSVNPQID 188
+ + E + T I+ + R + + + + V VL + +
Sbjct: 102 SATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGN 161
Query: 189 PDIASIIGVSTALSISELPFLG---------------------PLGVAK------VGYID 221
A I V AL + +P + L V + I
Sbjct: 162 LFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIG 221
Query: 222 GKYILNPTTEQLKKSHLDLLVAGTEKAIITV--ESESKQLPEDIILNAIIFGHEKMKIAI 279
+++++ T ++ S LLV+ T K ++T + L + I + G K+
Sbjct: 222 YRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKRVGKVLH 281
Query: 280 NAINELVQN 288
++ +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 = 5e-12
Identities = 30/83 (36%), Positives = 48/83 (57%), Gaps = 2/83 (2%)
Query: 673 KRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKE 732
+ +E L + ++ G V G+V + +FGA + I +DGL+HIS +S K V + +K
Sbjct: 643 QEGVESL-KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKA 701
Query: 733 NQKVRVKVLGID-DRGRIKLSMI 754
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 = 60.9 bits (148), Expect = 9e-12
Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 302 DKTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLI----DNENLTIDINDI 357
D L ++I+ ++KA QI+ K+ ++ + + + + + ++E + D+
Sbjct: 10 DADLQAEIVGKYNADLQKAVQIEEKKASEIATEAVKEHVTAEYEERYAEHEEHDRIMRDV 69
Query: 358 NCILYDLESKIIRKQILDKGLRID 381
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 = 60.5 bits (147), Expect = 2e-11
Identities = 16/95 (16%), Positives = 31/95 (32%), Gaps = 3/95 (3%)
Query: 291 QKKVNWDPIVKDKTLISKIINISEHKIRKAYQI--KNKQIRDLTFKNISKDIYSSLIDNE 348
++ I+ K+ + +K RD I D L + +
Sbjct: 4 GSSGPQKIFTPSAEIVKYTKIIAMEKLYAVFTDYEHDKVSRDEAVNKIRLDTEEHLKE-K 62
Query: 349 NLTIDINDINCILYDLESKIIRKQILDKGLRIDNR 383
+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: 616 APRLITIKIDPSKIRDVIGKGGSTIRTLTEETG-TQIDINDE-GIITIASFNSVSGQEAK 673
+ + + IG G+ I+ + G T ID++++ I + + ++A+
Sbjct: 2 SRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKAR 61
Query: 674 RRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKEN 733
+E + +Q+ + G V + G +I+ + K G++ + + N+ +E
Sbjct: 62 SFLEFAEDVIQVPRNLVGKV--IGKNGKLIQEIVDKSGVVRVRIEAENEKNVP----QEE 115
Query: 734 QKVRVKVLG 742
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: 537 EKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSY 596
E+ ++ D++G + + A V G+TA+ +D
Sbjct: 6 EQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFH----------------- 48
Query: 597 ILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETG-TQIDIND 655
I + + V K ++ L I++ + + VIGK G I+ + +++G ++ I
Sbjct: 49 IYGEDQDAVKKARSFLE---FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEA 105
Query: 656 EGIITIASFNSVSG----------QEAKRRIEKLTESVQ 684
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: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 430
+ L + R+D R + R + I G + G G+T+ + +
Sbjct: 16 LEALRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISC-----QIAQP 67
Query: 431 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL----------LPVLP 480
F F++ + P A + E+ R+ ++++ L ++
Sbjct: 68 YEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVA 127
Query: 481 NNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP-------------------- 520
+++R + +G AS L+ P
Sbjct: 128 --GSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPV 185
Query: 521 ---ISEHVAGIAMGLIKDGEKV----------VILSDILGDEDRCGDMDFKVAGTVNG-I 566
I + + + + D E+ D V N +
Sbjct: 186 PLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKNREV 245
Query: 567 TALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRL 619
+ + + ++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: 611 ELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG--------IITIA 662
L++ P + + + +IG+GG TIR++ + +G +I + E +I I+
Sbjct: 8 ILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKIS 67
Query: 663 SFNSVSGQEAKRRIEKLTESVQ 684
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 = 62.0 bits (150), Expect = 7e-10
Identities = 115/762 (15%), Positives = 197/762 (25%), Gaps = 325/762 (42%)
Query: 79 ISIEIGEIARQATSSVLVSIEDTVILATVVSCKD------PTSTYNF---------FPLT 123
+++ G + +LV + +A+ + ++ P T F L
Sbjct: 9 LTLSHGSL----EHVLLVP-TASFFIASQL--QEQFNKILPEPTEGFAADDEPTTPAELV 61
Query: 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 183
++ Y + + K + + +++ + F YL
Sbjct: 62 GKFL--GYVSSLV------EPSKVGQFDQVLNLCLTE-----FENCYLEG---------- 98
Query: 184 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 243
N DI ++ + L ++ + + K YI + + ++ S L
Sbjct: 99 N-----DIHAL--AAKLLQENDTTLVKTKELIKN-YITARIMAKRPFDKKSNSAL-FRAV 149
Query: 244 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVN--WDPIVK 301
G A + IFG GQ + ++
Sbjct: 150 GEGNAQLVA----------------IFG------------------GQGNTDDYFE---- 171
Query: 302 DKTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCIL 361
E +R Y Y L+ +L I L
Sbjct: 172 ------------E--LRDLY-----------------QTYHVLV--GDL---IKFSAETL 195
Query: 362 YDL-ESKIIRKQILDKGLRIDN--RGVNDIR--------PISI----------------R 394
+L + + +++ +GL I ++ PIS
Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKL 255
Query: 395 TGILP---RTHGSSLFTRGDTQALVVAT-LGTSRDEQKIDALMGEFTDSF--MLHYNMPP 448
G P R++ Q LV A + + + F S +
Sbjct: 256 LGFTPGELRSYLKGATGHS--QGLVTAVAIAETDSWE-------SFFVSVRKAITV---L 303
Query: 449 FATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNG---SSSMA 505
F IGV R + +L P + E + N S M
Sbjct: 304 F------FIGV---R--CYEAYPNTSLPP-------------SILEDSLENNEGVPSPML 339
Query: 506 SVCGGCLALLDAGV-------PISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFK 558
S+ + V P + V I+ L+ G +
Sbjct: 340 SISNLTQEQVQDYVNKTNSHLPAGKQVE-IS--LV------------------NGAKNLV 378
Query: 559 VAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPR 618
V+G +LY GL+ L K K AP
Sbjct: 379 VSGPP---------------------QSLY----GLNLTLRKAK-------------APS 400
Query: 619 LITIKIDPSKI----RDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKR 674
+D S+I R + + R L + + F+S A
Sbjct: 401 ----GLDQSRIPFSERKLKF----SNRFLP--------------VA-SPFHSHLLVPASD 437
Query: 675 RIEK--LTESVQIGKVYTGI-VLRLFDFGAIIRILSGKDGLLHISQISSKRVN------- 724
I K + +V I V FD G+ +R+LSG + I V
Sbjct: 438 LINKDLVKNNVSFNAKDIQIPVYDTFD-GSDLRVLSGSISERIVDCIIRLPVKWETTTQF 496
Query: 725 ----IITDF--------------LKENQKVRVKVLGIDDRGR 748
I+ DF K+ VRV V G D
Sbjct: 497 KATHIL-DFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINP 537
Score = 51.2 bits (122), Expect = 1e-06
Identities = 105/646 (16%), Positives = 183/646 (28%), Gaps = 239/646 (36%)
Query: 49 DHHSRRGLIMMKGNFLFNKIIKSFKYGSYKISIEI-------GEIAR--------QATSS 93
D +S R L + +GS + + + + + T
Sbjct: 2 DAYSTRPLTL--------------SHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEG 47
Query: 94 VLVSIEDTVI-------LATVVSCKDPTSTYNFFP---LTVDYIEKAY--------AAGR 135
E T L V S +P+ F L + E Y A +
Sbjct: 48 FAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAK 107
Query: 136 IPGSFFKREGKPSERETII------SRLIDRPIRP-----LF------------------ 166
+ + + + +I + RP LF
Sbjct: 108 LLQE---NDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQG 164
Query: 167 -PEGYLNEIQIV--VYVLSVNPQIDP-----------------------DIAS-IIGVST 199
+ Y E++ + Y + V I +I + S
Sbjct: 165 NTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSN 224
Query: 200 ALSISEL---PFLGPL-GVAKVG-YIDGKYILNPTTEQLKKS------HLDLLVAGTEKA 248
L P PL GV ++ Y+ +L T +L+ H LV A
Sbjct: 225 TPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVT----A 280
Query: 249 IITVESESKQLPEDIILNAI--IF-----GHE---KMKIAINAINELVQNVGQKKVNWDP 298
+ E++S + + AI +F +E + + + + ++N + P
Sbjct: 281 VAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLEN-NEGV----P 335
Query: 299 IVKDKTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLI---DNENLT---I 352
+ + I N+++ +++ N + K + SL+ N ++
Sbjct: 336 -----SPMLSISNLTQEQVQDYVNKTNSHLPA------GKQVEISLVNGAKNLVVSGPPQ 384
Query: 353 DINDINCILYDLESKIIRKQILDKGL---RIDNRGVNDIRPISIRTGILPRT---HGSSL 406
LY L +RK GL RI R + LP H S L
Sbjct: 385 S-------LYGLNLT-LRKAKAPSGLDQSRIPFSE----RKLKFSNRFLPVASPFH-SHL 431
Query: 407 FTRGDTQALVVATLGTSRDEQKIDALMGEFT-DSFMLHYNMPPFATGDIGRIGVPKRREI 465
L + D D + + ++ + +P + T D
Sbjct: 432 -------------LVPASDLINKDLVKNNVSFNAKDIQ--IPVYDTFD------------ 464
Query: 466 GHG-RLAKRALLPVLPNNNKFNYSIRLVSEITES-----NGSSSMASVCGGCLALLDAGV 519
G R+ ++ R+V I + A+ +LD G
Sbjct: 465 GSDLRVLSGSISE------------RIVDCIIRLPVKWETTTQFKAT------HILDFG- 505
Query: 520 PISEHVAGIAMGL------IKDGEKV-VILSDILGDEDRCGDMDFK 558
P G A GL KDG V VI++ L D + D FK
Sbjct: 506 P------GGASGLGVLTHRNKDGTGVRVIVAGTL-DINPDDDYGFK 544
Score = 42.3 bits (99), Expect = 6e-04
Identities = 48/319 (15%), Positives = 97/319 (30%), Gaps = 121/319 (37%)
Query: 433 MGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLV 492
MG M Y A +++ RA + + +SI
Sbjct: 1631 MG------MDLYKTSKAA------------QDV-----WNRADNHFK---DTYGFSI--- 1661
Query: 493 SEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDG----EKVV-----ILS 543
+I +N + + GG + G I E+ + + I DG EK+ +
Sbjct: 1662 LDIVINNPVN-LTIHFGG-----EKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHST 1715
Query: 544 DIL--GDEDRCGDMDFKVAGTVN---GITALQM----DIKIFGITYDIIQIALYKAKKGL 594
++ T +T ++ D+K G+ I A G
Sbjct: 1716 SYTFRSEKGLLSA-------TQFTQPALTLMEKAAFEDLKSKGL----IPADATFA--GH 1762
Query: 595 S---Y-----------------ILEK----MKTEVPKCKNELSKFAPRLITIKIDPSKIR 630
S Y ++ M+ VP+ + S + I I+P ++
Sbjct: 1763 SLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYG----MIAINPGRV- 1817
Query: 631 DVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNS------VSGQ-EA----------- 672
++ + E G + ++ I ++N +G A
Sbjct: 1818 -AASFSQEALQYVVERVGKRTG----WLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFI 1872
Query: 673 -KRRIE--KLTESVQIGKV 688
++I+ +L +S+ + +V
Sbjct: 1873 KLQKIDIIELQKSLSLEEV 1891
Score = 42.3 bits (99), Expect = 7e-04
Identities = 43/276 (15%), Positives = 87/276 (31%), Gaps = 78/276 (28%)
Query: 74 YGSYKISIEIGEIARQATSSVL-VSIEDTVILATVVSCKDPTS-TYNFFPLTVDYIEKAY 131
Y + K + ++ A SI D VI +P + T +F I + Y
Sbjct: 1636 YKTSKAAQDVWNRADNHFKDTYGFSILDIVI-------NNPVNLTIHFGGEKGKRIRENY 1688
Query: 132 AAGRIPGSFFKREGKPSER---ETIISRLIDRPIRPLF--PEGYLN--EI-QIVVYVLSV 183
+A E + E I + + F +G L+ + Q + ++
Sbjct: 1689 SA-------MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEK 1741
Query: 184 -------NPQIDPDIASIIGVS----TAL-SISE-LPF-------------------LGP 211
+ + P A+ G S AL S+++ +
Sbjct: 1742 AAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDE 1801
Query: 212 LGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKAIITVESESKQLPEDII-LNA--- 267
LG + G I +NP + + + V + L E I+ N
Sbjct: 1802 LGRSNYGMIA----INPG-----RVAASFSQEALQYVVERVGKRTGWLVE-IVNYNVENQ 1851
Query: 268 --IIFGHEKMKIAINAINELVQNVGQKKVNWDPIVK 301
+ G + A++ + ++ + +K+ I++
Sbjct: 1852 QYVAAGDLR---ALDTVTNVLNFIKLQKI---DIIE 1881
Score = 37.3 bits (86), Expect = 0.021
Identities = 47/240 (19%), Positives = 82/240 (34%), Gaps = 88/240 (36%)
Query: 16 SRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGNFLFNKIIKSFKYG 75
S T+ T Q AL F+ +K +GLI F G
Sbjct: 1727 SATQF-T-----QPALTLMEK----AAFED-LKS----KGLIPADATFA----------G 1761
Query: 76 -SYKISIEIGEI-ARQATSSVLVSIEDTV-------ILATVVSCKDPTSTYNFFPLTVDY 126
S +GE A + + V+ SIE V + V +D N+ + ++
Sbjct: 1762 HS------LGEYAALASLADVM-SIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAIN- 1813
Query: 127 IEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVN-- 184
GR+ + F +E + ++ R+ R G+L EI VN
Sbjct: 1814 ------PGRV-AASFSQEAL----QYVVERVGKR-------TGWLVEI--------VNYN 1847
Query: 185 -P--QIDPDIAS--IIGVSTALSISELPFLGPLGVAKVGYID-GKYILNPTTEQLKKSHL 238
Q +A+ + + T ++ L K+ ID + + + E++ + HL
Sbjct: 1848 VENQQY---VAAGDLRALDTVTNV--------LNFIKLQKIDIIELQKSLSLEEV-EGHL 1895
Score = 32.3 bits (73), Expect = 0.75
Identities = 50/298 (16%), Positives = 79/298 (26%), Gaps = 127/298 (42%)
Query: 287 QNVG-----------QKKVNWD---------------PIVKD--KTLISKIINISEHKIR 318
Q G + V W+ IV + L +IR
Sbjct: 1627 QEQGMGMDLYKTSKAAQDV-WNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIR 1685
Query: 319 KAYQ-------IKNKQIRDLTFKNISKDIYSSLI---DNE--NLTIDINDIN---CILYD 363
+ Y + K + FK I++ +S + + T +
Sbjct: 1686 ENYSAMIFETIVDGKLKTEKIFKEINEHS-TSYTFRSEKGLLSATQ-----FTQPALT-- 1737
Query: 364 LESKIIRKQILDKGLRIDNR-----------------GVNDIRPISIRTGI-LPRTHGSS 405
L K + + KGL + V +SI + + +
Sbjct: 1738 LMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADV-----MSIESLVEV------- 1785
Query: 406 LFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREI 465
+F RG T + V RDE +Y M + GR+ +E
Sbjct: 1786 VFYRGMTMQVAVP-----RDELG------------RSNYGM---IAINPGRVAASFSQEA 1825
Query: 466 GHG---RLAKRA--LL-PVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDA 517
R+ KR L+ V NY N + V G L LD
Sbjct: 1826 LQYVVERVGKRTGWLVEIV-------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 = 54.0 bits (130), Expect = 3e-09
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI----NDEGIITIASFNSVSGQEAKRR 675
T+ I R VIGK G ++ L +T T+I I + I I ++A+
Sbjct: 19 ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITG-TKEGIEKARHE 77
Query: 676 IEKLTE 681
+ ++
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 = 7e-09
Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 5/80 (6%)
Query: 609 KNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG----IITIASF 664
K L P I +++ R VIG+ GS IR + +E I + II I
Sbjct: 8 KEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITG- 66
Query: 665 NSVSGQEAKRRIEKLTESVQ 684
+ + 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 = 53.9 bits (129), Expect = 2e-08
Identities = 25/126 (19%), Positives = 52/126 (41%), Gaps = 12/126 (9%)
Query: 637 GSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTE--SVQIGKVYTGIVL 694
G I + E + + G + A + ++ ++E ++ + G V G V+
Sbjct: 7 GDRIGSAEEYVKGEGVYEEGGELFAAVAGKLIIKDRVAKVESISPIPEIVKGDVVLGRVV 66
Query: 695 RLFDFGAIIRILSGKD----------GLLHISQISSKRVNIITDFLKENQKVRVKVLGID 744
L + A+I + S K G+LH+S + V I++ + ++ +V+G +
Sbjct: 67 DLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIGDN 126
Query: 745 DRGRIK 750
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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG-------IITIASFNSVSGQEA 672
+++ +DP +IG+ G+ I + E I D+ ITI + + A
Sbjct: 19 LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITG-YEKNTEAA 77
Query: 673 KRRIEKLTESVQ 684
+ I ++ ++
Sbjct: 78 RDAILRIVGELE 89
>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 = 54.9 bits (131), Expect = 9e-08
Identities = 73/447 (16%), Positives = 145/447 (32%), Gaps = 116/447 (25%)
Query: 1 MTIKNNIKASIILDNSRT------KNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRR 54
+ +KN +L+ + N T + + + RI+ + + +K
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD-HSSNIKLRIHSIQAELRRLLKSKPYEN 245
Query: 55 GLIMMKGNFLFN----KIIKSFKYGSYKI-----SIEIGEIARQATSSVLVSIEDTV--- 102
L++ L N K +F KI ++ + AT++ +S++
Sbjct: 246 CLLV-----LLNVQNAKAWNAFNLSC-KILLTTRFKQVTDFLSAATTTH-ISLDHHSMTL 298
Query: 103 -------ILATVVSCKD---PTSTYNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERET 152
+L + C+ P P + I ++ G +K
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDK---- 354
Query: 153 IISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSI--SELPFLG 210
++ +I+ + L P E + + LSV P I +I+ LS+ ++
Sbjct: 355 -LTTIIESSLNVLEP----AEYRKMFDRLSVFPP-SAHIPTIL-----LSLIWFDVI--- 400
Query: 211 PLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKAIITVES----ESKQLPEDIILN 266
D ++N + K S L+ +++ I++ S +L + L
Sbjct: 401 --------KSDVMVVVN---KLHKYS---LVEKQPKESTISIPSIYLELKVKLENEYAL- 445
Query: 267 AIIFGHEKMKIAINAINELVQNVGQKKVNWD--PIVKDKTLISKI----INISEHK---- 316
H + ++ N+ + + D P D+ S I NI +
Sbjct: 446 -----HRSI------VDHY--NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL 492
Query: 317 IRKAYQ----IKNKQIRDLTFKNISKDI---------YSSLI-DNEN-LTIDINDINCIL 361
R + ++ K D T N S I Y I DN+ +N I L
Sbjct: 493 FRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFL 552
Query: 362 YDLESKIIR---KQILDKGLRIDNRGV 385
+E +I +L L ++ +
Sbjct: 553 PKIEENLICSKYTDLLRIALMAEDEAI 579
Score = 43.3 bits (101), Expect = 3e-04
Identities = 40/331 (12%), Positives = 88/331 (26%), Gaps = 103/331 (31%)
Query: 464 EIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISE 523
E G + + +L V + N+ + V ++ +S L + +
Sbjct: 10 ETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKS--------------ILSKEEI---D 52
Query: 524 HVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDII 583
H+ + + L L + F V L+++ Y +
Sbjct: 53 HI----IMSKDAVSGTLRLFWTLLSKQEEMVQKF-----VE--EVLRIN-------YKFL 94
Query: 584 QIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVI---------- 633
+ ++ S + + + N+ FA ++ K+R +
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL 154
Query: 634 --GKGGSTIRTLTEETGTQIDI---NDEGI--ITIASFNS-------------------V 667
G GS + + + D I + + + NS
Sbjct: 155 IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214
Query: 668 SGQEAKRRIEKLTESVQIGK------------------VYTGIVLRLFDFGAIIRILSGK 709
S + I+ S+Q V F+ +IL
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC--KIL--- 269
Query: 710 DGLLHISQISSKRVNIITDFLKENQKVRVKV 740
++++ +TDFL + +
Sbjct: 270 --------LTTRFKQ-VTDFLSAATTTHISL 291
Score = 42.9 bits (100), Expect = 4e-04
Identities = 65/550 (11%), Positives = 158/550 (28%), Gaps = 162/550 (29%)
Query: 219 YIDGKYILNPTTEQLKKSHLDLLVAGTEKAIITVESESKQL-PEDIILNAIIFGHEKMK- 276
YI+ + L + K ++ + + + +L P + +I G +
Sbjct: 112 YIEQRDRLYNDNQVFAKYNVS-----RLQPYLKLRQALLELRPAKNV---LIDG---VLG 160
Query: 277 -----IAINAI-NELVQNVGQKKVNWDPIVKDKTLISKIINISEHKIRKAYQIKNKQIRD 330
+A++ + VQ K+ W +N+ + ++ Q
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFW-------------LNLKNCNSPET-VLEMLQ--K 204
Query: 331 LTFKNISKDIYSSLIDN-ENLTIDINDINCILYDLESKIIRKQILDKGLRI-DNRGVNDI 388
L ++ I + ++S D+ N+ + I+ I L ++++ + + L + N V +
Sbjct: 205 LLYQ-IDPN-WTSRSDHSSNIKLRIHSIQAEL----RRLLKSKPYENCLLVLLN--VQNA 256
Query: 389 RPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGE------------- 435
+ + F + L T+R +Q D L
Sbjct: 257 KAWN-------------AF---NLSC---KILLTTRFKQVTDFLSAATTTHISLDHHSMT 297
Query: 436 FTDS-----FMLHYNMP------------PFATGDIGRIGVPKRREIGHGRLAKRALLPV 478
T + + + P + I R + K
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR---LSIIAESIRDGLATWDNWKH----- 349
Query: 479 LPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEK 538
N +K I + E M L++ I + + + +
Sbjct: 350 -VNCDKLTTIIESSLNVLEPAEYRKMFDR----LSVFPPSAHIPTILLSLIWFDVIKSDV 404
Query: 539 VVILSDI----LGDEDRCG------DMDFKVAGTVNGITALQMDIKIFGIT-YDIIQ--- 584
+V+++ + L ++ + ++ + AL I + Y+I +
Sbjct: 405 MVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI----VDHYNIPKTFD 460
Query: 585 ----------------IA--LYKAKKG------------LSYILEKMKTEVPKCKNELSK 614
I L + ++ +K++ + N
Sbjct: 461 SDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAW-NASGS 519
Query: 615 FAPRLITIKIDPSKIRDVIGKGGSTIRTLTE---ETGTQIDINDE-GIITIASFNSVSG- 669
L +K I D K + + + + + + ++ IA
Sbjct: 520 ILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAI 579
Query: 670 -QEAKRRIEK 678
+EA +++++
Sbjct: 580 FEEAHKQVQR 589
Score = 31.7 bits (71), Expect = 0.97
Identities = 13/99 (13%), Positives = 29/99 (29%), Gaps = 29/99 (29%)
Query: 7 IKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRR-GLIMMKGNFLF 65
++ I D + + + + L +K +I D+ + L+ +FL
Sbjct: 503 LEQKIRHD--------STAWNASGSILNTLQQLKF-YKPYICDNDPKYERLVNAILDFLP 553
Query: 66 N---KIIKS-----------FKYGSYKISIEIGEIARQA 90
+I S + + E +Q
Sbjct: 554 KIEENLICSKYTDLLRIALMAEDEAI-----FEEAHKQV 587
>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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI------NDEGIITIA-SFNSVSGQEA 672
I + + + VIG+ G I+ + + G +I E I I + + A
Sbjct: 13 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRC--EHA 70
Query: 673 KRRIEKLTESVQ 684
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: 586 ALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTE 645
+ +A + + IL + +NE I + + + VIG+ G I+ +
Sbjct: 59 KVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQN 118
Query: 646 ETGTQIDI------NDEGIITIA-SFNSVSGQEAKRRIEKLTESVQIG 686
+ 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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG 657
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 = 8e-07
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG----IITIASFNSVSGQEAKRR 675
+ I ID R +IGK G+ I + ++ + I + +I I + Q+AKR
Sbjct: 7 VEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEG-DPQGVQQAKRE 65
Query: 676 IEKL 679
+ +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 = 1e-06
Identities = 16/71 (22%), Positives = 25/71 (35%), Gaps = 8/71 (11%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI-----NDEGIITIA-SFNSVSGQEAK 673
+ +D +IG G IR + +E I D +T+ +V +EA
Sbjct: 19 EDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENV--EEAI 76
Query: 674 RRIEKLTESVQ 684
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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI--------NDEGIITIA-SFNSVSGQ 670
I I K VIGKGG TI+ L E G ++ + N + + I V Q
Sbjct: 16 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKV--Q 73
Query: 671 EAKRRIEKL 679
+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: 621 TIKIDPSKI-RDVIGKGGSTIRTLTEETGTQ--------IDINDEGIITIASFNSVSGQE 671
+K+ P + +D+ + E + +D+ D G + + +
Sbjct: 10 VVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHP 69
Query: 672 AKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNII----- 726
++ ++ G V+ + +FG+ +R L DGL+H+SQI V+
Sbjct: 70 VVFETLVY--IPEMYELIEGEVVDVVEFGSFVR-LGPLDGLIHVSQIMDDYVSYDPKREA 126
Query: 727 ------TDFLKENQKVRVKVLGIDDRGR------IKLSM 753
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: 596 YILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND 655
+K ++ + + E R ++I P+K+ VIG+ S ++TL E+T +I +
Sbjct: 126 VAFDKTRSPLLTVQGEGLGRIVRGKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR 185
Query: 656 EGIITIASFNSVSGQEAKRRIEKLTESVQIG 686
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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG---------IITIA-SFNSVSG 669
+T I K VIG+GG ++ + ++TG ++I+ + + I S +
Sbjct: 9 MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQI-- 66
Query: 670 QEAKRRI-EKLTESVQIG 686
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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG 657
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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG-------IITI-ASFNSVSGQE 671
+ + I + +IGK G I+ L+ I I ++ I + +
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQ--FK 62
Query: 672 AKRRIEKL--TESVQIGKVYTGIVLRLFDFGAIIRILSGKDG--LLHISQISSKRVNIIT 727
A+ RI E+ K + + + + GK G + + +++ V +
Sbjct: 63 AQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 122
Query: 728 DFL-KENQKVRVKVLG 742
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 = 2e-05
Identities = 29/135 (21%), Positives = 58/135 (42%), Gaps = 16/135 (11%)
Query: 622 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND----EGIITI-ASFNSVSGQEAKRRI 676
+ + ++ +IGK G +++ + EE+G +I+I++ E IIT+ N++ +A I
Sbjct: 9 LLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAI--FKAFAMI 66
Query: 677 EKLTESVQIGKVYTG-------IVLRLFDFGAIIRILSGKDGLL--HISQISSKRVNIIT 727
E + + LRL + L GK G I + + +V +
Sbjct: 67 IDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG 126
Query: 728 DFLKENQKVRVKVLG 742
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: 590 AKKGLSYILEKMKTEVPKCKNELSKFAPRLITIK--IDPSKIRDVIGKGGSTIRTLTEET 647
K + I++K++ ++ + + +T++ + S+ +IGKGG I+ + E T
Sbjct: 59 IFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIREST 118
Query: 648 GTQIDI-------NDEGIITIA-SFNSVSGQEAKRRI-EKLTES 682
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 = 43.2 bits (102), Expect = 2e-05
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND------EGIITIA-SFNSVSGQEA 672
K+ + +IG+GG I + +E+G +I I E + + SV Q A
Sbjct: 17 EEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESV--QSA 74
Query: 673 KRRIEKLTESVQIG 686
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 = 3e-05
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND------EGIITIA-SFNSVSGQEA 672
+ I +IGKGG I+ + E+G I I++ + IITI + + + Q A
Sbjct: 16 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQI--QNA 73
Query: 673 KRRIEKL 679
+ ++
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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND------EGIITIA-SFNSVSGQEA 672
+ I +IGKGG I+ + E+G I I++ + IITI + + + Q A
Sbjct: 9 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQI--QNA 66
Query: 673 KRRIEKL 679
+ ++
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 = 1e-04
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 12/75 (16%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG---------IITIA-SFNSVSG 669
+ I + + + ++GKGG T+ E TG +I I+ +G +TI S +
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT-- 62
Query: 670 QEAKRRIEKLTESVQ 684
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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG 657
+ + + + + ++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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI---NDEGIITIASFNSVSGQEAKRRI 676
I +++ + V+G G+TI+ + + T T I + E + + + + A+ I
Sbjct: 12 IQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAV-TGMPENVDRAREEI 70
Query: 677 E 677
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: 620 ITIKI--DPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG----IITI-ASFNSVSGQEA 672
+TI++ ++ +IGK G +++ + EE+G +I+I++ IIT+ N++ +A
Sbjct: 5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAI--FKA 62
Query: 673 KRRI-EKLTE 681
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 = 40.0 bits (94), Expect = 2e-04
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG------IITIA-SFNSVSGQEA 672
+ I + I +IG+ G+ I + + +G QI I + +TI S S+ A
Sbjct: 8 HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASI--SLA 65
Query: 673 KRRIE 677
+ I
Sbjct: 66 QYLIN 70
>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 = 41.8 bits (98), Expect = 2e-04
Identities = 31/158 (19%), Positives = 63/158 (39%), Gaps = 28/158 (17%)
Query: 621 TIKIDPSKIRDVIGK------GGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEA-- 672
++I P++ + + + ++ G + I + + T V G A
Sbjct: 10 IVRIPPNEFGKPLNEIALNELRQQYQEKILKDLGLVLAILN--VKTSEEGMLVFGDGATY 67
Query: 673 -KRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIIT---- 727
+ + +T + +V G VL++ ++G + L DGL+HISQI+ +
Sbjct: 68 HEVEFDMITYVPVVQEVVEGEVLQVDNYGVFVN-LGPMDGLVHISQITDDTLKYDNVRGI 126
Query: 728 -------DFLKENQKVRVKVLGIDD-----RGRIKLSM 753
+++ 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: 626 PSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQI 685
P +IG+ G T + + E +G + + + + I + + + AK IEKL
Sbjct: 137 PRVRGRIIGRKGRTRQIIEEMSGASVSVYGKTVAIIGNPIQI--EIAKTAIEKLARGSPH 194
Query: 686 GKVY 689
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: 604 EVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITI 661
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 = 8e-04
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 9/70 (12%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND------EGIITIA-SFNSVSGQEA 672
+ I I +IG+ G+ I + + +G QI I + + +TI S S+ A
Sbjct: 7 HELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASI--SLA 64
Query: 673 KRRIEKLTES 682
+ 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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI------NDEGIITI-ASFNSVSGQEA 672
I + I + VIG+ G I+ + + G +I E I I + Q A
Sbjct: 5 IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRA--QHA 62
Query: 673 KRRIEKLTESVQ 684
I L SVQ
Sbjct: 63 AEIITDLLRSVQ 74
Score = 35.6 bits (82), Expect = 0.023
Identities = 10/38 (26%), Positives = 22/38 (57%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG 657
+ 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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG 657
+ + I +IGKGG TI L +ETG I ++
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSK 45
Score = 39.1 bits (91), Expect = 0.002
Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 12/75 (16%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI--------NDEGIITIA-SFNSVSGQ 670
+ I + S +IGKGG+T++ + E++G + + ++T++ +
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQN--R 163
Query: 671 EAKRRI-EKLTESVQ 684
+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: 622 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITIAS 663
+K+ P ++ VIG G + TGT I ++ + ++ +
Sbjct: 8 VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEP 50
Score = 39.2 bits (91), Expect = 0.002
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 632 VIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 689
+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: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEE-TGTQIDINDEG----IITIA-SFNSVSGQEAK 673
+ + I +IG G IR++ EE G I EG + I + V ++AK
Sbjct: 19 VEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDV--EKAK 76
Query: 674 RRIEKLTESVQ 684
+++ 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: 664 FNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGK-DGLLHISQISSKR 722
+ ++ QE +R+ + + + + IV RL G + + G +H S+ ++
Sbjct: 131 WGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERYAE- 189
Query: 723 VNIITDFLKENQKVRVKVLGID-DRGRIKLSM 753
+ Q + +V+G + LS+
Sbjct: 190 -------PRLGQVLDARVIGFREVDRTLNLSL 214
Score = 34.9 bits (80), Expect = 0.068
Identities = 14/88 (15%), Positives = 36/88 (40%), Gaps = 7/88 (7%)
Query: 670 QEAKRRIEKLTESVQIGKVYTGIVLRLF-DFGAIIRI-LSGKDGLLHISQISSKRVNIIT 727
+ K R+ L + + G V + D G + L K+ ++ + + +
Sbjct: 54 MKQKLRLTTLEVTATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKEL--- 110
Query: 728 DFLKENQKVRVKVLGIDDRGRIKLSMIY 755
+ K+ ++ +++ +D + RI + Y
Sbjct: 111 -WPKKGDQLYIRLE-VDKKDRIWGLLAY 136
Score = 31.8 bits (72), Expect = 0.76
Identities = 7/72 (9%), Positives = 22/72 (30%), Gaps = 12/72 (16%)
Query: 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 741
+ + G+++ D ++ G+ L + V+
Sbjct: 3 NTNLASFIVGLIIDENDRFYFVQK-DGQTYALAKEEGQ----------HTVGDTVKGFAY 51
Query: 742 GIDDRGRIKLSM 753
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 = 40.0 bits (94), Expect = 0.003
Identities = 14/105 (13%), Positives = 35/105 (33%), Gaps = 19/105 (18%)
Query: 656 EGIITIASFNSVSGQEAKRRIEKLTESV----QIGKVYTGIVLRLFDFGAIIRILS-GKD 710
I + N+ + ++A+R + Q +V+ +V+ A + I D
Sbjct: 370 AAHIAESQMNADATRQAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFD 429
Query: 711 GLLHISQISSKRVNIITDFLKENQKVRVKVLGID-DRGRIKLSMI 754
++ ++V+ ID + R++ +
Sbjct: 430 VQVNTP-------------AAPGTALQVQFADIDLPQMRVRARSV 461
>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 = 36.2 bits (83), Expect = 0.005
Identities = 13/66 (19%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 622 IKIDPSKIRDVIGKGGSTIRTLTEETG-TQIDINDE-GIITIASFNSVSGQEAKRRIEKL 679
+ + IG GS I+ + G T I+++++ G I ++ + ++A+ +E +
Sbjct: 19 FVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLEFV 78
Query: 680 TESVQI 685
+ +Q+
Sbjct: 79 EDFIQV 84
>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 = 0.005
Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 5/68 (7%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEE-TGTQIDIND-EGIITIA-SFNSVSGQEAKRRI 676
++ R +IGK G + +T++ I+ + E IT+ V A+ +I
Sbjct: 29 SSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKITLEGPTEDV--SVAQEQI 86
Query: 677 EKLTESVQ 684
E + + +
Sbjct: 87 EGMVKDLI 94
>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 = 35.0 bits (80), Expect = 0.018
Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 3/76 (3%)
Query: 681 ESVQIGKVYTGIVLRLFDFGAIIRI-LSGKDGLLHISQISS-KRVNIITDFLKENQKVRV 738
E+++ G + TG V L D G ++ I + G L + + R LK Q +
Sbjct: 17 EALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNC 76
Query: 739 KVLGID-DRGRIKLSM 753
V + + G + LS+
Sbjct: 77 IVEKVKGNGGVVSLSV 92
>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 = 0.25
Identities = 20/78 (25%), Positives = 27/78 (34%), Gaps = 11/78 (14%)
Query: 675 RIEKLTESVQIGKVYTGIVLRLFD----FGAIIRILSGKDGLLHISQISSKRVNIITDFL 730
R T G VY G+ + F G I G D LHIS + + V
Sbjct: 49 RTFSATVRASQGPVYKGVC-KCFCRSKGHGFITPADGGPDIFLHISDVEGEYV------P 101
Query: 731 KENQKVRVKVLGIDDRGR 748
E +V K+ I +
Sbjct: 102 VEGDEVTYKMCSIPPKNE 119
>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA
binding, cell cycle; 2.79A {Caenorhabditis elegans}
Length = 376
Score = 33.4 bits (75), Expect = 0.28
Identities = 12/103 (11%), Positives = 35/103 (33%), Gaps = 15/103 (14%)
Query: 593 GLSYILEKMKTEVP-KCKNELSKFAPRLITIKIDPSKI--RDVIGKGG--STIRTLTEET 647
+++I + +P + + P +T+ ++ + G + ++ ET
Sbjct: 2 AMAHIHQLKAQGLPLPSNIPMIEINPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAET 61
Query: 648 GTQIDINDEGIITIASFN-----SVSG-----QEAKRRIEKLT 680
T I + D + +++G A+ + +
Sbjct: 62 NTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNC 104
>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 = 0.38
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 16/72 (22%)
Query: 629 IRDVIGKGGSTIRTLTEETGTQIDINDEGI----------------ITIASFNSVSGQEA 672
V G G S ++ + ETG ++ + +G I I+ A
Sbjct: 30 KEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA 89
Query: 673 KRRIEKLTESVQ 684
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 = 31.1 bits (69), Expect = 0.79
Identities = 7/35 (20%), Positives = 13/35 (37%), Gaps = 10/35 (28%)
Query: 602 KTEVPKCKNELSKFAPRLITIKID--PS-KIRDVI 633
K + K + L +A D P+ I+ +
Sbjct: 19 KQALKKLQASLKLYAD-------DSAPALAIKATM 46
Score = 29.9 bits (66), Expect = 1.5
Identities = 6/17 (35%), Positives = 11/17 (64%), Gaps = 3/17 (17%)
Query: 673 KRRIEKLTESVQIGKVY 689
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 = 29.7 bits (67), Expect = 3.2
Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 7/50 (14%)
Query: 616 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE-------TGTQIDINDEGI 658
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 = 29.7 bits (66), Expect = 3.3
Identities = 9/73 (12%), Positives = 25/73 (34%), Gaps = 14/73 (19%)
Query: 685 IGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITD--------------FL 730
+G++ TG + + G + +L D + + + + +
Sbjct: 81 LGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYF 140
Query: 731 KENQKVRVKVLGI 743
N+K+R ++
Sbjct: 141 DVNEKIRFRIERE 153
>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 = 29.7 bits (67), Expect = 3.8
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 624 IDPSKIRDVIGK--GGSTIRTLTEETGTQIDINDEGIITIASFNSVS 668
DP +RD G G T+ T ++ G I G T SF SVS
Sbjct: 16 FDPRALRDAFGAFATGVTVVTASDAAGKPI-----GF-TANSFTSVS 56
>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 = 4.5
Identities = 8/57 (14%), Positives = 22/57 (38%), Gaps = 12/57 (21%)
Query: 614 KFAPRLITIKIDPSKIRDVI-----------GKGGS-TIRTLTEETGTQIDINDEGI 658
+ + ++ D ++I+ V+ G+ G I + T ++ + + G
Sbjct: 230 ETDNEDLRVEADRTRIKQVLINLVQNAIEATGENGKIKITSEDMYTKVRVSVWNSGP 286
>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 = 5.4
Identities = 8/57 (14%), Positives = 22/57 (38%), Gaps = 12/57 (21%)
Query: 614 KFAPRLITIKIDPSKIRDVI-----------GKGGS-TIRTLTEETGTQIDINDEGI 658
+ + ++ 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 = 5.7
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 698 DFGAIIRILSGKDGLLHISQISSKRVN 724
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 = 6.6
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 632 VIGKGGSTIRTLTEETGTQIDINDEG 657
++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 = 7.4
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 616 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE----TGTQIDIN 654
A + + + +K VIG+GG IR L EE TG + +N
Sbjct: 60 AADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALN 102
>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 = 8.7
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 7/46 (15%)
Query: 616 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE-------TGTQIDIN 654
P I I ++ ++V+G+ G IR LT +++
Sbjct: 42 TPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFNFLENGVELY 87
>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 = 8.9
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 616 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE----TGTQIDIN 654
+ 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 = 9.2
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 616 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE----TGTQIDIN 654
+ I + I ++ VIGK G + L + G IN
Sbjct: 59 PAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQIN 101
>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 = 9.6
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 616 APRLITIKIDPSKIRDVIGKGGSTIRTLTEE 646
P I I ++ ++V+G+ G IR LT
Sbjct: 42 TPTRTEIIILATRTQNVLGEKGRRIRELTAV 72
>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 = 27.1 bits (60), Expect = 9.9
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 632 VIGKGGSTIRTLTEETGTQIDINDEGIIT 660
+IG G+T++ + +E +I I +G +
Sbjct: 27 LIGPRGNTLKNIEKECNAKIMIRGKGSVK 55
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 0.385
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: 11,604,251
Number of extensions: 758176
Number of successful extensions: 2034
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1863
Number of HSP's successfully gapped: 179
Length of query: 755
Length of database: 6,701,793
Length adjustment: 101
Effective length of query: 654
Effective length of database: 3,881,772
Effective search space: 2538678888
Effective search space used: 2538678888
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)