RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3755
(692 letters)
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 1117 bits (2891), Expect = 0.0
Identities = 394/690 (57%), Positives = 518/690 (75%), Gaps = 1/690 (0%)
Query: 1 MFRFILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 60
MF I+KS ++G +++E G++ARQA +VLV DTV+L TVV+ K+P +FFPLT
Sbjct: 1 MFNKIVKSIEFGGRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKEGQDFFPLT 60
Query: 61 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
VDY EK YAAG+IPG FFKREG+PSE+ET+ SRLIDRPIRPLFP+G+ NE+Q+V VLSV
Sbjct: 61 VDYEEKTYAAGKIPGGFFKREGRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSV 120
Query: 121 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 180
+P+ DPDI ++IG S ALSIS +PF GP+ +VGYIDG+++LNPT E+L++S LDL+VA
Sbjct: 121 DPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGEFVLNPTVEELEESDLDLVVA 180
Query: 181 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 240
GT+ A++ VESE+K+L E+++L AI FGHE ++ I+A EL G K W P D+
Sbjct: 181 GTKDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG-PKWEWQPPEVDE 239
Query: 241 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 300
L + + ++E K+++AYQI +KQ R+ I +++ +L E D +I
Sbjct: 240 ELKAAVKELAEAKLKEAYQITDKQEREAALDAIKEEVLEALAAEEEEEEDEKEIKEAFKK 299
Query: 301 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 360
LE KI+R++IL++G+RID R +++IRPISI G+LPRTHGS+LFTRG+TQALVVATLGT
Sbjct: 300 LEKKIVRRRILEEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTL 359
Query: 361 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 420
RDEQ ID L GE+ FMLHYN PP++ G+ GR+G P RREIGHG LA+RAL PVLP+
Sbjct: 360 RDEQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPGRREIGHGALAERALEPVLPSEE 419
Query: 421 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 480
+F Y+IR+VSEI ESNGSSSMASVCG LAL+DAGVPI VAGIAMGLIK+G+K +L+
Sbjct: 420 EFPYTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLT 479
Query: 481 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKT 540
DILGDED GDMDFKVAGT +GITALQMDIKI GIT +I++ AL +AK+G +IL KM
Sbjct: 480 DILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNE 539
Query: 541 EVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIAS 600
+ + + ELS +APR+ TIKI P KIRDVIG GG TIR +TEETG +IDI D+G + IA+
Sbjct: 540 AISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAA 599
Query: 601 FNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV 660
+ + + AK RIE +T ++G++Y G V+R+ DFGA + IL GKDGL+HIS+I+ +RV
Sbjct: 600 TDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERV 659
Query: 661 NIITDFLKENQKVRVKVLGIDDRGRIKLSM 690
+ D LKE +V+VKVL ID RGRI+LS
Sbjct: 660 EKVEDVLKEGDEVKVKVLEIDKRGRIRLSR 689
>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family)
[Transcription, Degradation of RNA].
Length = 684
Score = 1048 bits (2713), Expect = 0.0
Identities = 383/684 (55%), Positives = 506/684 (73%), Gaps = 5/684 (0%)
Query: 10 KYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYA 69
+YG +++E G+IARQA +V+V DTV+L TVV+ K+ +FFPLTV+Y EK YA
Sbjct: 1 EYGGRTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEGQDFFPLTVNYQEKFYA 60
Query: 70 AGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIA 129
AG+IPG FFKREG+PSE+ET+ SRLIDRPIRPLFP+G+ NE+Q+V VLS +P+ DPDI
Sbjct: 61 AGKIPGGFFKREGRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSYDPENDPDIL 120
Query: 130 SIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKAIITV 189
+IIG S AL+IS +PF GP+ +VGYIDG+Y+LNPT ++L+KS LDL+VAGT+ A++ V
Sbjct: 121 AIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLNPTVDELEKSDLDLVVAGTKDAVLMV 180
Query: 190 ESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKII-N 248
ESE+K+L E+++L AI FGHE+++ I AI EL + G++K + D+ L +K+
Sbjct: 181 ESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKWEFVAPEVDEELKAKVKEL 240
Query: 249 ISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDN---ENLTIDINDINCILYDLESKI 305
E +++AYQI KQ R I +++ +L + E +I DLE KI
Sbjct: 241 AYEAGLKEAYQITEKQERYAALDAIKEEVLEALAEEEEEEEEADREKEIKEAFKDLEKKI 300
Query: 306 IRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQK 365
+R++IL +G RID R ++ IRPISI G+LPRTHGS+LFTRG+TQALVV TLGT RDEQ
Sbjct: 301 VRERILKEGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQI 360
Query: 366 IDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYS 425
ID L GE+ FMLHYN PP++ G++GR+G P RREIGHG LA+RAL VLP+ +F Y+
Sbjct: 361 IDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRREIGHGALAERALKAVLPSEEEFPYT 420
Query: 426 IRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDG-EKVVILSDILG 484
IR+VSEI ESNGSSSMASVCGG LAL+DAGVPI VAGIAMGLIK+G E+ +LSDILG
Sbjct: 421 IRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDERFAVLSDILG 480
Query: 485 DEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPK 544
DED GDMDFKVAGT +GITALQMDIKI GIT +I++ AL +AK+G +IL +M + +
Sbjct: 481 DEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVISE 540
Query: 545 CKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSV 604
+ ELS +APR+ TIKI+P KIRDVIG GG IR +TEETG +IDI D+G + IA+ +
Sbjct: 541 PRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGE 600
Query: 605 SGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIIT 664
+ + A + IE +T ++GK+Y G V+R+ DFGA + IL GKDGL+HIS+I+++RV +
Sbjct: 601 AAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVE 660
Query: 665 DFLKENQKVRVKVLGIDDRGRIKL 688
D LKE +V+VKVL ID +GRIKL
Sbjct: 661 DVLKEGDEVKVKVLEIDKQGRIKL 684
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 933 bits (2413), Expect = 0.0
Identities = 387/691 (56%), Positives = 510/691 (73%), Gaps = 3/691 (0%)
Query: 1 MFRFILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 60
MF I+K+ ++G +++E G+IARQA +VLV DTV+LATVV P +FFPLT
Sbjct: 1 MFNKIVKTIEWGGRTLTLETGKIARQANGAVLVRYGDTVVLATVV-ASKPKEGQDFFPLT 59
Query: 61 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
V+Y EK YAAG+IPG FFKREG+PSE+E + SRLIDRPIRPLFP+G+ NE+QIV VLSV
Sbjct: 60 VNYEEKTYAAGKIPGGFFKREGRPSEKEILTSRLIDRPIRPLFPKGFRNEVQIVNTVLSV 119
Query: 121 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 180
+P+ DPDI +++G S ALS+S +PFLGP+G +VGYIDG ++LNPT E+L++S LDL+VA
Sbjct: 120 DPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGIFVLNPTLEELEESKLDLVVA 179
Query: 181 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 240
GT+ A+ VESE+ +L E+++L A+ FGHE ++ INA EL VG+KK +P D+
Sbjct: 180 GTKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDE 239
Query: 241 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 300
L +K+ +++E ++++A I+ KQ R I + I L E + +I IL
Sbjct: 240 ELEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEEELSGEEES--SLKEIKAILEK 297
Query: 301 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 360
LE K +R+ IL+ +RID R +++RPI I G+LPRTHGS+LFTRG+TQALVV TLGT
Sbjct: 298 LEKKPVRRLILEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTP 357
Query: 361 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 420
RD Q ID L GE+ F+LHYN PPF+ G+ GR+G P RREIGHG LA+RAL PVLP+
Sbjct: 358 RDAQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRREIGHGALAERALAPVLPSEE 417
Query: 421 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 480
+F Y+IR+VSEI ESNGSSSMASVCGG LAL+DAGVPI VAGIAMGLIK+G+K +LS
Sbjct: 418 EFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLS 477
Query: 481 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKT 540
DILGDED GDMDFKVAGT +GITALQMDIKI GIT +I++ AL +AK +IL M
Sbjct: 478 DILGDEDHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNE 537
Query: 541 EVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIAS 600
+ + + ELS +APR+ TIKIDP KIRDVIG GG TI+ +TEETG +IDI D+G + IA+
Sbjct: 538 AISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAA 597
Query: 601 FNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV 660
+ S ++AK RIE +T V++G+VY G V+R+ DFGA + +L GKDGL+HISQ++ +RV
Sbjct: 598 SDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERV 657
Query: 661 NIITDFLKENQKVRVKVLGIDDRGRIKLSMI 691
+ D LKE +V+VKV+ ID +GRI+LS+
Sbjct: 658 EKVEDVLKEGDEVKVKVIEIDKQGRIRLSIK 688
>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 584 bits (1507), Expect = 0.0
Identities = 286/736 (38%), Positives = 431/736 (58%), Gaps = 57/736 (7%)
Query: 11 YGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAA 70
G I +E G I RQA+ SV V+ +T++ +V P+ +FFPL+V Y E+ AA
Sbjct: 86 VGDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQERFSAA 145
Query: 71 GRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIAS 130
GR G FFKREG+ + E +I RLIDRP+RP P+G+ +E QI+ +VLS + PD +
Sbjct: 146 GRTSGGFFKREGRTKDHEVLICRLIDRPLRPTMPKGFYHETQILSWVLSYDGLHSPDSLA 205
Query: 131 IIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKAIITVE 190
+ A+++SE+P L + +VG I GK+I+NPTT+++++S LDL++AGT+ AI+ +E
Sbjct: 206 VTAAGIAVALSEVPNLKAIAGVRVGLIGGKFIVNPTTKEMEESELDLIMAGTDSAILMIE 265
Query: 191 SESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKIINIS 250
LPE+ +L A+ G + ++ I LV+ G+ K+ + L + I+
Sbjct: 266 GYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGKPKMLDAIKLPPPELYKHVKEIA 325
Query: 251 EHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDIN------------------ 292
++ KA QI+ K R ++ + + S L + ++ D +
Sbjct: 326 GDELVKALQIRGKIPRRKALSSLEEKVLSILTEEGYVSKDESFGTSETRADLLEDEDEDE 385
Query: 293 ------------------------------DINCILYDLESKIIRKQILDKGLRIDNRGV 322
D+ + ++ SK +R++I++ G R D R
Sbjct: 386 EVVVDGEVDEGDVHIKPIPRKSSPLLFSEVDVKLVFKEVTSKFLRRRIVEGGKRSDGRTP 445
Query: 323 NDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMG-EFTDSFMLHY 381
++IRPI+ G+LPR HGS+LFTRG+TQAL V TLG + Q+ID L+ + F L Y
Sbjct: 446 DEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQY 505
Query: 382 NMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSM 441
+ PP G++GRIG P RREIGHG LA+RAL P+LP+ + F Y+IR+ S ITESNGSSSM
Sbjct: 506 SFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSSM 565
Query: 442 ASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKV------VILSDILGDEDRCGDMDFK 495
ASVCGGCLAL DAGVP+ +AGIAMG++ D E+ +ILSDI G ED GDMDFK
Sbjct: 566 ASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFK 625
Query: 496 VAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPR 555
VAG +GITA QMDIK+ GIT I++ AL +AK G +IL +M P LSK+AP
Sbjct: 626 VAGNEDGITAFQMDIKVGGITLPIMERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPL 685
Query: 556 LITIKIDPSKIRDVIGKGGSTIRTLTEETGTQ-IDINDEGIITIASFNSVSGQEAKRRIE 614
+ +K+ P K+ +IG GG ++++ EETG + ID D+G + I + + S +++K I
Sbjct: 686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIIS 745
Query: 615 KLTESVQIGKVYTGIVLR-LFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 673
LT +G +Y ++ + +GA + I G++GL HIS++SS + D K ++
Sbjct: 746 SLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRI 805
Query: 674 RVKVLGIDDRGRIKLS 689
VK++ ++D+G+++LS
Sbjct: 806 DVKLIEVNDKGQLRLS 821
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase
I/polynucleotide phosphorylase. Sohlberg, et al present
characterization of two proteins from Streptomyces
coelicolor. The protein in this family was shown to have
poly(A) polymerase activity and may be responsible for
polyadenylating RNA in this species. Reference 2 showed
that a nearly identical plasmid-encoded protein from
Streptomyces antibioticus is a bifunctional enzyme that
acts also as a guanosine pentaphosphate synthetase.
Length = 719
Score = 568 bits (1466), Expect = 0.0
Identities = 293/708 (41%), Positives = 427/708 (60%), Gaps = 32/708 (4%)
Query: 10 KYGSYKISIEIGEIARQATSSVLVSI-EDTVILATVVSCKDPTSTYNFFPLTVDYIEKAY 68
++G+ I E G +ARQA SV+ + ++T++L+ + K P ++FFPLTVD E+ Y
Sbjct: 13 RFGTRTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKDQFDFFPLTVDVEERMY 72
Query: 69 AAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDI 128
AAGRIPGSFF+REG+PS + RLIDRP+RP F +G NE+Q+VV VLS+NP D+
Sbjct: 73 AAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPSFVKGLRNEVQVVVTVLSLNPDHLYDV 132
Query: 129 ASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGT-----E 183
+I S + ++ LPF GP+G +V IDG+++ PT EQL+ + D++VAG +
Sbjct: 133 VAINAASASTQLAGLPFSGPIGGVRVALIDGQWVAFPTHEQLEGAVFDMVVAGRVLENGD 192
Query: 184 KAIITVESESKQLPEDIILNA--------IIFGHEKMKIAINAINELVQNVGQK--KVNW 233
AI+ VE+E+ + D++ + G E K I + ++ +K K
Sbjct: 193 VAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAEKAAKPTG 252
Query: 234 D-PIVKDKT--LISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTID 290
+ P+ D + + + ++ A I KQ R+ + + + L E
Sbjct: 253 EFPLFPDYQDDVYEAVEGAVKDELSAALTIAGKQEREEALDEVKALVAAKLA--EQFEGR 310
Query: 291 INDINCILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQ 350
+I+ + K++R+++L +G+RID RGV DIRP+ ++PR HGS+LF RG+TQ
Sbjct: 311 EKEISAAYRAVTKKLVRERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQ 370
Query: 351 ALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKR 410
L V TL + EQ+ID+L E + +M HYN PP++TG+ GR+G PKRREIGHG LA+R
Sbjct: 371 ILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYSTGETGRVGSPKRREIGHGALAER 430
Query: 411 ALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLI 470
AL+PVLP+ +F Y+IR VSE SNGS+SM SVC L+LL+AGVP+ VAGIAMGLI
Sbjct: 431 ALVPVLPSREEFPYAIRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIAMGLI 490
Query: 471 K---DGE-KVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYK 526
DGE + V L+DILG ED GDMDFKVAGT +TALQ+D K+ GI ++ AL +
Sbjct: 491 SDEVDGETRYVALTDILGAEDAFGDMDFKVAGTSEFVTALQLDTKLDGIPASVLASALKQ 550
Query: 527 AKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGT 586
A+ IL+ M E +E+S +APR+IT+KI KI +VIG G I + +ETG
Sbjct: 551 ARDARLAILDVM-AEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGA 609
Query: 587 QIDINDEGIITIASFNSVSGQEAKRRIEKLTESV--QIGKVYTGIVLRLFDFGAIIRILS 644
+I I D+G + I + + S + A+ I + ++G+ + G V++ FGA + +L
Sbjct: 610 EISIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLLP 669
Query: 645 GKDGLLHISQI----SSKRVNIITDFLKENQKVRVKVLGIDDRGRIKL 688
GKDGLLHISQI KRV + D L QK++V++ IDDRG++ L
Sbjct: 670 GKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSL 717
>gnl|CDD|206769 cd11364, RNase_PH_PNPase_2, Polyribonucleotide
nucleotidyltransferase, repeat 2. Polyribonucleotide
nucleotidyltransferase (PNPase) is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally, all members
of this family form hexameric rings. In the case of
PNPase the complex is a trimer, since each monomer
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction and in
quality control of ribosomal RNA precursors, with the
second repeat containing the active site. PNPase is part
of the RNA degradosome complex and binds to the
scaffolding domain of the endoribonuclease RNase E.
Length = 223
Score = 396 bits (1020), Expect = e-135
Identities = 143/222 (64%), Positives = 174/222 (78%), Gaps = 1/222 (0%)
Query: 324 DIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNM 383
+IRPIS G+LPRTHGS+LFTRG+TQ L TLGT D QKID+L GE + FMLHYN
Sbjct: 1 EIRPISCEVGLLPRTHGSALFTRGETQVLCTVTLGTLEDAQKIDSLGGEKSKRFMLHYNF 60
Query: 384 PPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMAS 443
PP++ G+ GR+G P RREIGHG LA+RALLPVLP+ F Y+IR+VSE+ ESNGSSSMAS
Sbjct: 61 PPYSVGETGRVGGPGRREIGHGALAERALLPVLPSPEDFPYTIRVVSEVLESNGSSSMAS 120
Query: 444 VCGGCLALLDAGVPISEHVAGIAMGLIKDG-EKVVILSDILGDEDRCGDMDFKVAGTVNG 502
VCGG LAL+DAGVPI VAGIAMGLI +G + +L+DILG ED GDMDFKVAGT +G
Sbjct: 121 VCGGSLALMDAGVPIKAPVAGIAMGLITEGIDDYRVLTDILGLEDHLGDMDFKVAGTRDG 180
Query: 503 ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPK 544
ITALQMDIKI GIT +I++ AL +AK+G +IL+ M+ + +
Sbjct: 181 ITALQMDIKIPGITLEIMREALQQAKEGRLHILDIMEKAISE 222
>gnl|CDD|206768 cd11363, RNase_PH_PNPase_1, Polyribonucleotide
nucleotidyltransferase, repeat 1. Polyribonucleotide
nucleotidyltransferase (PNPase) is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally, all members
of this family form hexameric rings. In the case of
PNPase the complex is a trimer, since each monomer
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction and in
quality control of ribosomal RNA precursors. It is part
of the RNA degradosome complex and binds to the
scaffolding domain of the endoribonuclease RNase E.
Length = 229
Score = 334 bits (858), Expect = e-111
Identities = 118/227 (51%), Positives = 165/227 (72%)
Query: 7 KSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEK 66
G ++ E G++A+QA SV+V DTV+L T VS K P +FFPLTVDY EK
Sbjct: 3 FEVLVGGRTLTFETGKLAKQADGSVVVQYGDTVVLVTAVSSKKPKEGIDFFPLTVDYREK 62
Query: 67 AYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDP 126
YAAG+IPG FFKREG+PSE+E + SRLIDRPIRPLFP+G+ NE+Q++ VLSV+ DP
Sbjct: 63 LYAAGKIPGGFFKREGRPSEKEILTSRLIDRPIRPLFPKGFRNEVQVIATVLSVDGVNDP 122
Query: 127 DIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKAI 186
D+ +I G S ALS+S++PF GP+G +VG IDG++++NPT E+L++S LDL+VAGT+ A+
Sbjct: 123 DVLAINGASAALSLSDIPFNGPVGAVRVGRIDGEFVVNPTREELEESDLDLVVAGTKDAV 182
Query: 187 ITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNW 233
+ VE+ +K++ E+ +L AI FGHE ++ I A EL VG++K +
Sbjct: 183 LMVEAGAKEVSEEDMLEAIKFGHEAIQQLIAAQEELAAEVGKEKREY 229
Score = 44.8 bits (107), Expect = 5e-05
Identities = 50/194 (25%), Positives = 80/194 (41%), Gaps = 25/194 (12%)
Query: 326 RPISIRTGILPR-THGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFML--HYN 382
R ++ TG L + GS + GDT LV A E D F L Y
Sbjct: 10 RTLTFETGKLAKQADGSVVVQYGDTVVLVTAVSSKKPKEG---------IDFFPLTVDYR 60
Query: 383 MPPFATGDI-----GRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNG 437
+A G I R G P +EI RL R + P+ P F +++++ + +G
Sbjct: 61 EKLYAAGKIPGGFFKREGRPSEKEILTSRLIDRPIRPLFPKG--FRNEVQVIATVLSVDG 118
Query: 438 --SSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFK 495
+ ++ G AL + +P + V + +G I DGE V+ +E D+D
Sbjct: 119 VNDPDVLAINGASAALSLSDIPFNGPVGAVRVGRI-DGE-FVVNPTR--EELEESDLDLV 174
Query: 496 VAGTVNGITALQMD 509
VAGT + + ++
Sbjct: 175 VAGTKDAVLMVEAG 188
>gnl|CDD|216323 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1. This
family includes 3'-5' exoribonucleases. Ribonuclease PH
contains a single copy of this domain, and removes
nucleotide residues following the -CCA terminus of tRNA.
Polyribonucleotide nucleotidyltransferase (PNPase)
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction. The
exosome is a 3'-5' exoribonuclease complex that is
required for 3' processing of the 5.8S rRNA. Three of
its five protein components contain a copy of this
domain. A hypothetical protein from S. pombe appears to
belong to an uncharacterized subfamily. This subfamily
is found in both eukaryotes and archaebacteria.
Length = 129
Score = 121 bits (307), Expect = 1e-32
Identities = 46/134 (34%), Positives = 66/134 (49%), Gaps = 5/134 (3%)
Query: 324 DIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNM 383
++RPI I TG+L + GS+L GDT+ L T +++ D F + Y
Sbjct: 1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPQKERD----FFPGELTVEYEE 56
Query: 384 PPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMAS 443
PFA+G+ G P REI RL RAL P +P + IR+ + +GS A+
Sbjct: 57 SPFASGERPE-GRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDGSLLDAA 115
Query: 444 VCGGCLALLDAGVP 457
+ LAL DAG+P
Sbjct: 116 INAASLALADAGIP 129
Score = 106 bits (266), Expect = 5e-27
Identities = 56/135 (41%), Positives = 73/135 (54%), Gaps = 14/135 (10%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATVV-SCKDPTSTYNFFP--LTVDYIEKAYAAG 71
I IE G + QA S LV + DT +LATV + P +FFP LTV+Y E +A+G
Sbjct: 4 PIEIETG-VLSQADGSALVELGDTKVLATVTGPIEPPQKERDFFPGELTVEYEESPFASG 62
Query: 72 RIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYL--NEIQIVVYVLSVNPQIDPDIA 129
P EG+PSERE +SRLIDR +RP P EI+I V VLS + A
Sbjct: 63 ERP------EGRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDG--SLLDA 114
Query: 130 SIIGVSTALSISELP 144
+I S AL+ + +P
Sbjct: 115 AINAASLALADAGIP 129
>gnl|CDD|206766 cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucleases. RNase
PH-like 3'-5' exoribonucleases are enzymes that catalyze
the 3' to 5' processing and decay of RNA substrates.
Evolutionarily related members can be fond in
prokaryotes, archaea, and eukaryotes. Bacterial
ribonuclease PH contains a single copy of this domain,
and removes nucleotide residues following the -CCA
terminus of tRNA. Polyribonucleotide
nucleotidyltransferase (PNPase) contains two tandem
copies of the domain and is involved in mRNA degradation
in a 3'-5' direction. Archaeal exosomes contain two
individually encoded RNase PH-like 3'-5'
exoribonucleases and are required for 3' processing of
the 5.8S rRNA. The eukaryotic exosome core is composed
of six individually encoded RNase PH-like subunits, but
it is not a phosphorolytic enzyme per se; it directly
associates with Rrp44 and Rrp6, which are hydrolytic
exoribonucleases related to bacterial RNase II/R and
RNase D. All members of the RNase PH-like family form
ring structures by oligomerization of six domains or
subunits, except for a total of 3 subunits with tandem
repeats in the case of PNPase, with a central channel
through which the RNA substrate must pass to gain access
to the phosphorolytic active sites.
Length = 218
Score = 118 bits (299), Expect = 2e-30
Identities = 53/223 (23%), Positives = 91/223 (40%), Gaps = 26/223 (11%)
Query: 325 IRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMP 384
RP+ I TG+L + GS+L G+T+ + T D L + ++ +
Sbjct: 1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEP----DKLERPDKGTLYVNVEIS 56
Query: 385 PFATGDIGRIGVPKRREIGHGRLAKRALLPVLP---NNNKFNYSIRLVSEITESNGSSSM 441
P A G+ R G P E+ RL +R + + + K ++ + + ++ +G
Sbjct: 57 PGAVGER-RQGPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDGGLLD 115
Query: 442 ASVCGGCLALLDAGVP-------------ISEHVAGIAMGLIKDGEKVVILSDILGDEDR 488
A AL DAG+P + + + +++G I DG V+L D G+E+
Sbjct: 116 ACWNAAIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGISDG---VLLLDPTGEEEE 172
Query: 489 CGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKG 530
D VA +G + L T + I+ L AKK
Sbjct: 173 LADSTLTVAVDKSGKLCLLSKVGGGSLDT-EEIKECLELAKKR 214
Score = 75.8 bits (187), Expect = 1e-15
Identities = 46/222 (20%), Positives = 78/222 (35%), Gaps = 35/222 (15%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATVVSC----KDPTSTYNFFPLTVDYIEKAYAA 70
+ IE G + QA S LV + +T ++ V + D + L V+ A
Sbjct: 3 PVEIETGVL-NQADGSALVKLGNTKVICAV-TGPIVEPDKLERPDKGTLYVNVEISPGAV 60
Query: 71 GRIPGSFFKREGKPSERETIISRLIDRPIR-----PLFPEGYLNEIQIVVYVLSVNPQID 125
G R+G P + E ISRL++R I + + + VLS + +
Sbjct: 61 GER------RQGPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDGGLL 114
Query: 126 PDIASIIGVSTAL-------------SISELPFLGPLGVAKVGYI-DGKYILNPTTEQLK 171
A AL S L + VG I DG +L+PT E+ +
Sbjct: 115 D--ACWNAAIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGISDGVLLLDPTGEEEE 172
Query: 172 KSHLDLLVAGTEK-AIITVESESKQLPE-DIILNAIIFGHEK 211
+ L VA + + + + + I + ++
Sbjct: 173 LADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAKKR 214
>gnl|CDD|235187 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional.
Length = 244
Score = 107 bits (269), Expect = 3e-26
Identities = 76/240 (31%), Positives = 118/240 (49%), Gaps = 25/240 (10%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGT----SRDE 363
K IL+ GLR+D R +++RPI I G+L GS+ G+ + + A G R
Sbjct: 7 KLILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKI-IAAVYGPREMHPRHL 65
Query: 364 QKID-ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKF 422
Q D A++ + YNM PF+ + R G P RR I ++ + AL P +
Sbjct: 66 QLPDRAVL-------RVRYNMAPFSVDERKRPG-PDRRSIEISKVIREALEPAIMLELFP 117
Query: 423 NYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDI 482
I + E+ +++ + +A + LAL DAG+P+ + VAG A+G + DG V+ D+
Sbjct: 118 RTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKV-DGVIVL---DL 173
Query: 483 LGDEDRCGDMDFKVAGTVNG--ITALQMDIKIFG-ITYDIIQIALYKAKKGLSYILEKMK 539
+ED G+ D VA IT LQ+D G +T + AL AKKG+ I + +
Sbjct: 174 NKEEDNYGEADMPVAIMPRLGEITLLQLD----GNLTREEFLEALELAKKGIKRIYQLQR 229
Score = 32.7 bits (75), Expect = 0.48
Identities = 47/185 (25%), Positives = 71/185 (38%), Gaps = 43/185 (23%)
Query: 16 ISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTS-------------TYNFFPLTVD 62
I IE+G + A S + + I+A V ++ YN P +VD
Sbjct: 27 IKIEVGVLKN-ADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVD 85
Query: 63 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRP-----LFPEGYLNEIQIVVYV 117
E+ KR G P R IS++I + P LFP I + + V
Sbjct: 86 --ER------------KRPG-PDRRSIEISKVIREALEPAIMLELFPR---TVIDVFIEV 127
Query: 118 LSVNPQIDPD--IASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHL 175
L Q D +A I S AL+ + +P + VG +DG +L+ E+
Sbjct: 128 L----QADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLNKEEDNYGEA 183
Query: 176 DLLVA 180
D+ VA
Sbjct: 184 DMPVA 188
>gnl|CDD|131120 TIGR02065, ECX1, archaeal exosome-like complex exonuclease 1. This
family contains the archaeal protein orthologous to the
eukaryotic exosome protein Rrp41. It is somewhat more
distantly related to the bacterial protein ribonuclease
PH. An exosome-like complex has been demonstrated
experimentally for the Archaea in Sulfolobus
solfataricus, so members of this family are designated
exosome complex exonuclease 1, after usage in SwissProt
[Transcription, Degradation of RNA].
Length = 230
Score = 102 bits (255), Expect = 2e-24
Identities = 74/236 (31%), Positives = 117/236 (49%), Gaps = 23/236 (9%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS----RDE 363
K IL+ G+R+D R +++RPI I G+L GS+ G T+ + A G R
Sbjct: 1 KLILEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYLEFGGTKI-LAAVYGPREAHPRHL 59
Query: 364 QKID-ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKF 422
Q D A++ + Y+M PF+T + R G P RREI ++ + AL P +
Sbjct: 60 QLPDRAVL-------RVRYHMAPFSTDERKRPG-PSRREIEISKVIREALEPAILLEQFP 111
Query: 423 NYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDI 482
I + E+ +++G + A + LAL DAG+P+ + V G+A+G + V++ D+
Sbjct: 112 RTVIDVFIEVLQADGGTRCAGLTAASLALADAGIPMRDLVVGVAVGKVDG----VVVLDL 167
Query: 483 LGDEDRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILE 536
+ED G+ D VA IT LQ+D +T D + AL A +G+ I E
Sbjct: 168 SEEEDMYGEADMPVAIMPKTGEITLLQLD---GDLTPDEFRQALDLAVEGIKRIYE 220
Score = 35.5 bits (82), Expect = 0.055
Identities = 47/185 (25%), Positives = 71/185 (38%), Gaps = 43/185 (23%)
Query: 16 ISIEIGEIARQATSSVLVSIEDTVILATVVSCKDP-------------TSTYNFFPLTVD 62
I IE G + + A S + T ILA V ++ Y+ P + D
Sbjct: 21 IKIEAG-VLKNADGSAYLEFGGTKILAAVYGPREAHPRHLQLPDRAVLRVRYHMAPFSTD 79
Query: 63 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRP-----LFPEGYLNEIQIVVYV 117
E+ KR G PS RE IS++I + P FP I + + V
Sbjct: 80 --ER------------KRPG-PSRREIEISKVIREALEPAILLEQFPR---TVIDVFIEV 121
Query: 118 LSVNPQIDPD--IASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHL 175
L Q D A + S AL+ + +P + VG +DG +L+ + E+
Sbjct: 122 L----QADGGTRCAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLSEEEDMYGEA 177
Query: 176 DLLVA 180
D+ VA
Sbjct: 178 DMPVA 182
>gnl|CDD|239918 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase
(PNPase), ), S1-like RNA-binding domain. PNPase is a
polyribonucleotide nucleotidyl transferase that degrades
mRNA. It is a trimeric multidomain protein. The
C-terminus contains the S1 domain which binds ssRNA.
This family is classified based on the S1 domain. PNPase
nonspecifically removes the 3' nucleotides from mRNA,
but is stalled by double-stranded RNA structures such as
a stem-loop. Evidence shows that a minimum of 7-10
unpaired nucleotides at the 3' end, is required for
PNPase degradation. It is suggested that PNPase also
dephosphorylates the RNA 5' end. This additional
activity may regulate the 5'-dependent activity of
RNaseE in vivo.
Length = 68
Score = 93.8 bits (234), Expect = 2e-23
Identities = 37/68 (54%), Positives = 51/68 (75%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 682
GK+Y G V+++ DFGA + IL GKDGL+HIS++S +RV + D LK +V+VKV+ +DD
Sbjct: 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD 60
Query: 683 RGRIKLSM 690
RGRI LS
Sbjct: 61 RGRISLSR 68
>gnl|CDD|223761 COG0689, Rph, RNase PH [Translation, ribosomal structure and
biogenesis].
Length = 230
Score = 95.8 bits (239), Expect = 3e-22
Identities = 68/241 (28%), Positives = 107/241 (44%), Gaps = 24/241 (9%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 367
+ G+R D R +++RPI I G+L GSSL G+T+ + + E
Sbjct: 1 MLESEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTV---SGPREPVPR 57
Query: 368 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPV-----LPNNNKF 422
L G Y M P +T + + + R RL RAL V LP +
Sbjct: 58 FLRGTGKGWLTAEYGMLPRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPES--- 114
Query: 423 NYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDI 482
+I + ++ +++G + AS+ G LAL DAG+P+ + VA I++G++ VI+ D+
Sbjct: 115 --TIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIVDG----VIVLDL 168
Query: 483 LGDEDRCGDMDFKVAGTVNG----ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 538
+ED + D V T NG I L D T D + L A KG + + E
Sbjct: 169 DYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGP---FTEDELLELLDLAIKGCNELRELQ 225
Query: 539 K 539
+
Sbjct: 226 R 226
Score = 45.0 bits (107), Expect = 5e-05
Identities = 60/227 (26%), Positives = 95/227 (41%), Gaps = 38/227 (16%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTY----NFFPLTVDYIEKAYAA 70
I I G + + A S L+ +T ++ TV ++P + LT +Y
Sbjct: 20 PIKITRG-VLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEY------- 71
Query: 71 GRIPGSFFKREG-KPSERETI-ISRLIDRPIRP-----LFPEGYLNEIQIVVYVLSVNPQ 123
G +P S +R+ + T ISRLI R +R L PE + I I VL Q
Sbjct: 72 GMLPRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPE---STIDIDCDVL----Q 124
Query: 124 IDPDI--ASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAG 181
D ASI G S AL+ + +P + VG +DG +L+ E+ + D+ V
Sbjct: 125 ADGGTRTASITGASLALADAGIPLRDLVAAISVGIVDGVIVLDLDYEEDSAAEADMNVVM 184
Query: 182 TEKA-IITVE--SESKQLPEDIILNAIIFGHEKMKIAINAINELVQN 225
T ++ ++ +E ED +L + +AI NEL +
Sbjct: 185 TGNGGLVEIQGLAEDGPFTEDELLEL-------LDLAIKGCNELREL 224
>gnl|CDD|206771 cd11366, RNase_PH_archRRP41, RRP41 subunit of archaeal exosome.
The RRP41 subunit of the archaeal exosome is a member of
the RNase_PH family, named after the bacterial
Ribonuclease PH, a 3'-5' exoribonuclease. Structurally
all members of this family form hexameric rings (trimers
of dimers). In archaea, the ring is formed by three
Rrp41:Rrp42 dimers. The central chamber within the ring
contains three phosphorolytic active sites located in an
Rrp41 pocket at the interface between Rrp42 and Rrp41.
The ring is capped by three copies of Rrp4 and/or Csl4
which contain putative RNA interaction domains. The
archaeal exosome degrades single-stranded RNA (ssRNA) in
the 3'-5' direction, but also can catalyze the reverse
reaction of adding nucleoside diphosphates to the 3'-end
of RNA which has been shown to lead to the formation of
poly-A-rich tails on RNA.
Length = 214
Score = 94.3 bits (235), Expect = 6e-22
Identities = 70/224 (31%), Positives = 108/224 (48%), Gaps = 25/224 (11%)
Query: 324 DIRPISIRTGILPRTHGSSLFTRGDTQALVVATLG----TSRDEQKID-ALMGEFTDSFM 378
++RPI I G+L GS+ G+ + + A G R Q D A++
Sbjct: 1 ELRPIKIEVGVLKNADGSAYVEWGNNKIIA-AVYGPREVHPRHLQLPDRAVI-------R 52
Query: 379 LHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGS 438
+ YNM PF+ + R G P RREI ++ K AL P + +I + E+ +++
Sbjct: 53 VRYNMAPFSVDERKRPG-PDRREIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAG 111
Query: 439 SSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAG 498
+ +A + LAL DAG+P+ + VA A G + K+V+ D+ +ED G+ D +A
Sbjct: 112 TRVAGLNAASLALADAGIPMRDLVAACAAGKV--DGKIVL--DLNKEEDNYGEADMPIAM 167
Query: 499 TVNG--ITALQMDIKIFG-ITYDIIQIALYKAKKGLSYILEKMK 539
N IT LQ+D G +T D + A+ AKKG I E K
Sbjct: 168 MPNLGEITLLQLD----GDLTPDEFKQAIELAKKGCKRIYELQK 207
Score = 32.7 bits (75), Expect = 0.41
Identities = 47/186 (25%), Positives = 71/186 (38%), Gaps = 43/186 (23%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTST-------------YNFFPLTV 61
I IE+G + A S V + I+A V ++ YN P +V
Sbjct: 4 PIKIEVGVLKN-ADGSAYVEWGNNKIIAAVYGPREVHPRHLQLPDRAVIRVRYNMAPFSV 62
Query: 62 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRP-----LFPEGYLNEIQIVVY 116
D E+ KR G P RE IS++I + P FP I + V
Sbjct: 63 D--ER------------KRPG-PDRREIEISKVIKEALEPAIILEEFPR---TAIDVFVE 104
Query: 117 VLSVNPQIDPD--IASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSH 174
VL Q D +A + S AL+ + +P + G +DGK +L+ E+
Sbjct: 105 VL----QADAGTRVAGLNAASLALADAGIPMRDLVAACAAGKVDGKIVLDLNKEEDNYGE 160
Query: 175 LDLLVA 180
D+ +A
Sbjct: 161 ADMPIA 166
>gnl|CDD|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein
S1 (RPS1) domain. RPS1 is a component of the small
ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog.
Autoantibodies to double-stranded DNA from patients with
systemic lupus erythematosus cross-react with the human
RPS1 homolog.
Length = 69
Score = 83.5 bits (207), Expect = 9e-20
Identities = 38/68 (55%), Positives = 45/68 (66%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 682
G V G V RL FGA + + G GL+HISQI+ KRV + D LKE KV+VKVL ID
Sbjct: 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA 60
Query: 683 RGRIKLSM 690
RGRI LS+
Sbjct: 61 RGRISLSI 68
>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K
homology RNA-binding domain (KH). PNPase is a
polyribonucleotide nucleotidyl transferase that degrades
mRNA in prokaryotes and plant chloroplasts. The
C-terminal region of PNPase contains domains homologous
to those in other RNA binding proteins: a KH domain and
an S1 domain. KH domains bind single-stranded RNA and
are found in a wide variety of proteins including
ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 61
Score = 82.2 bits (204), Expect = 2e-19
Identities = 32/61 (52%), Positives = 45/61 (73%)
Query: 554 PRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRI 613
PR+ T+KI P KIRDVIG GG TI+ + EETG +IDI D+G + IA+ + + ++AK+ I
Sbjct: 1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMI 60
Query: 614 E 614
E
Sbjct: 61 E 61
>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 390
Score = 85.7 bits (213), Expect = 8e-18
Identities = 40/94 (42%), Positives = 57/94 (60%), Gaps = 2/94 (2%)
Query: 598 IASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISS 657
I S +V +E + E+L S++ G V G V RL DFGA + I G DGL+HIS++S
Sbjct: 168 ILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSH 226
Query: 658 KRVNIITDFLKENQKVRVKVLGID-DRGRIKLSM 690
+RV ++ + Q+V VKVL ID + RI LS+
Sbjct: 227 ERVEKPSEVVSVGQEVEVKVLSIDWETERISLSL 260
Score = 82.2 bits (204), Expect = 1e-16
Identities = 35/78 (44%), Positives = 51/78 (65%), Gaps = 1/78 (1%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 673
E + E + G V G V RL DFGA + +L G +GL+HISQIS K + ++ L+E Q+V
Sbjct: 269 EGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEV 328
Query: 674 RVKVLGID-DRGRIKLSM 690
+VKVL ++ + RI LS+
Sbjct: 329 KVKVLEVNEEEKRISLSI 346
Score = 36.8 bits (86), Expect = 0.032
Identities = 21/66 (31%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 618 ESVQIGKVYTGIVLRLFDFGAIIRILSGK-DGLLHISQISSKRVNIITDFLKENQKVRVK 676
+ V++G V TG VL++ D + I K +G++ IS++S+ + I D +K ++ V
Sbjct: 13 KEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVY 72
Query: 677 VLGIDD 682
VL ++D
Sbjct: 73 VLKVED 78
Score = 29.5 bits (67), Expect = 6.3
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 4/83 (4%)
Query: 608 EAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFL 667
EA++ +KL E + G+V V + G ++ + G G + S IS++ V +DF
Sbjct: 91 EAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSDFK 149
Query: 668 KENQKVRVKVLGIDDRG-RIKLS 689
+ + VK++ +D R+ LS
Sbjct: 150 --GKTLEVKIIELDPEKNRVILS 170
>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain.
Length = 72
Score = 72.3 bits (178), Expect = 8e-16
Identities = 28/71 (39%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 680
++G V G V + GA + + +G +GL+ IS++S KRV + LK +V+VKVL +
Sbjct: 1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV 60
Query: 681 D-DRGRIKLSM 690
D ++GRI LS+
Sbjct: 61 DEEKGRIILSL 71
>gnl|CDD|235614 PRK05807, PRK05807, hypothetical protein; Provisional.
Length = 136
Score = 73.6 bits (181), Expect = 1e-15
Identities = 30/70 (42%), Positives = 46/70 (65%), Gaps = 1/70 (1%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 680
+ G + G V+ + +FGA + + GK GL+HIS+++ V I + LKE KV+VKV+ I
Sbjct: 4 KAGSILEGTVVNITNFGAFVE-VEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISI 62
Query: 681 DDRGRIKLSM 690
DD G+I LS+
Sbjct: 63 DDNGKISLSI 72
>gnl|CDD|240189 cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N-terminal S1
domain of human ATP-dependent RNA helicase DHX8, a DEAH
(Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA
helicases are thought to play key roles in pre-mRNA
splicing and DHX8 facilitates nuclear export of spliced
mRNA by releasing the RNA from the spliceosome. DHX8 is
also known as HRH1 (human RNA helicase 1) in Homo
sapiens and PRP22 in Saccharomyces cerevisiae.
Length = 79
Score = 71.5 bits (176), Expect = 2e-15
Identities = 32/72 (44%), Positives = 46/72 (63%), Gaps = 5/72 (6%)
Query: 623 GKVYTGIVLRLFDFGAIIRILS---GKDGLLHISQISSK-RVNIITDFLKENQKVRVKVL 678
GK+Y G V + DFG +++ K+GL+HISQ+S + RV +D +K QKV+VKV+
Sbjct: 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVI 60
Query: 679 GIDDRGRIKLSM 690
I G+I LSM
Sbjct: 61 SI-QNGKISLSM 71
>gnl|CDD|224023 COG1098, VacB, Predicted RNA binding protein (contains ribosomal
protein S1 domain) [Translation, ribosomal structure and
biogenesis].
Length = 129
Score = 72.3 bits (178), Expect = 3e-15
Identities = 30/72 (41%), Positives = 46/72 (63%)
Query: 619 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 678
S+++G G + + +GA + + GK GL+HIS+I+ V I D LK Q+V+VKVL
Sbjct: 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVL 61
Query: 679 GIDDRGRIKLSM 690
ID+ G+I LS+
Sbjct: 62 DIDENGKISLSI 73
>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase/S1 RNA-binding domain protein; Reviewed.
Length = 647
Score = 78.8 bits (195), Expect = 4e-15
Identities = 35/93 (37%), Positives = 56/93 (60%), Gaps = 2/93 (2%)
Query: 598 IASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISS 657
+ S ++ +E +++ E+ S++ G V G V RL DFGA + I G DGLLH+S+IS
Sbjct: 453 VLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISW 511
Query: 658 KRVNIITDFLKENQKVRVKVLGID-DRGRIKLS 689
RV +D LK +++V +L ID + ++ LS
Sbjct: 512 GRVEKPSDVLKVGDEIKVYILDIDKENKKLSLS 544
Score = 75.4 bits (186), Expect = 4e-14
Identities = 32/78 (41%), Positives = 50/78 (64%), Gaps = 1/78 (1%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 673
E + E +G + G V+R+ FGA + + G DGL+HISQIS KR++ D L E ++V
Sbjct: 554 ENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEV 613
Query: 674 RVKVLGID-DRGRIKLSM 690
+ K+L +D + RI+LS+
Sbjct: 614 KAKILEVDPEEKRIRLSI 631
Score = 32.6 bits (75), Expect = 0.83
Identities = 15/83 (18%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 608 EAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFL 667
E + +L + ++ G + G V+ + + + + +G++ + +++ ++ + + +
Sbjct: 288 EQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESV 347
Query: 668 KENQKVRVKVLGI-DDRGRIKLS 689
K ++ VKVL + D+ G + LS
Sbjct: 348 KVGDEIEVKVLKLEDEDGYVVLS 370
>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal
structure and biogenesis].
Length = 541
Score = 77.0 bits (190), Expect = 1e-14
Identities = 43/131 (32%), Positives = 74/131 (56%), Gaps = 8/131 (6%)
Query: 561 IDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESV 620
+D +RD+ G + E +D ++ S +V +E + E+L +
Sbjct: 137 VDVRPVRDLDPLIGKELEFKILE----LDKKRNNVV--LSRRAVLEEERSEQREELLNKL 190
Query: 621 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 680
++G+V G+V + D+GA + I G DGLLHIS+IS KRV+ ++ +K +V+VKV+ +
Sbjct: 191 EVGEVVEGVVKNITDYGAFVDI-GGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISL 249
Query: 681 D-DRGRIKLSM 690
D +RGR+ LS+
Sbjct: 250 DEERGRVSLSL 260
Score = 71.6 bits (176), Expect = 6e-13
Identities = 30/78 (38%), Positives = 47/78 (60%), Gaps = 1/78 (1%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 673
E + + +G G V L D+GA + I G +GL+H+S+IS + N+ ++ +K Q+V
Sbjct: 269 EGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEV 328
Query: 674 RVKVLGID-DRGRIKLSM 690
VKVL ID +R RI L +
Sbjct: 329 EVKVLDIDPERRRISLGL 346
Score = 48.5 bits (116), Expect = 8e-06
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 673
E+ + +G V G V + DFGA + + G DGL+H+S +S R + K+ +V
Sbjct: 355 EEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEV 414
Query: 674 RVKVLGID-DRGRIKLS 689
KVL +D ++ RI L
Sbjct: 415 EAKVLAVDKEKERISLG 431
Score = 36.1 bits (84), Expect = 0.067
Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 602 NSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVN 661
S E +R EKL E+ + G++ G + G + I G L S + + V
Sbjct: 85 LSRRKAERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDI-EGVRAFLPGSLVDVRPVR 143
Query: 662 IITDFLKENQKVRVKVLGID-DRGRIKLS 689
+ +++ K+L +D R + LS
Sbjct: 144 DLDPL--IGKELEFKILELDKKRNNVVLS 170
Score = 33.8 bits (78), Expect = 0.35
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 682
G V G V + D GA + + G +GL+ +S++S LK +V V+ ID
Sbjct: 450 GSVVKGKVKSVKDKGAFVELGGGVEGLIRLSELSRDV-------LKVGDEVEAVVVSIDK 502
Query: 683 R-GRIKLS 689
+ +I LS
Sbjct: 503 KNRKILLS 510
Score = 32.3 bits (74), Expect = 1.1
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 617 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVK 676
E + G V G V+ + G ++ I +G++ IS+ S++ V D ++ +V V
Sbjct: 16 DEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVE---DVVQVGDEVEVL 72
Query: 677 VLGI-DDRGRIKLS 689
VL + D G + LS
Sbjct: 73 VLRVEDGEGELVLS 86
>gnl|CDD|240193 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein
S1 (RPS1) domain. RPS1 is a component of the small
ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 3 (ec3) of the Escherichia coli RPS1.
Autoantibodies to double-stranded DNA from patients with
systemic lupus erythematosus cross-react with the human
RPS1 homolog.
Length = 68
Score = 67.3 bits (165), Expect = 4e-14
Identities = 31/69 (44%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 622 IGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID 681
G V G V + DFGA + L G DGLLHIS +S RV ++ + +V VKVL ID
Sbjct: 1 EGDVVEGTVKSITDFGAFVD-LGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKID 59
Query: 682 -DRGRIKLS 689
+R RI L
Sbjct: 60 KERKRISLG 68
>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 75.2 bits (186), Expect = 5e-14
Identities = 33/85 (38%), Positives = 54/85 (63%), Gaps = 4/85 (4%)
Query: 607 QEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDF 666
+ +R E+L E+++ G+V G+V + D+GA + L G DGLLHI+ IS KRVN ++
Sbjct: 188 RAEER--EELLENLEEGQVVEGVVKNITDYGAFVD-LGGVDGLLHITDISWKRVNHPSEV 244
Query: 667 LKENQKVRVKVLGID-DRGRIKLSM 690
+ +V+VKVL D ++ R+ L +
Sbjct: 245 VNVGDEVKVKVLKFDKEKKRVSLGL 269
Score = 58.6 bits (143), Expect = 7e-09
Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 14/97 (14%)
Query: 608 EAKRRI------------EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQI 655
E KRRI E+ E +G V G V + DFGA + + G DGL+H+S I
Sbjct: 347 EEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDI 406
Query: 656 S-SKRVNIITDFLKENQKVRVKVLGID-DRGRIKLSM 690
S K+ + K+ +V VL +D ++ RI L +
Sbjct: 407 SWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGI 443
Score = 57.9 bits (141), Expect = 1e-08
Identities = 24/79 (30%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 672
E + + +G G V + D+GA + + G +GL+H+S++S +K+ + + Q+
Sbjct: 278 EAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQE 337
Query: 673 VRVKVLGID-DRGRIKLSM 690
V V VL ID ++ RI L +
Sbjct: 338 VEVMVLEIDEEKRRISLGL 356
Score = 55.2 bits (134), Expect = 8e-08
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 673
E+ + + G + TG V + D GA + + G +GL+ S++S RV T+ LK +V
Sbjct: 452 EEFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEV 511
Query: 674 RVKVLGIDDRGR-IKLSM 690
KV+ ID + R I LS+
Sbjct: 512 EAKVINIDRKNRRISLSI 529
>gnl|CDD|216000 pfam00575, S1, S1 RNA binding domain. The S1 domain occurs in a
wide range of RNA associated proteins. It is
structurally similar to cold shock protein which binds
nucleic acids. The S1 domain has an OB-fold structure.
Length = 74
Score = 66.1 bits (162), Expect = 1e-13
Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 619 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 678
+ G V G V R+ GA + + +G +G + IS+IS RV + LK +V VKVL
Sbjct: 1 KPEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVL 60
Query: 679 GID-DRGRIKLSM 690
+D +RGRI LS+
Sbjct: 61 KVDKERGRIILSI 73
>gnl|CDD|206775 cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryotic exosome. The
RRP41 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 226
Score = 69.1 bits (170), Expect = 3e-13
Identities = 50/207 (24%), Positives = 89/207 (42%), Gaps = 21/207 (10%)
Query: 314 GLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLG----TSRDEQKIDAL 369
GLR+D R N++R I R G+ GS+ +G+T+ L G +R + D
Sbjct: 1 GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVY-GPHEPRNRSQALHDRA 59
Query: 370 MGEFTDSFMLHYNMPPFATGDIGRIGVPKRR--EIGHGRLAKRALLPVLPNNNKFNYSIR 427
Y+M F+TG+ R G RR E+ ++ V+ + I
Sbjct: 60 ------VVNCEYSMATFSTGERKRRGKGDRRSTELSL--AIRQTFEAVILTHLYPRSQID 111
Query: 428 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 487
+ ++ +++G A + LAL+DAG+P+ ++V + G + L D+ E+
Sbjct: 112 IYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYLDS----TPLLDLNYLEE 167
Query: 488 RCGDMDFKVA--GTVNGITALQMDIKI 512
D VA + + LQM+ ++
Sbjct: 168 SGDLPDLTVAVLPKSDKVVLLQMESRL 194
>gnl|CDD|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding
domain. Found in a wide variety of RNA-associated
proteins. Originally identified in S1 ribosomal protein.
This superfamily also contains the Cold Shock Domain
(CSD), which is a homolog of the S1 domain. Both domains
are members of the Oligonucleotide/oligosaccharide
Binding (OB) fold.
Length = 65
Score = 62.0 bits (151), Expect = 2e-12
Identities = 26/65 (40%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 626 YTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDR-G 684
TG V+ + FG + + G +GL+HIS++S K V ++ K +V VKVL +D G
Sbjct: 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKG 60
Query: 685 RIKLS 689
RI LS
Sbjct: 61 RISLS 65
>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1. This model describes
ribosomal protein S1, RpsA. This protein is found in
most bacterial genomes in a single copy, but is not
present in the Mycoplasmas. It is heterogeneous with
respect to the number of repeats of the S1 RNA binding
domain described by PFAM model pfam00575: six repeats in
E. coli and most other bacteria, four in Bacillus
subtilis and some other species. rpsA is an essential
gene in E. coli but not in B. subtilis. It is associated
with the cytidylate kinase gene cmk in many species, and
fused to it in Treponema pallidum. RpsA is proposed
(Medline:97323001) to assist in mRNA degradation. This
model provides trusted hits to most long form (6 repeat)
examples of RpsA. Among homologs with only four repeats
are some to which other (perhaps secondary) functions
have been assigned [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 516
Score = 68.2 bits (167), Expect = 6e-12
Identities = 36/84 (42%), Positives = 56/84 (66%), Gaps = 2/84 (2%)
Query: 608 EAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFL 667
E + E+L E+++ G V G+V + DFGA + L G DGLLHI+ +S KRV ++++
Sbjct: 173 ERSQAREELLENLKEGDVVKGVVKNITDFGAFV-DLGGVDGLLHITDMSWKRVKHPSEYV 231
Query: 668 KENQKVRVKVLGID-DRGRIKLSM 690
K Q+V+VKV+ D ++GRI LS+
Sbjct: 232 KVGQEVKVKVIKFDKEKGRISLSL 255
Score = 54.0 bits (130), Expect = 2e-07
Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 672
E + + +G TG V L D+G + I G +GL+H+S++S K+ + + +K+ +
Sbjct: 264 EAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDE 323
Query: 673 VRVKVLGID-DRGRIKLSM 690
V V +L ID +R R+ L +
Sbjct: 324 VEVMILDIDPERRRLSLGL 342
Score = 45.1 bits (107), Expect = 1e-04
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 673
EK ++G V G V + DFGA + + G +GL+ S++S R TD +K +V
Sbjct: 438 EKFAAKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEV 497
Query: 674 RVKVLGID-DRGRIKLS 689
KV+ ID ++ LS
Sbjct: 498 EAKVVDIDKKNRKVSLS 514
Score = 42.4 bits (100), Expect = 6e-04
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 672
E+ E +G TG + ++ DFGA + + G DGL+H+S IS K K+ +
Sbjct: 351 EQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDE 410
Query: 673 VRVKVLGIDDRG-RIKLS 689
+ VL +D RI L
Sbjct: 411 IEAVVLAVDKEKKRISLG 428
>gnl|CDD|217697 pfam03726, PNPase, Polyribonucleotide nucleotidyltransferase, RNA
binding domain. This family contains the RNA binding
domain of Polyribonucleotide nucleotidyltransferase
(PNPase) PNPase is involved in mRNA degradation in a
3'-5' direction.
Length = 80
Score = 59.2 bits (144), Expect = 3e-11
Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 241 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 300
L K+ ++E ++ +AY I KQ R I D+ ++ E+ +D +I I
Sbjct: 1 ELEEKVAALAEERLSEAYTITGKQERYAALDEIKADVVAAFAA-EDDELDEKEIKAIFKA 59
Query: 301 LESKIIRKQILDKGLRIDNRG 321
LE K++R +ILD G RID RG
Sbjct: 60 LEKKVVRSRILDGGPRIDGRG 80
>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional.
Length = 491
Score = 65.9 bits (161), Expect = 3e-11
Identities = 34/88 (38%), Positives = 48/88 (54%), Gaps = 5/88 (5%)
Query: 607 QEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDF 666
+E K +E E+V+ G V G V RL FGA + + G +G++HIS++S RV +
Sbjct: 187 REQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEA 246
Query: 667 LKENQKVRVKVLGIDDRG-----RIKLS 689
+ VRVKVLGI+ RI LS
Sbjct: 247 VSVGDTVRVKVLGIERAKKGKGLRISLS 274
Score = 59.7 bits (145), Expect = 3e-09
Identities = 30/79 (37%), Positives = 48/79 (60%), Gaps = 2/79 (2%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 672
+ + + ++ G TG V+RL FGA + IL G +GL+H+S++S ++RVN D +
Sbjct: 284 DTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDA 343
Query: 673 VRVKVLGID-DRGRIKLSM 690
V VK+ ID + RI LS+
Sbjct: 344 VAVKIKDIDPAKRRISLSL 362
Score = 30.8 bits (70), Expect = 2.8
Identities = 26/89 (29%), Positives = 32/89 (35%), Gaps = 12/89 (13%)
Query: 609 AKRRI------------EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS 656
AKRRI + E G TG V + FG + + G GLL S IS
Sbjct: 354 AKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVIS 413
Query: 657 SKRVNIITDFLKENQKVRVKVLGIDDRGR 685
+ LK V + V ID R
Sbjct: 414 RAGKPATYEKLKPGDSVTLVVEEIDTAKR 442
>gnl|CDD|240190 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a
transcription accessory factor called Tex, which has
been characterized in Bordetella pertussis and
Pseudomonas aeruginosa. The tex gene is essential in
Bortella pertusis and is named for its role in toxin
expression. Tex has two functional domains, an
N-terminal domain homologous to the Escherichia coli
maltose repression protein, which is a poorly defined
transcriptional factor, and a C-terminal S1 RNA-binding
domain. Tex is found in prokaryotes, eukaryotes, and
archaea.
Length = 68
Score = 58.0 bits (141), Expect = 6e-11
Identities = 29/68 (42%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID- 681
G V G+V + DFGA + I +DGL+HIS+++ + V+ +D + V VKV+ ID
Sbjct: 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDE 60
Query: 682 DRGRIKLS 689
+RGRI LS
Sbjct: 61 ERGRISLS 68
>gnl|CDD|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit
alpha; Validated.
Length = 262
Score = 60.2 bits (147), Expect = 5e-10
Identities = 28/66 (42%), Positives = 41/66 (62%), Gaps = 3/66 (4%)
Query: 628 GIVLRLFDFGAIIRIL--SGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID-DRG 684
G V + DFGA + + GK+G +HIS+++S V I D +KE QKV KV+ +D +G
Sbjct: 14 GTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKG 73
Query: 685 RIKLSM 690
I LS+
Sbjct: 74 HIDLSL 79
>gnl|CDD|239899 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of
translation Initiation Factor 2, S1-like RNA-binding
domain. S1-like RNA-binding domains are found in a wide
variety of RNA-associated proteins. Eukaryotic and
archaeal Initiation Factor 2 (e- and aIF2, respectively)
are heterotrimeric proteins with three subunits (alpha,
beta, and gamma). IF2 plays a crucial role in the
process of translation initiation. The IF2 gamma subunit
contains a GTP-binding site. The IF2 beta and gamma
subunits together are thought to be responsible for
binding methionyl-initiator tRNA. The ternary complex
consisting of IF2, GTP, and the methionyl-initiator tRNA
binds to the small subunit of the ribosome, as part of a
pre-initiation complex that scans the mRNA to find the
AUG start codon. The IF2-bound GTP is hydrolyzed to GDP
when the methionyl-initiator tRNA binds the AUG start
codon, at which time the IF2 is released with its bound
GDP. The large ribosomal subunit then joins with the
small subunit to complete the initiation complex, which
is competent to begin translation. The IF2a subunit is a
major site of control of the translation initiation
process, via phosphorylation of a specific serine
residue. This alpha subunit is well conserved in
eukaryotes and archaea but is not present in bacteria.
IF2 is a cold-shock-inducible protein.
Length = 76
Score = 55.7 bits (135), Expect = 6e-10
Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 622 IGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLG 679
G++ V + D GA + +L +G++ +S++S +R+ I +K +K VKV+
Sbjct: 3 EGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIR 62
Query: 680 ID-DRGRIKLSM 690
+D ++G I LS
Sbjct: 63 VDKEKGYIDLSK 74
>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated.
Length = 123
Score = 56.6 bits (137), Expect = 9e-10
Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 616 LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRV 675
+ ++G V TG V + +GA + + GL+HIS+I+ V I DFL +V+V
Sbjct: 1 MMSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKV 60
Query: 676 KVLGID-DRGRIKLSM 690
KVL +D ++G+I LS+
Sbjct: 61 KVLSVDEEKGKISLSI 76
>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit
(eIF-2alpha) [Translation, ribosomal structure and
biogenesis].
Length = 269
Score = 59.6 bits (145), Expect = 1e-09
Identities = 31/83 (37%), Positives = 49/83 (59%), Gaps = 6/83 (7%)
Query: 611 RRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLK 668
+ + E G++ G V ++ D+GA + + GK+G +HIS+++S V I D++K
Sbjct: 3 MKRREYPE---EGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVK 59
Query: 669 ENQKVRVKVLGID-DRGRIKLSM 690
E QKV KVL +D RG I LS+
Sbjct: 60 EGQKVVAKVLRVDPKRGHIDLSL 82
>gnl|CDD|206777 cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryotic exosome. The
RRP46 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 199
Score = 58.0 bits (141), Expect = 1e-09
Identities = 44/167 (26%), Positives = 72/167 (43%), Gaps = 41/167 (24%)
Query: 325 IRPISIRTGILPRTHGSSLFTRGDTQALVVATLG----TSRDEQKIDALMGEFTDSFMLH 380
+RP+S G+L R GS+ F++GDT L G R E
Sbjct: 1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVY-GPIEVKLRKE----------------- 42
Query: 381 YNMPPFATGDI---GRIGVPKRREIGHGRLAKRALLPVL-----PNNNKFNYSIRLVSEI 432
+P AT ++ + G+P +E L + L P++ P I +V ++
Sbjct: 43 --LPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIILLHLHPRT-----LISVVLQV 95
Query: 433 TESNGSSSMASVC--GGCLALLDAGVPISEHVAGIAMGLIKDGEKVV 477
+ +GS + + CLALLDAGVP+ A + + +DGE ++
Sbjct: 96 LQDDGS--LLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIIL 140
>gnl|CDD|236305 PRK08582, PRK08582, hypothetical protein; Provisional.
Length = 139
Score = 55.8 bits (135), Expect = 2e-09
Identities = 29/71 (40%), Positives = 44/71 (61%)
Query: 619 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 678
S+++G G V + +FGA + + GK GL+HIS+++ V I D LK +V VKVL
Sbjct: 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVL 61
Query: 679 GIDDRGRIKLS 689
++D G+I LS
Sbjct: 62 NVEDDGKIGLS 72
>gnl|CDD|235268 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42;
Provisional.
Length = 271
Score = 57.6 bits (140), Expect = 4e-09
Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 303 SKIIRKQILD---KGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 353
+I + IL KG RID R +++ RPI I TG++ + GS+L G+TQ L
Sbjct: 9 PEIKKDYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLA 62
>gnl|CDD|236126 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 486
Score = 58.5 bits (142), Expect = 6e-09
Identities = 27/71 (38%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 680
IG++ G V +L FGA +R+ G +GL+HIS+++ + V + ++ +V VKV+ I
Sbjct: 292 AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDI 351
Query: 681 D-DRGRIKLSM 690
D +R RI LS+
Sbjct: 352 DLERRRISLSL 362
Score = 51.2 bits (123), Expect = 1e-06
Identities = 28/71 (39%), Positives = 48/71 (67%), Gaps = 2/71 (2%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 680
Q G+V G+V + +FGA + L G DGL+H+S++S K ++ ++ ++ Q+V V+VL +
Sbjct: 207 QKGQVRKGVVSSIVNFGAFVD-LGGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDV 265
Query: 681 D-DRGRIKLSM 690
D DR R+ LS+
Sbjct: 266 DMDRERVSLSL 276
>gnl|CDD|215657 pfam00013, KH_1, KH domain. KH motifs bind RNA in vitro.
Autoantibodies to Nova, a KH domain protein, cause
paraneoplastic opsoclonus ataxia.
Length = 59
Score = 52.2 bits (126), Expect = 7e-09
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG--IITIASFNSVSGQEAKRRI 613
I I P K+ +IGKGGS I+ + EETG +I I D+ +TI+ ++AK I
Sbjct: 2 ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDDTVTISG-TPEQVEKAKELI 59
>gnl|CDD|131021 TIGR01966, RNasePH, ribonuclease PH. This bacterial enzyme,
ribonuclease PH, performs the final 3'-trimming and
modification of tRNA precursors. This model is
restricted absolutely to bacteria. Related families
outside the model include proteins described as probable
exosome complex exonucleases (rRNA processing) and
polyribonucleotide nucleotidyltransferases (mRNA
degradation). The most divergent member within the
family is RNase PH from Deinococcus radiodurans
[Transcription, RNA processing].
Length = 236
Score = 55.8 bits (135), Expect = 1e-08
Identities = 59/209 (28%), Positives = 91/209 (43%), Gaps = 37/209 (17%)
Query: 316 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALM-GEFT 374
R D R + +RP+SI L GS L G+T+ L A++ E+K+ + G
Sbjct: 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASV-----EEKVPPFLRGSGE 55
Query: 375 DSFMLHYNMPPFATGDIGRIGVPKRREIGHG----------RLAKRALLPVLPNNNKFNY 424
Y M P AT RRE G RL RAL V+
Sbjct: 56 GWITAEYGMLPRATQT------RNRRESAKGKQSGRTQEIQRLIGRALRAVVDLEALGER 109
Query: 425 SIRLVSEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDG 473
+I + ++ +++G + AS+ G +AL DA PI + VA +++G++ DG
Sbjct: 110 TIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIV-DG 168
Query: 474 EKVVILSDILGDEDRCGDMDFKVAGTVNG 502
E V+ D+ +ED D+D V T +G
Sbjct: 169 EPVL---DLDYEEDSAADVDMNVVMTGSG 194
Score = 33.5 bits (77), Expect = 0.30
Identities = 62/253 (24%), Positives = 94/253 (37%), Gaps = 66/253 (26%)
Query: 15 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFP-LTV 61
+SI + A SVL+ +T +L T V K P T+ Y P T
Sbjct: 12 PVSITRD-FLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQ 70
Query: 62 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVN 121
+ A G+ G R I RLI R +R + L E I
Sbjct: 71 TRNRRESAKGKQSG-----------RTQEIQRLIGRALRAVVDLEALGERTIW------- 112
Query: 122 PQIDPDI---------ASIIG--VSTALSISEL---------PFLGPLGVAKVGYIDGKY 161
ID D+ ASI G V+ A +IS+L P + VG +DG+
Sbjct: 113 --IDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIVDGEP 170
Query: 162 ILNPTTEQLKKSHLDLLVAGTEK-AIITVE--SESKQLPEDIILNAIIFGHEKMKIAINA 218
+L+ E+ + +D+ V T + V+ +E D LN + + +A
Sbjct: 171 VLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRD-ELNKL------LDLAKKG 223
Query: 219 INELVQNVGQKKV 231
I EL++ QK+
Sbjct: 224 IRELIE--LQKQA 234
>gnl|CDD|225094 COG2183, Tex, Transcriptional accessory protein [Transcription].
Length = 780
Score = 56.9 bits (138), Expect = 3e-08
Identities = 32/81 (39%), Positives = 48/81 (59%), Gaps = 2/81 (2%)
Query: 613 IEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQK 672
+E +T+ ++ G + G V + DFGA + I +DGL+HISQ+S K V + +K
Sbjct: 650 VESITD-LKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDI 708
Query: 673 VRVKVLGID-DRGRIKLSMIY 692
V+VKV+ +D R RI LSM
Sbjct: 709 VKVKVIEVDTARKRIALSMRL 729
>gnl|CDD|217696 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2. This
family includes 3'-5' exoribonucleases. Ribonuclease PH
contains a single copy of this domain, and removes
nucleotide residues following the -CCA terminus of tRNA.
Polyribonucleotide nucleotidyltransferase (PNPase)
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction. The
exosome is a 3'-5' exoribonuclease complex that is
required for 3' processing of the 5.8S rRNA. Three of
its five protein components contain a copy of this
domain. A hypothetical protein from S. pombe appears to
belong to an uncharacterized subfamily. This subfamily
is found in both eukaryotes and archaebacteria.
Length = 68
Score = 50.6 bits (122), Expect = 3e-08
Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 147 GPLGVAKVGYIDGKYILNPTTEQ--LKKSHLDLLVAGTEKAIIT-VESESKQLPEDIILN 203
GP+ VG IDG+ +L+PT E+ L S L ++VAGT + + E +L E+ +L
Sbjct: 1 GPVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGEIVALMKEGGGAELTEEELLE 60
Query: 204 AIIFGHEK 211
A+ HE
Sbjct: 61 ALELAHEG 68
Score = 37.2 bits (87), Expect = 0.001
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 7/71 (9%)
Query: 462 VAGIAMGLIKDGEKVVILSDILGDEDRC--GDMDFKVAGTVNGITALQMDIKIFGITYDI 519
VA + +G I ++ D +E+ D+ VAGT + ++ +T +
Sbjct: 3 VAAVTVGKIDGE----LVLDPTLEEESLADSDLTIVVAGTGEIVALMKEGGGAE-LTEEE 57
Query: 520 IQIALYKAKKG 530
+ AL A +G
Sbjct: 58 LLEALELAHEG 68
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA. There are two different KH domains that belong
to different protein folds, but they share a single KH
motif. The KH motif is folded into a beta alpha alpha
beta unit. In addition to the core, type II KH domains
(e.g. ribosomal protein S3) include N-terminal extension
and type I KH domains (e.g. hnRNP K) contain C-terminal
extension.
Length = 64
Score = 49.9 bits (120), Expect = 4e-08
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 9/65 (13%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI------NDEGIITI-ASFNSVSGQEA 609
+ + S + +IGKGGSTI+ + EETG +I I ++E I+TI + +V ++A
Sbjct: 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAV--EKA 59
Query: 610 KRRIE 614
K I
Sbjct: 60 KELIL 64
>gnl|CDD|240213 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5
is found in eukaryotes but not in prokaryotes or
archaea.
Length = 77
Score = 50.0 bits (120), Expect = 6e-08
Identities = 27/70 (38%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 623 GKVYTGIVLRLFDFGAIIRI-LSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID 681
G+ G V R+ D+G I I + GL H S+IS RV + + KVR KVL ID
Sbjct: 3 GQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKID 62
Query: 682 -DRGRIKLSM 690
++ RI L +
Sbjct: 63 AEKKRISLGL 72
>gnl|CDD|206767 cd11362, RNase_PH_bact, Ribonuclease PH. Ribonuclease PH (RNase
PH)-like 3'-5' exoribonucleases are enzymes that
catalyze the 3' to 5' processing and decay of RNA
substrates. Structurally all members of this family form
hexameric rings (trimers of dimers). Bacterial RNase PH
forms a homohexameric ring, and removes nucleotide
residues following the -CCA terminus of tRNA.
Length = 227
Score = 53.0 bits (128), Expect = 9e-08
Identities = 56/205 (27%), Positives = 91/205 (44%), Gaps = 45/205 (21%)
Query: 324 DIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALM-----GEFTDSFM 378
+RPISI G GS L GDT+ L A++ E+K+ + G T
Sbjct: 1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASV-----EEKVPPFLRGKGKGWVT---- 51
Query: 379 LHYNMPPFATGDIGRIGVPKRREIGHG----------RLAKRALLPVLPNNNKFNYSIRL 428
Y+M P +T + R +RE G RL R+L + +I +
Sbjct: 52 AEYSMLPRSTHE--R----TQREASKGKQSGRTQEIQRLIGRSLRAAVDLEALGERTITI 105
Query: 429 VSEITESNGSSSMASVCGGCLALLDA-------GV----PISEHVAGIAMGLIKDGEKVV 477
++ +++G + AS+ G +AL DA GV P+ VA +++G++ DGE ++
Sbjct: 106 DCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIV-DGEPLL 164
Query: 478 ILSDILGDEDRCGDMDFKVAGTVNG 502
D+ +ED D+D V T +G
Sbjct: 165 ---DLDYEEDSAADVDMNVVMTGSG 186
Score = 31.4 bits (72), Expect = 1.2
Identities = 54/204 (26%), Positives = 73/204 (35%), Gaps = 58/204 (28%)
Query: 16 ISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVDY 63
ISI G + A SVL+ DT +L T V K P T+ Y+ P
Sbjct: 5 ISITRG-FNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGKGKGWVTAEYSMLP----- 58
Query: 64 IEKAYAAGRIPGSFFKRE---GKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
R +RE GK S R I RLI R +R L E I
Sbjct: 59 --------RSTHERTQREASKGKQSGRTQEIQRLIGRSLRAAVDLEALGERTI------- 103
Query: 121 NPQIDPDI---------ASIIGVSTALS-----------ISELPFLGPLGVAKVGYIDGK 160
ID D+ ASI G AL+ + E P + VG +DG+
Sbjct: 104 --TIDCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIVDGE 161
Query: 161 YILNPTTEQLKKSHLDLLVAGTEK 184
+L+ E+ + +D+ V T
Sbjct: 162 PLLDLDYEEDSAADVDMNVVMTGS 185
>gnl|CDD|206770 cd11365, RNase_PH_archRRP42, RRP42 subunit of archaeal exosome.
The RRP42 subunit of the archaeal exosome is a member of
the RNase_PH family, named after the bacterial
Ribonuclease PH, a 3'-5' exoribonuclease. Structurally
all members of this family form hexameric rings (trimers
of dimers). In archaea, the ring is formed by three
Rrp41:Rrp42 dimers. The central chamber within the ring
contains three phosphorolytic active sites located in an
Rrp41 pocket at the interface between Rrp42 and Rrp41.
The ring is capped by three copies of Rrp4 and/or Csl4
which contain putative RNA interaction domains. The
archaeal exosome degrades single-stranded RNA (ssRNA) in
the 3'-5' direction, but also can catalyze the reverse
reaction of adding nucleoside diphosphates to the 3'-end
of RNA which has been shown to lead to the formation of
poly-A-rich tails on RNA. It is required for 3'
processing of the 5.8S rRNA.
Length = 256
Score = 52.6 bits (127), Expect = 2e-07
Identities = 25/54 (46%), Positives = 33/54 (61%), Gaps = 3/54 (5%)
Query: 303 SKIIRKQILD---KGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 353
KI R IL KG RID RG+++ R I I TG++P+ GS+L G+TQ L
Sbjct: 1 PKIKRDYILSLLEKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLA 54
>gnl|CDD|240191 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-binding domain.
pNO40 is a nucleolar protein of unknown function with an
N-terminal S1 RNA binding domain, a CCHC type zinc
finger, and clusters of basic amino acids representing a
potential nucleolar targeting signal. pNO40 was
identified through a yeast two-hybrid interaction screen
of a human kidney cDNA library using the pinin (pnn)
protein as bait. pNO40 is thought to play a role in
ribosome maturation and/or biogenesis.
Length = 73
Score = 48.2 bits (115), Expect = 2e-07
Identities = 23/71 (32%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILS-GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLG 679
+ +++ G V + ++GA ++I K GL+H S +SS RV+ ++ + +KV VKV+G
Sbjct: 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIG 61
Query: 680 IDDRGRIKLSM 690
+ + ++KLS+
Sbjct: 62 REMKDKMKLSL 72
>gnl|CDD|225034 COG2123, COG2123, RNase PH-related exoribonuclease [Translation,
ribosomal structure and biogenesis].
Length = 272
Score = 52.0 bits (125), Expect = 4e-07
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 300 DLESKIIRKQI----LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVA 355
I+++ L KG+RID R ++ RP+ I TG++P+ +GS+L G+TQ +V
Sbjct: 4 SEIISEIKREYILNLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGV 63
Query: 356 TLGTSR 361
Sbjct: 64 KAEIGE 69
>gnl|CDD|239908 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo
sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae
S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting
factor important for biogenesis of both the 40S and 60S
eukaryotic ribosomal subunits. Rrp5 has two distinct
regions, an N-terminal region containing tandemly
repeated S1 RNA-binding domains (12 S1 repeats in S.
cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5)
and a C-terminal region containing tetratricopeptide
repeat (TPR) motifs thought to be involved in
protein-protein interactions. Mutational studies have
shown that each region represents a specific functional
domain. Deletions within the S1-containing region
inhibit pre-rRNA processing at either site A3 or A2,
whereas deletions within the TPR region confer an
inability to support cleavage of A0-A2. This CD includes
H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7.
Rrp5 is found in eukaryotes but not in prokaryotes or
archaea.
Length = 83
Score = 47.6 bits (114), Expect = 5e-07
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 618 ESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKV 677
++ G V G V + +G + L G GL S IS + V + K+ Q V KV
Sbjct: 10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKV 69
Query: 678 LGID-DRGRIKLSM 690
+D ++ R LS+
Sbjct: 70 TSVDEEKQRFLLSL 83
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 45.0 bits (107), Expect = 3e-06
Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 5/64 (7%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI----NDEGIITIASFNSVSGQEAKRR 612
I + I K+ +IGKGGSTI+ + EETG +IDI ++E ++ I + ++A
Sbjct: 5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPE-NVEKAAEL 63
Query: 613 IEKL 616
I ++
Sbjct: 64 ILEI 67
>gnl|CDD|240195 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein
S1 (RPS1) domain. RPS1 is a component of the small
ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 5 (ec5) of the Escherichia coli RPS1.
Autoantibodies to double-stranded DNA from patients with
systemic lupus erythematosus cross-react with the human
RPS1 homolog.
Length = 69
Score = 43.3 bits (102), Expect = 1e-05
Identities = 28/68 (41%), Positives = 41/68 (60%), Gaps = 2/68 (2%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQKVRVKVLGID 681
G V +G + + DFG + + G DGL+HIS IS ++RV ++ K+ Q+V VL ID
Sbjct: 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID 60
Query: 682 -DRGRIKL 688
+R RI L
Sbjct: 61 VERERISL 68
>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed.
Length = 318
Score = 47.5 bits (113), Expect = 1e-05
Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 4/82 (4%)
Query: 611 RR--IEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLK 668
RR +E+ +++G+V G V + +GA I I G GLLHIS+IS + +
Sbjct: 183 RRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFN 241
Query: 669 ENQKVRVKVLGID-DRGRIKLS 689
N +++V ++ +D +RGRI LS
Sbjct: 242 VNDEMKVMIIDLDAERGRISLS 263
>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal
protein S1; Provisional.
Length = 863
Score = 47.0 bits (111), Expect = 3e-05
Identities = 30/85 (35%), Positives = 47/85 (55%), Gaps = 2/85 (2%)
Query: 607 QEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDF 666
+ A++ E+ SV I +G+V FGA I L G DGLLH++ +S V +F
Sbjct: 478 ERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFID-LGGFDGLLHVNDMSWGHVARPREF 536
Query: 667 LKENQKVRVKVLGIDD-RGRIKLSM 690
+K+ Q + +KV+ +D RI LS+
Sbjct: 537 VKKGQTIELKVIRLDQAEKRINLSL 561
Score = 42.0 bits (98), Expect = 0.001
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 622 IGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQKVRVKVLGI 680
+ V G V ++ DFGA I + G +GL HIS+ S K+ + +D +K +V +LG
Sbjct: 578 VNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGY 637
Query: 681 D-DRGRIKLSM 690
D GR+ L +
Sbjct: 638 DIQAGRVSLGL 648
Score = 29.7 bits (66), Expect = 6.0
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 614 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 672
E++ +G +T ++++ + GA I + G DG LH+ +S KR L+ ++
Sbjct: 657 EEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKE 716
Query: 673 VRVKVLGIDDRGR 685
+ V+ D + R
Sbjct: 717 IECMVIECDPQAR 729
>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding
domain_vigilin_like. The vigilin family is a large and
extended family of multiple KH-domain proteins,
including vigilin, also called high density lipoprotein
binding protien (HBP), fungal Scp160 and bicaudal-C.
Yeast Scp160p has been shown to bind RNA and to
associate with both soluble and membrane-bound
polyribosomes as a mRNP component. Bicaudal-C is a
RNA-binding molecule believed to function in embryonic
development at the post-transcriptional level. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 62
Score = 39.4 bits (93), Expect = 2e-04
Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG----IITI 598
++I R +IGK GS IR + EETG +I D G ITI
Sbjct: 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITI 47
>gnl|CDD|206776 cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic exosome. The
MTR3 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 210
Score = 42.2 bits (100), Expect = 3e-04
Identities = 48/192 (25%), Positives = 81/192 (42%), Gaps = 27/192 (14%)
Query: 325 IRPISIRTGILPRTHGSSLFTRGDTQALVVATLG---TSRDEQKIDALMGEFTDS--FML 379
IRPI ++TG++ + GS+ G+T+ ++ + G EF+D
Sbjct: 1 IRPIFLKTGVVSQAKGSAYVELGNTK-VICSVYGPRPIPGRT--------EFSDRGRLNC 51
Query: 380 HYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLP-VLPNNNKF-NYSIRLVSEITESNG 437
PFAT R E L +AL P V K+ I + + ES+G
Sbjct: 52 EVKFAPFATPGRRR-HGQDSEERELSSLLHQALEPAVRL--EKYPKSQIDVFVTVLESDG 108
Query: 438 SS-SMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKV 496
S + A LAL DAG+ + + V + LI G+++++ D +E+ +
Sbjct: 109 SVLAAAITAAS-LALADAGIEMYDLVTACSAALI--GDELLL--DPTREEEEASSGGVML 163
Query: 497 AG--TVNGITAL 506
A ++N +T L
Sbjct: 164 AYMPSLNQVTQL 175
>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4;
Provisional.
Length = 235
Score = 42.6 bits (101), Expect = 3e-04
Identities = 19/40 (47%), Positives = 23/40 (57%)
Query: 559 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITI 598
++I P K+ VIGK GS I L EETG I + G I I
Sbjct: 149 VEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQNGRIWI 188
>gnl|CDD|239900 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like
RNA-binding domain. RNase E is an essential
endoribonuclease in the processing and degradation of
RNA. In addition to its role in mRNA degradation, RNase
E has also been implicated in the processing of rRNA,
and the maturation of tRNA, 10Sa RNA and the M1
precursor of RNase P. RNase E associates with PNPase (3'
to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and
enolase (glycolytic enzyme) to form the RNA
degradosome. RNase E tends to cut mRNA within
single-stranded regions that are rich in A/U
nucleotides. The N-terminal region of RNase E contains
the catalytic site. Within the conserved N-terminal
domain of RNAse E and RNase G, there is an S1-like
subdomain, which is an ancient single-stranded
RNA-binding domain. S1 domain is an RNA-binding module
originally identified in the ribosomal protein S1. The
S1 domain is required for RNA cleavage by RNase E. RNase
G is paralogous to RNase E with an N-terminal catalytic
domain that is highly homologous to that of RNase E.
RNase G not only shares sequence similarity with RNase
E, but also functionally overlaps with RNase E. In
Escherichia coli, RNase G is involved in the maturation
of the 5' end of the 16S rRNA. RNase G plays a secondary
role in mRNA decay.
Length = 88
Score = 39.1 bits (92), Expect = 5e-04
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 618 ESVQIGKVYTGIVLRLFDF--GAIIRILSGKDGLLHISQISS---KRVNIITDFLKENQK 672
+G +Y G V ++ A + I GK+G LH+S I K+ I LKE Q+
Sbjct: 3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQE 62
Query: 673 VRVKV 677
+ V+V
Sbjct: 63 ILVQV 67
>gnl|CDD|180908 PRK07252, PRK07252, hypothetical protein; Provisional.
Length = 120
Score = 40.1 bits (94), Expect = 5e-04
Identities = 22/71 (30%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 680
+IG G + + +GA + + +G GL+HIS+I + ++ I LK ++V V+V+
Sbjct: 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDF 61
Query: 681 DD-RGRIKLSM 690
D+ G+ LS+
Sbjct: 62 DEYTGKASLSL 72
>gnl|CDD|206772 cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryotic exosome. The
RRP42 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 272
Score = 41.8 bits (99), Expect = 6e-04
Identities = 17/40 (42%), Positives = 23/40 (57%)
Query: 314 GLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 353
+R D R D RPI + TG+L T+GS+ G+T LV
Sbjct: 17 NIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLV 56
>gnl|CDD|240196 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein
S1 (RPS1) domain. RPS1 is a component of the small
ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 6 (ec6) of the Escherichia coli RPS1.
Autoantibodies to double-stranded DNA from patients with
systemic lupus erythematosus cross-react with the human
RPS1 homolog.
Length = 73
Score = 38.0 bits (89), Expect = 9e-04
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 682
G + TG V + GA +++ G +G L +++S RV T+ K +V K+ +D
Sbjct: 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60
Query: 683 RGR-IKLS 689
+ R I LS
Sbjct: 61 KNRKISLS 68
>gnl|CDD|240203 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes H. sapiens S1 repeat 6 (hs6) and S.
cerevisiae S1 repeat 5 (sc5). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 70
Score = 37.6 bits (88), Expect = 0.001
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 628 GIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID-DRGRI 686
G ++++ G I+ + G L S++S + + + Q V+VKVL D ++ R+
Sbjct: 6 GTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRL 65
Query: 687 KLS 689
LS
Sbjct: 66 LLS 68
>gnl|CDD|178914 PRK00173, rph, ribonuclease PH; Reviewed.
Length = 238
Score = 40.9 bits (97), Expect = 0.001
Identities = 55/220 (25%), Positives = 89/220 (40%), Gaps = 59/220 (26%)
Query: 316 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS-----RDEQK--IDA 368
R D R + +RP++I GS L GDT+ L A++ + + + + A
Sbjct: 2 RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTA 61
Query: 369 LMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHG----------RLAKRAL-----L 413
Y M P AT R RE G RL R+L L
Sbjct: 62 -----------EYGMLPRATHT--R----NDREAAKGKQGGRTQEIQRLIGRSLRAVVDL 104
Query: 414 PVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDA-------GV----PISEHV 462
L +I + ++ +++G + AS+ G +AL DA G P+ + V
Sbjct: 105 KALGER-----TITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQV 159
Query: 463 AGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG 502
A +++G++ DGE V+ D+ +ED + D V T +G
Sbjct: 160 AAVSVGIV-DGEPVL---DLDYEEDSAAETDMNVVMTGSG 195
>gnl|CDD|239919 cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain of the
archaea-specific RecJ-like exonuclease. The function of
this family is not fully understood. In Escherichia
coli, RecJ degrades single-stranded DNA in the 5'-3'
direction and participates in homologous recombination
and mismatch repair.
Length = 77
Score = 37.6 bits (88), Expect = 0.001
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 617 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVK 676
E +++GK+Y G V + +G + + GL+H S N++ D+ + +V V+
Sbjct: 11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRS-------NLLRDY-EVGDEVIVQ 62
Query: 677 VLGIDDRGRIKLS 689
V I + G I L
Sbjct: 63 VTDIPENGNIDLI 75
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 39.5 bits (93), Expect = 0.002
Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 559 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITI 598
+KI +I +IGK G T + + E TG +++I+ + G + I
Sbjct: 7 VKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVII 47
Score = 32.5 bits (75), Expect = 0.34
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 569 VIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 626
+IG+GG T R + E TG I + + + I V + A+ IE L E G VY
Sbjct: 109 IIGEGGKTRRIIEELTGVDISVYGKTVAIIGDPEQV--EIAREAIEMLIEGAPHGTVY 164
>gnl|CDD|221895 pfam13014, KH_3, KH domain. KH motifs bind RNA in vitro. This
RNA-binding domain is required for the efficient
anchoring of ASH1-mRNA to the distal tip of the daughter
cell. ASH1 is a specific repressor of transcription that
localizes asymmetrically to the daughter cell nucleus.
RNA localisation is a widespread mechanism for achieving
localised protein synthesis.
Length = 42
Score = 36.0 bits (84), Expect = 0.002
Identities = 17/40 (42%), Positives = 24/40 (60%), Gaps = 6/40 (15%)
Query: 565 KIRDVIGKGGSTIRTLTEETGTQIDI------NDEGIITI 598
+ +IGKGG TI+ + EETG +I I + E I+TI
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTI 40
>gnl|CDD|240194 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Ribosomal protein
S1 (RPS1) domain. RPS1 is a component of the small
ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 4 (ec4) of the Escherichia coli RPS1.
Autoantibodies to double-stranded DNA from patients with
systemic lupus erythematosus cross-react with the human
RPS1 homolog.
Length = 72
Score = 37.2 bits (86), Expect = 0.002
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 627 TGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNII-TDFLKENQKVRVKVLGID-DRG 684
G V L D+G + + G +GL+H+S++ NI + + +V V VL ID +R
Sbjct: 8 FGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERR 67
Query: 685 RIKL 688
RI L
Sbjct: 68 RISL 71
>gnl|CDD|239907 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain.
S1-like RNA-binding domains are found in a wide variety
of RNA-associated proteins. RpoE is subunit E of
archaeal RNA polymerase. Archaeal cells contain a single
RNA polymerase made up of 12 subunits, which are
homologous to the 12 subunits (RPB1-12) of eukaryotic
RNA polymerase II. RpoE is homologous to Rpa43 of
eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA
polymerase II, and Rpc25 of eukaryotic RNA polymerase
III. RpoE is composed of two domains, the N-terminal RNP
(ribonucleoprotein) domain and the C-terminal S1 domain.
This S1 domain binds ssRNA and ssDNA. This family is
classified based on the C-terminal S1 domain. The
function of RpoE is not fully understood. In eukaryotes,
RPB7 and RPB4 form a heterodimer that reversibly
associates with the RNA polymerase II core.
Length = 99
Score = 36.9 bits (86), Expect = 0.005
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 18/80 (22%)
Query: 628 GIVLRLFDFGAIIRILSGKDGLLHISQIS-------SKRVNIITD----FLKENQKVRVK 676
G V+ + DFGA +RI DGLLHISQI K +I + LK VR +
Sbjct: 5 GEVVEVVDFGAFVRI-GPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRAR 63
Query: 677 VLGI------DDRGRIKLSM 690
++ + +I L+M
Sbjct: 64 IVAVSLKERRPRESKIGLTM 83
>gnl|CDD|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain
protein. This family of proteins is universal among the
41 archaeal genomes analyzed in and is not observed
outside of the archaea. The proteins contain a single KH
domain (pfam00013) which is likely to confer the ability
to bind RNA.
Length = 172
Score = 37.5 bits (88), Expect = 0.008
Identities = 16/41 (39%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 559 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITI 598
+KI +I +IGKGG T + + E TG ++DI+ + G + I
Sbjct: 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKI 42
Score = 31.4 bits (72), Expect = 0.84
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 569 VIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 626
+IG+GG T R + E TG I + + + I V Q A+ IE L E G VY
Sbjct: 103 IIGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQV--QIAREAIEMLIEGAPHGTVY 158
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 38.5 bits (90), Expect = 0.013
Identities = 23/127 (18%), Positives = 52/127 (40%), Gaps = 11/127 (8%)
Query: 554 PRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRI 613
+K+ I VIGKGG I+ + ++ G +ID+ G++ I
Sbjct: 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDV-------KPLEEEEEGEKVPVEI 537
Query: 614 EKLTES--VQIGKVYTGIVLRLF-DFGAIIRILSGKDGLLHISQISSKRVNIITDFLKEN 670
E+ + + +G + G +R++ + + G++ I + S+ I + +
Sbjct: 538 EEKGKHIVLYVGPDFAGKPVRIYAGDEYLFTATVSRKGVVKIRK-DSEVGKEIEEAIDNG 596
Query: 671 QKVRVKV 677
+ +R +
Sbjct: 597 RDIRASL 603
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 38.3 bits (90), Expect = 0.014
Identities = 23/147 (15%), Positives = 54/147 (36%), Gaps = 22/147 (14%)
Query: 546 KNELSKFAP----------RLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGI 595
+ E+ ++ P + + I VIGKGG I+ + ++ G ID+
Sbjct: 462 EREIKRYLPGPVEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521
Query: 596 ITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD-----FGAIIRILSGKDGLL 650
+ + + + +G Y G + ++ F A + + G +
Sbjct: 522 EPGEEAEEGEEVTVEETKKHVI--LIVGPDYAGKTVDVYAGGEYLFTATV----SRKGEI 575
Query: 651 HISQISSKRVNIITDFLKENQKVRVKV 677
+++ +S + + E + +RV+
Sbjct: 576 KVAK-NSAIAKELLRAIDEGEDIRVRP 601
>gnl|CDD|236547 PRK09521, PRK09521, exosome complex RNA-binding protein Csl4;
Provisional.
Length = 189
Score = 36.9 bits (86), Expect = 0.015
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 10/74 (13%)
Query: 619 SVQIGKVYTGIVLRLFDFGAIIRILS----------GKDGLLHISQISSKRVNIITDFLK 668
++ G + G V+ + + A++RI+S K +HISQ+S V +TD K
Sbjct: 61 LLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFK 120
Query: 669 ENQKVRVKVLGIDD 682
VR KV+ D
Sbjct: 121 IGDIVRAKVISYTD 134
>gnl|CDD|206774 cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryotic exosome. The
RRP43 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 261
Score = 37.5 bits (88), Expect = 0.016
Identities = 14/45 (31%), Positives = 25/45 (55%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL 352
++ L + +R D R +++ RP S+ G + GS+L G+T L
Sbjct: 10 RRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVL 54
>gnl|CDD|224022 COG1097, RRP4, RNA-binding protein Rrp4 and related proteins
(contain S1 domain and KH domain) [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 36.9 bits (86), Expect = 0.019
Identities = 18/38 (47%), Positives = 24/38 (63%)
Query: 559 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGII 596
+KI PSK+ VIGK GS + L E+TG +I + G I
Sbjct: 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNGRI 187
>gnl|CDD|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E';
Provisional.
Length = 187
Score = 36.3 bits (85), Expect = 0.020
Identities = 27/88 (30%), Positives = 42/88 (47%), Gaps = 20/88 (22%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILSGK-DGLLHISQISSKRVNIITD-----------FLK 668
++ +V G V+ + +FGA +RI G DGLLHISQI ++ LK
Sbjct: 80 ELQEVVEGEVVEVVEFGAFVRI--GPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLK 137
Query: 669 ENQKVRVKVLGI-----DDRG-RIKLSM 690
VR +++ + RG +I L+M
Sbjct: 138 VGDVVRARIVAVSLKERRPRGSKIGLTM 165
>gnl|CDD|223631 COG0557, VacB, Exoribonuclease R [Transcription].
Length = 706
Score = 37.8 bits (88), Expect = 0.021
Identities = 23/103 (22%), Positives = 46/103 (44%), Gaps = 19/103 (18%)
Query: 607 QEAKRRIEKLTESV----QIGKVYTGIVLRLFDFGAIIRILS-GKDGLLHISQISSKRV- 660
QEA+R + L ++ ++G+ + G+V + FG + + G +GL+HIS +
Sbjct: 603 QEAERDVIDLLKAEYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYH 662
Query: 661 -----------NIITDFLKENQKVRVKVLGID-DRGRIKLSMI 691
+ + +V+VKV +D D +I ++
Sbjct: 663 FDERGQALVGEKSGKVY-RLGDEVKVKVTSVDLDERKIDFELV 704
>gnl|CDD|240192 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal
protein S1 (RPS1) domain. RPS1 is a component of the
small ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 1 of the Escherichia coli and Homo sapiens
RPS1 (ec1 and hs1, respectively). Autoantibodies to
double-stranded DNA from patients with systemic lupus
erythematosus cross-react with the human RPS1 homolog.
Length = 70
Score = 33.7 bits (78), Expect = 0.025
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 682
G + G V+ + D ++ I +G++ IS+ S + D +K +V V VL ++D
Sbjct: 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVED 60
Query: 683 R-GRIKLS 689
G + LS
Sbjct: 61 EEGNVVLS 68
>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like.
Members of this group possess KH domains in a tandem
arrangement. Most members, similar to the poly(C)
binding proteins (PCBPs) and Nova, containing three KH
domains, with the first and second domains, which are
represented here, in tandem arrangement, followed by a
large spacer region, with the third domain near the
C-terminal end of the protein. The poly(C) binding
proteins (PCBPs) can be divided into two groups, hnRNPs
K/J and the alphaCPs, which share a triple KH domain
configuration and poly(C) binding specificity. They
play roles in mRNA stabilization, translational
activation, and translational silencing. Nova-1 and
Nova-2 are nuclear RNA-binding proteins that regulate
splicing. This group also contains plant proteins that
seem to have two tandem repeat arrrangements, like Hen4,
a protein that plays a role in AGAMOUS (AG) pre-mRNA
processing and important step in plant development. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 65
Score = 32.8 bits (76), Expect = 0.048
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 10/53 (18%)
Query: 569 VIGKGGSTIRTLTEETGTQIDI-------NDEGIITI-ASFNSVSGQEAKRRI 613
+IGKGGSTI+ + EETG +I + + E ++TI ++V Q+A I
Sbjct: 14 IIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAV--QKALLLI 64
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E'
[Transcription].
Length = 183
Score = 35.3 bits (82), Expect = 0.048
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 12/70 (17%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-------SKRVNIITD----FLKENQ 671
G+V G V+ + +FGA +RI DGL+H+SQI K +I + LK
Sbjct: 82 GEVVEGEVVEVVEFGAFVRIGP-LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGD 140
Query: 672 KVRVKVLGID 681
KVR +++G+
Sbjct: 141 KVRARIVGVS 150
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 35.5 bits (82), Expect = 0.12
Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 7/76 (9%)
Query: 617 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVK 676
E V+ GK Y GIV R+ +G + + S GL+H + + D ++ V+
Sbjct: 117 MEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGDPDYAVGD------EIIVQ 170
Query: 677 VLGIDDRGRIKLSMIY 692
V + ++
Sbjct: 171 VSDVRPEKG-EIDFEP 185
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 35.1 bits (81), Expect = 0.13
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 569 VIGKGGSTIRTLTEETGTQIDIND-EGIITIASFNSVSGQEAKRRIEKLTESVQI 622
+IG+ G IR TG + I+D + I+SFN + + A+ +EKL +I
Sbjct: 213 IIGREGRNIRAFEGLTGVDLIIDDTPEAVVISSFNPIRREIARLTLEKLLADGRI 267
>gnl|CDD|206773 cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryotic exosome. The
RRP45 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 259
Score = 34.4 bits (80), Expect = 0.14
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 311 LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVAT 356
L +GLR+D RG+++ RPI I +G + G T+ L +
Sbjct: 13 LKEGLRLDGRGLDEFRPIKIT---FGLEYGCVEVSLGKTRVLAQVS 55
Score = 28.6 bits (65), Expect = 8.7
Identities = 31/115 (26%), Positives = 43/115 (37%), Gaps = 34/115 (29%)
Query: 4 FILKSFK----------YGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCK--DPT 51
FILK+ K I I G V VS+ T +LA VSC+ +P
Sbjct: 8 FILKALKEGLRLDGRGLDEFRPIKITFG----LEYGCVEVSLGKTRVLA-QVSCEIVEPK 62
Query: 52 STY---NFFPLTVDY---IEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIR 100
+ V+ A+ GR PSE E +SRL++R +R
Sbjct: 63 PDRPNEGILFINVELSPMASPAFEPGR-----------PSEEEVELSRLLERALR 106
>gnl|CDD|239049 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA is
an essential multifunctional transcription elongation
factor that is universally conserved among prokaryotes
and archaea. NusA anti-termination function plays an
important role in the expression of ribosomal rrn
operons. During transcription of many other genes,
NusA-induced RNAP pausing provides a mechanism for
synchronizing transcription and translation . The
N-terminal RNAP-binding domain (NTD) is connected
through a flexible hinge helix to three globular
domains, S1, KH1 and KH2. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices.
Length = 61
Score = 31.0 bits (71), Expect = 0.22
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI 590
+ + ++ IGKGG +R ++ G +IDI
Sbjct: 27 ARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 33.0 bits (76), Expect = 0.26
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 564 SKIRD-VIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQI 622
+I+ +IG+ G T R + E TG I + + + I F V + A+ +E L
Sbjct: 110 RRIKGRIIGREGKTRRAIEELTGVYISVYGKTVAIIGGFEQV--EIAREAVEMLINGAPH 167
Query: 623 GKVY 626
GKVY
Sbjct: 168 GKVY 171
Score = 31.5 bits (72), Expect = 0.83
Identities = 20/101 (19%), Positives = 44/101 (43%), Gaps = 10/101 (9%)
Query: 552 FAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITI----ASFNSVSG 606
+KI +I +IGK G + + E+TG ++ I+ G +TI + + ++
Sbjct: 5 AEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLAL 64
Query: 607 QEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKD 647
+A+ ++ + K L+L + + ++ KD
Sbjct: 65 LKARDVVKAIGRGFPPEK-----ALKLLEDDYYLEVIDLKD 100
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 33.6 bits (78), Expect = 0.38
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 569 VIGKGGSTIRTLTEETGTQIDINDE-GIITIASFNSVSGQEAKRRIEKL 616
+IG+ G IR L TG + I+D + ++ F+ + + A+ +EKL
Sbjct: 225 IIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPIRREIARLALEKL 273
>gnl|CDD|198433 cd10035, UDG_like_3, Uncharacterized subfamily of Uracil-DNA
glycosylases. This is a subfamily of Uracil-DNA
glycosylase superfamily. Uracil-DNA glycosylases (UDG)
catalyze the removal of uracil from DNA to initiate DNA
base excision repair pathway. Uracil in DNA can arise as
a result of mis-incorporation of dUMP residues by DNA
polymerase or deamination of cytosine. Uracil mispaired
with guanine in DNA is one of the major pro-mutagenic
events, causing G:C->A:T mutations. UDG is an essential
enzyme for maintaining the integrity of genetic
information. This ubiquitously found enzyme hydrolyzes
the N-glycosidic bond of deoxyuridine in DNA.
Length = 133
Score = 31.2 bits (71), Expect = 0.82
Identities = 10/39 (25%), Positives = 17/39 (43%)
Query: 379 LHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLP 417
+ +N+ P+ G+ P E+ G LL +LP
Sbjct: 63 VLWNVVPWHPHTPGKNRTPTPAEVEAGLRYLAELLALLP 101
>gnl|CDD|180524 PRK06309, PRK06309, DNA polymerase III subunit epsilon; Validated.
Length = 232
Score = 31.7 bits (72), Expect = 1.1
Identities = 14/27 (51%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 581 TEETGTQIDINDEGIITIASFNSVSGQ 607
TE TGTQID + II IA++N V+ +
Sbjct: 9 TETTGTQID--KDRIIEIAAYNGVTSE 33
>gnl|CDD|132299 TIGR03255, PhnV, 2-aminoethylphosphonate ABC transport system,
membrane component PhnV. This membrane component of an
ABC transport system is found in Salmonella and
Burkholderia lineages in the vicinity of enzymes for the
breakdown of 2-aminoethylphosphonate.
Length = 272
Score = 31.5 bits (71), Expect = 1.1
Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 14/85 (16%)
Query: 122 PQIDPDIASIIGVSTALSISEL--------PFLGPLGVAKVGYIDGKYILNPTTEQLKKS 173
P + P I + + + ALS+ EL P L +A G D I + +
Sbjct: 194 PLLMPAIMAALALGFALSLGELGATLMIYPPGFATLPIAIFGATDRGNIADAAALSI--- 250
Query: 174 HLDLLVAGTEKAIITVESESKQLPE 198
LL+A + A+I + + +K+L +
Sbjct: 251 ---LLLAASLLALIAIAAIAKRLGQ 272
>gnl|CDD|240212 cd05707, S1_Rrp5_repeat_sc11, S1_Rrp5_repeat_sc11: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5
is found in eukaryotes but not in prokaryotes or
archaea.
Length = 68
Score = 29.2 bits (66), Expect = 1.2
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID- 681
G V G V + + G + + G D + +S++S + K Q V+ K++ ID
Sbjct: 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDP 60
Query: 682 DRGRIKLS 689
D GRI+++
Sbjct: 61 DNGRIEMT 68
>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription].
Length = 190
Score = 31.0 bits (71), Expect = 1.3
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 555 RLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDE 593
+ + + P ++ IGKGG +R ++ TG +IDI
Sbjct: 142 HVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180
>gnl|CDD|224021 COG1096, COG1096, Predicted RNA-binding protein (consists of S1
domain and a Zn-ribbon domain) [Translation, ribosomal
structure and biogenesis].
Length = 188
Score = 30.8 bits (70), Expect = 1.4
Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 10/71 (14%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKD----------GLLHISQISSKRVNIITDFLKENQK 672
G + G V + + A++RI+ + +H+SQ+ V ++D +
Sbjct: 65 GDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDI 124
Query: 673 VRVKVLGIDDR 683
VR +V+ D
Sbjct: 125 VRARVISTGDP 135
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 31.8 bits (73), Expect = 1.5
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDE-GIITIASFNSVSGQEAKRRIEK 615
+ + D K R +IG+ G IR L TG + I+D + ++ F+ V + A+ +EK
Sbjct: 208 VNLPNDEMKGR-IIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEK 266
Query: 616 L 616
L
Sbjct: 267 L 267
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 29.0 bits (66), Expect = 1.7
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 553 APRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND 592
P + + I S+ VIGKGGS I+ L +E I++
Sbjct: 23 TPNRVIVVIRTSQPGIVIGKGGSNIKKLGKELRKLIELEG 62
>gnl|CDD|233116 TIGR00757, RNaseEG, ribonuclease, Rne/Rng family. This model
describes ribonuclease G (formerly CafA, cytoplasmic
axial filament protein A), the N-terminal domain of
ribonuclease E in which ribonuclease activity resides,
and related proteins. In E. coli, both RNase E and RNase
G have been shown to play a role in the maturation of
the 5' end of 16S RNA. The C-terminal half of RNase E
(excluded from the seed alignment for this model) lacks
ribonuclease activity but participates in mRNA
degradation by organizing the degradosome
[Transcription, Degradation of RNA].
Length = 414
Score = 31.5 bits (72), Expect = 1.8
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 14/79 (17%)
Query: 613 IEKLTESVQIGKVYTGIVLRLFDF--GAIIRILSGKDGLLHISQI------------SSK 658
IE+ G +Y G V R+ A + I K+G LH S I +
Sbjct: 16 IERPKSRQLKGNIYKGRVTRVLPSLQAAFVDIGLTKNGFLHASDIGPNSECLAPAEAKRE 75
Query: 659 RVNIITDFLKENQKVRVKV 677
I++ L+ Q V V+V
Sbjct: 76 AGASISELLRPGQSVLVQV 94
>gnl|CDD|214633 smart00357, CSP, Cold shock protein domain. RNA-binding domain
that functions as a RNA-chaperone in bacteria and is
involved in regulating translation in eukaryotes.
Contains sub-family of RNA-binding domains in the Rho
transcription termination factor.
Length = 64
Score = 28.3 bits (64), Expect = 1.8
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 630 VLRLFD--FGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGR 685
V++ F+ FG I GKD +H SQI + L+E +V KV+ + +
Sbjct: 3 VVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKS-----LREGDEVEFKVVSPEGGEK 55
>gnl|CDD|240207 cd05702, S1_Rrp5_repeat_hs11_sc8, S1_Rrp5_repeat_hs11_sc8: Rrp5 is
a trans-acting factor important for biogenesis of both
the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has
two distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes H. sapiens S1 repeat 11 (hs11) and S.
cerevisiae S1 repeat 8 (sc8). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 70
Score = 28.3 bits (64), Expect = 2.0
Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNII--TDFLKENQKVRVKVLGI 680
G + V + +++ G +H+S++ + + K QK++ +V+G
Sbjct: 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGG 60
Query: 681 DD 682
D
Sbjct: 61 HD 62
>gnl|CDD|239911 cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2: Ribosomal
protein S1 (RPS1) domain. RPS1 is a component of the
small ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain.While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 2 of the Escherichia coli and Homo sapiens
RPS1 (ec2 and hs2, respectively). Autoantibodies to
double-stranded DNA from patients with systemic lupus
erythematosus cross-react with the human RPS1 homolog.
Length = 67
Score = 28.2 bits (64), Expect = 2.1
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 637 GAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID-DRGRIKLS 689
G +I + G L SQ+ + V + +++ ++++ K++ ID +R I LS
Sbjct: 14 GGLIVDIEGVRAFLPASQVDLRPVEDLDEYV--GKELKFKIIEIDRERNNIVLS 65
>gnl|CDD|239094 cd02411, archeal_30S_S3_KH, K homology RNA-binding domain (KH) of
the archaeal 30S small ribosomal subunit S3 protein. S3
is part of the head region of the 30S ribosomal subunit
and is believed to interact with mRNA as it threads its
way from the latch into the channel. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA.
Length = 85
Score = 28.8 bits (65), Expect = 2.1
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 7/31 (22%)
Query: 569 VIGKGGSTIRTLTEETGT-------QIDIND 592
VIG+GG IR LTE T QID+ +
Sbjct: 52 VIGRGGKNIRELTEILETKFGLENPQIDVQE 82
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli
and is broadly distributed throughout the bacteria. In
E. coli, double mutants of this protein and
polynucleotide phosphorylase are not viable. Scoring
between trusted and noise cutoffs to the model are
shorter, divergent forms from the Chlamydiae, and
divergent forms from the Campylobacterales (including
Helicobacter pylori) and Leptospira interrogans
[Transcription, Degradation of RNA].
Length = 709
Score = 31.1 bits (71), Expect = 2.3
Identities = 18/87 (20%), Positives = 40/87 (45%), Gaps = 19/87 (21%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILSGK-DGLLHISQ--------------ISSKRVNIITD 665
+IG+ + G++ + FG + + + +GL+HIS + +R +
Sbjct: 626 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKV-- 683
Query: 666 FLKENQKVRVKVLGID-DRGRIKLSMI 691
+ +V+V+V+ D D G+I ++
Sbjct: 684 -FRLGDRVKVRVVKADLDTGKIDFELV 709
>gnl|CDD|240202 cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes H. sapiens S1 repeat 5 (hs5) and S.
cerevisiae S1 repeat 5 (sc5). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 69
Score = 28.4 bits (64), Expect = 2.4
Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID- 681
G+V G + +L G +++ GL+ ++ R+ K KV+ +VL ++
Sbjct: 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP 60
Query: 682 DRGRIKL 688
+R R+ L
Sbjct: 61 ERKRLVL 67
>gnl|CDD|130146 TIGR01074, rep, ATP-dependent DNA helicase Rep. Designed to
identify rep members of the uvrD/rep subfamily [DNA
metabolism, DNA replication, recombination, and repair].
Length = 664
Score = 30.9 bits (70), Expect = 2.9
Identities = 36/127 (28%), Positives = 55/127 (43%), Gaps = 16/127 (12%)
Query: 208 GHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKIINISEHKIRKAYQIKNKQIRD 267
G K ++ N I L+QN G K N + T +K E K R A + + R
Sbjct: 24 GSGKTRVITNKIAYLIQNCGYKARNIAAV----TFTNK--AAREMKERVAKTLGKGEARG 77
Query: 268 L---TFKNISKDI----YSSLIDNENLTI-DINDINCILYDLESKIIR--KQILDKGLRI 317
L TF + DI Y++L N ++ D D +L +L +I+ K +LDK +
Sbjct: 78 LTISTFHTLGLDIIKREYNALGYKSNFSLFDETDQLALLKELTEGLIKDDKDLLDKLIST 137
Query: 318 DNRGVND 324
+ ND
Sbjct: 138 ISNWKND 144
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 30.7 bits (69), Expect = 3.1
Identities = 10/38 (26%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 76 SFFKREGK--PSERETIISRLIDRPIRPLFPEGYLNEI 111
SF + E E+++ + RL +R +R + Y+ E+
Sbjct: 140 SFLESETTIVRKEKDSPLQRLGERLVREGMSQSYVEEM 177
>gnl|CDD|131211 TIGR02156, PA_CoA_Oxy1, phenylacetate-CoA oxygenase, PaaG subunit.
Phenylacetate-CoA oxygenase is comprised of a five gene
complex responsible for the hydroxylation of
phenylacetate-CoA (PA-CoA) as the second catabolic step
in phenylacetic acid (PA) degradation. Although the
exact function of this enzyme has not been determined,
it has been shown to be required for phenylacetic acid
degradation and has been proposed to function in a
multicomponent oxygenase acting on phenylacetate-CoA
[Energy metabolism, Other].
Length = 289
Score = 30.2 bits (68), Expect = 3.7
Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 9/57 (15%)
Query: 339 HGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIG 395
HG L+ TLG SR+E L G+ S + +N P DIG IG
Sbjct: 69 HGLYLYA-------AAETLGVSREELLDALLTGKAKYSSI--FNYPTLTWADIGVIG 116
>gnl|CDD|240201 cd05696, S1_Rrp5_repeat_hs4, S1_Rrp5_repeat_hs4: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is
found in eukaryotes but not in prokaryotes or archaea.
Length = 71
Score = 27.6 bits (62), Expect = 3.7
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 7/62 (11%)
Query: 618 ESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKV 677
+SV++ KV D GA+ + G G +HIS +S +V T K + ++
Sbjct: 5 DSVKVTKVEP-------DLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARI 57
Query: 678 LG 679
+G
Sbjct: 58 IG 59
>gnl|CDD|223281 COG0203, RplQ, Ribosomal protein L17 [Translation, ribosomal
structure and biogenesis].
Length = 116
Score = 28.7 bits (65), Expect = 4.1
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 536 EKMKTEVPKCKNELSKFAPRLIT 558
E+++T +PK K EL + +LIT
Sbjct: 32 ERIETTLPKAK-ELRRVVEKLIT 53
>gnl|CDD|239092 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II).
KH binds single-stranded RNA or DNA. It is found in a
wide variety of proteins including ribosomal proteins
(e.g. ribosomal protein S3), transcription factors (e.g.
NusA_K), and post-transcriptional modifiers of mRNA
(e.g. hnRNP K). There are two different KH domains that
belong to different protein folds, but they share a
single KH motif. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In addition to
their KH core domain, KH-II proteins have an N-terminal
alpha helical extension while KH-I proteins have a
C-terminal alpha helical extension.
Length = 68
Score = 27.2 bits (61), Expect = 4.9
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 3/35 (8%)
Query: 555 RLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQID 589
++ + P VIGK G IR L + +
Sbjct: 28 IIVVARGQPGL---VIGKKGQNIRALQKLLQKLLR 59
>gnl|CDD|218436 pfam05106, Phage_holin_3, Phage holin family (Lysis protein S).
This family represents one of a large number of mutually
dissimilar families of phage holins. Holins act against
the host cell membrane to allow lytic enzymes of the
phage to reach the bacterial cell wall. This family
includes the product of the S gene of phage lambda.
Length = 100
Score = 28.0 bits (63), Expect = 5.1
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 13/73 (17%)
Query: 351 ALVVATL-----GTSRDEQKIDALM--------GEFTDSFMLHYNMPPFATGDIGRIGVP 397
A V+A L G SR ++AL+ + F L ++ PFA G +G +GV
Sbjct: 28 AFVMALLRGRYGGGSRRRTLLEALLCGLLTLVARSALELFGLPPSLSPFAGGAVGFLGVD 87
Query: 398 KRREIGHGRLAKR 410
K RE+ + K+
Sbjct: 88 KIRELAKRLINKK 100
>gnl|CDD|184320 PRK13778, paaA, phenylacetate-CoA oxygenase subunit PaaA;
Provisional.
Length = 314
Score = 29.5 bits (67), Expect = 5.4
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 356 TLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIG 395
TLG SR+E D L G+ S + +Y +A D+G IG
Sbjct: 97 TLGVSREELIDDLLSGKAKYSSIFNYPTLTWA--DVGVIG 134
>gnl|CDD|237138 PRK12563, PRK12563, sulfate adenylyltransferase subunit 2;
Provisional.
Length = 312
Score = 29.4 bits (66), Expect = 6.1
Identities = 20/51 (39%), Positives = 24/51 (47%), Gaps = 10/51 (19%)
Query: 325 IRPISIRTGILPRTHGSSLF-----TRGDTQAL-----VVATLGTSRDEQK 365
P I GI+P HGS+L T+G QAL A G RDE+K
Sbjct: 101 HNPDGIARGIVPFRHGSALHTDVAKTQGLKQALDHHGFDAAIGGARRDEEK 151
>gnl|CDD|219444 pfam07516, SecA_SW, SecA Wing and Scaffold domain. SecA protein
binds to the plasma membrane where it interacts with
proOmpA to support translocation of proOmpA through the
membrane. SecA protein achieves this translocation, in
association with SecY protein, in an ATP dependent
manner. This family is composed of two C-terminal alpha
helical subdomains: the wing and scaffold subdomains.
Length = 213
Score = 29.1 bits (66), Expect = 6.1
Identities = 11/87 (12%), Positives = 33/87 (37%)
Query: 198 EDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKIINISEHKIRKA 257
+DI+ + + + E ++ + ++ D + ++ ++A
Sbjct: 69 DDIVEEYAPEKSYPEEWDLEGLEEELRELLGLDLDIDEEELEGLTEEELKERLIEAAKEA 128
Query: 258 YQIKNKQIRDLTFKNISKDIYSSLIDN 284
Y+ K ++ + + I + I +ID
Sbjct: 129 YEEKEAELGEELMREIERSIMLQVIDE 155
>gnl|CDD|235247 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
Length = 207
Score = 29.1 bits (66), Expect = 6.8
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 569 VIGKGGSTIRTLTEETGTQIDIND 592
VIG+GG IR LTE + + +
Sbjct: 54 VIGRGGKNIRELTEILEKKFGLEN 77
>gnl|CDD|233649 TIGR01945, rnfC, electron transport complex, RnfABCDGE type, C
subunit. The six subunit complex RnfABCDGE in
Rhodobacter capsulatus encodes an apparent NADH
oxidoreductase responsible for electron transport to
nitrogenase, necessary for nitrogen fixation. A closely
related complex in E. coli, RsxABCDGE (Reducer of SoxR),
reduces the 2Fe-2S-containing superoxide sensor SoxR,
active as a transcription factor when oxidized. This
family of putative NADH oxidoreductase complexes exists
in many of the same species as the related NQR, a
Na(+)-translocating NADH-quinone reductase, but is
distinct. This model describes the C subunit [Energy
metabolism, Electron transport].
Length = 435
Score = 29.6 bits (67), Expect = 6.9
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 222 LVQNVGQKKVNWDPIVKDKTLISKIINISEHKIRK 256
+VQNVG ++ +V K LI +++ ++ IR+
Sbjct: 261 VVQNVGTAFAIYEAVVNGKPLIERVVTVTGDAIRR 295
>gnl|CDD|225285 COG2429, COG2429, Archaeal GTP cyclohydrolase III [Nucleotide
transport and metabolism].
Length = 250
Score = 29.0 bits (65), Expect = 8.2
Identities = 18/87 (20%), Positives = 36/87 (41%), Gaps = 1/87 (1%)
Query: 592 DEGIITIASFNSVSGQEAKRRIEK-LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLL 650
+G + IA F+ I +I +VY ++ L GA++ L G + +
Sbjct: 128 TDGYVQIAHFDVNDATGTYTDIVSPYDTYTEIQRVYATLMRFLEKIGALLFFLGGDNIMA 187
Query: 651 HISQISSKRVNIITDFLKENQKVRVKV 677
+S+ V + ++ +V +KV
Sbjct: 188 VCPGLSAGDVLDAIAEVLDDAEVDLKV 214
>gnl|CDD|216176 pfam00890, FAD_binding_2, FAD binding domain. This family includes
members that bind FAD. This family includes the
flavoprotein subunits from succinate and fumarate
dehydrogenase, aspartate oxidase and the alpha subunit
of adenylylsulphate reductase.
Length = 401
Score = 29.2 bits (66), Expect = 8.3
Identities = 10/61 (16%), Positives = 20/61 (32%), Gaps = 6/61 (9%)
Query: 330 IRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATG 389
+ ++ +++AT G R+ + + G + PP TG
Sbjct: 173 VTGVVVENRRNGREVRIRAIAGVLLATGGFGRNAELLLPAAGYADTTG------PPANTG 226
Query: 390 D 390
D
Sbjct: 227 D 227
>gnl|CDD|130081 TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryotic/archaeal
type. This model describes ribosomal protein S3 of the
eukaryotic cytosol and of the archaea. TIGRFAMs model
TIGR01009 describes the bacterial/organellar type,
although the organellar types have a different
architecture with long insertions and may score poorly
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 195
Score = 28.5 bits (64), Expect = 8.6
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 7/77 (9%)
Query: 568 DVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYT 627
VIG+GG IR LTE+ + + E A+ + E++ S++
Sbjct: 51 LVIGRGGRRIRELTEKLQKKFGL--ENPQIDVEEVENPELNAQVQAERIARSLE-----R 103
Query: 628 GIVLRLFDFGAIIRILS 644
G+ R + A+ RI+
Sbjct: 104 GLHFRRAAYTAVRRIME 120
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.139 0.387
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 35,906,204
Number of extensions: 3721233
Number of successful extensions: 4113
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4008
Number of HSP's successfully gapped: 212
Length of query: 692
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 588
Effective length of database: 6,324,786
Effective search space: 3718974168
Effective search space used: 3718974168
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: 62 (27.6 bits)