RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3754
(755 letters)
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 1123 bits (2907), Expect = 0.0
Identities = 395/689 (57%), Positives = 519/689 (75%), Gaps = 1/689 (0%)
Query: 65 FNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTV 124
FNKI+KS ++G +++E G++ARQA +VLV DTV+L TVV+ K+P +FFPLTV
Sbjct: 2 FNKIVKSIEFGGRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKEGQDFFPLTV 61
Query: 125 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVN 184
DY EK YAAG+IPG FFKREG+PSE+ET+ SRLIDRPIRPLFP+G+ NE+Q+V VLSV+
Sbjct: 62 DYEEKTYAAGKIPGGFFKREGRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSVD 121
Query: 185 PQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAG 244
P+ DPDI ++IG S ALSIS +PF GP+ +VGYIDG+++LNPT E+L++S LDL+VAG
Sbjct: 122 PENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGEFVLNPTVEELEESDLDLVVAG 181
Query: 245 TEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKT 304
T+ A++ VESE+K+L E+++L AI FGHE ++ I+A EL G K W P D+
Sbjct: 182 TKDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG-PKWEWQPPEVDEE 240
Query: 305 LISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDL 364
L + + ++E K+++AYQI +KQ R+ I +++ +L E D +I L
Sbjct: 241 LKAAVKELAEAKLKEAYQITDKQEREAALDAIKEEVLEALAAEEEEEEDEKEIKEAFKKL 300
Query: 365 ESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSR 424
E KI+R++IL++G+RID R +++IRPISI G+LPRTHGS+LFTRG+TQALVVATLGT R
Sbjct: 301 EKKIVRRRILEEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLR 360
Query: 425 DEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNK 484
DEQ ID L GE+ FMLHYN PP++ G+ GR+G P RREIGHG LA+RAL PVLP+ +
Sbjct: 361 DEQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPGRREIGHGALAERALEPVLPSEEE 420
Query: 485 FNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSD 544
F Y+IR+VSEI ESNGSSSMASVCG LAL+DAGVPI VAGIAMGLIK+G+K +L+D
Sbjct: 421 FPYTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLTD 480
Query: 545 ILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTE 604
ILGDED GDMDFKVAGT +GITALQMDIKI GIT +I++ AL +AK+G +IL KM
Sbjct: 481 ILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEA 540
Query: 605 VPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASF 664
+ + + ELS +APR+ TIKI P KIRDVIG GG TIR +TEETG +IDI D+G + IA+
Sbjct: 541 ISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAAT 600
Query: 665 NSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVN 724
+ + + AK RIE +T ++G++Y G V+R+ DFGA + IL GKDGL+HIS+I+ +RV
Sbjct: 601 DGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVE 660
Query: 725 IITDFLKENQKVRVKVLGIDDRGRIKLSM 753
+ D LKE +V+VKVL ID RGRI+LS
Sbjct: 661 KVEDVLKEGDEVKVKVLEIDKRGRIRLSR 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 = 1051 bits (2721), Expect = 0.0
Identities = 383/684 (55%), Positives = 506/684 (73%), Gaps = 5/684 (0%)
Query: 73 KYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYA 132
+YG +++E G+IARQA +V+V DTV+L TVV+ K+ +FFPLTV+Y EK YA
Sbjct: 1 EYGGRTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEGQDFFPLTVNYQEKFYA 60
Query: 133 AGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIA 192
AG+IPG FFKREG+PSE+ET+ SRLIDRPIRPLFP+G+ NE+Q+V VLS +P+ DPDI
Sbjct: 61 AGKIPGGFFKREGRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSYDPENDPDIL 120
Query: 193 SIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKAIITV 252
+IIG S AL+IS +PF GP+ +VGYIDG+Y+LNPT ++L+KS LDL+VAGT+ A++ V
Sbjct: 121 AIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLNPTVDELEKSDLDLVVAGTKDAVLMV 180
Query: 253 ESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKII-N 311
ESE+K+L E+++L AI FGHE+++ I AI EL + G++K + D+ L +K+
Sbjct: 181 ESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKWEFVAPEVDEELKAKVKEL 240
Query: 312 ISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDN---ENLTIDINDINCILYDLESKI 368
E +++AYQI KQ R I +++ +L + E +I DLE KI
Sbjct: 241 AYEAGLKEAYQITEKQERYAALDAIKEEVLEALAEEEEEEEEADREKEIKEAFKDLEKKI 300
Query: 369 IRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQK 428
+R++IL +G RID R ++ IRPISI G+LPRTHGS+LFTRG+TQALVV TLGT RDEQ
Sbjct: 301 VRERILKEGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQI 360
Query: 429 IDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYS 488
ID L GE+ FMLHYN PP++ G++GR+G P RREIGHG LA+RAL VLP+ +F Y+
Sbjct: 361 IDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRREIGHGALAERALKAVLPSEEEFPYT 420
Query: 489 IRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDG-EKVVILSDILG 547
IR+VSEI ESNGSSSMASVCGG LAL+DAGVPI VAGIAMGLIK+G E+ +LSDILG
Sbjct: 421 IRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDERFAVLSDILG 480
Query: 548 DEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPK 607
DED GDMDFKVAGT +GITALQMDIKI GIT +I++ AL +AK+G +IL +M + +
Sbjct: 481 DEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVISE 540
Query: 608 CKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSV 667
+ ELS +APR+ TIKI+P KIRDVIG GG IR +TEETG +IDI D+G + IA+ +
Sbjct: 541 PRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGE 600
Query: 668 SGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIIT 727
+ + A + IE +T ++GK+Y G V+R+ DFGA + IL GKDGL+HIS+I+++RV +
Sbjct: 601 AAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVE 660
Query: 728 DFLKENQKVRVKVLGIDDRGRIKL 751
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 = 940 bits (2432), Expect = 0.0
Identities = 388/690 (56%), Positives = 511/690 (74%), Gaps = 3/690 (0%)
Query: 65 FNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTV 124
FNKI+K+ ++G +++E G+IARQA +VLV DTV+LATVV P +FFPLTV
Sbjct: 2 FNKIVKTIEWGGRTLTLETGKIARQANGAVLVRYGDTVVLATVV-ASKPKEGQDFFPLTV 60
Query: 125 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVN 184
+Y EK YAAG+IPG FFKREG+PSE+E + SRLIDRPIRPLFP+G+ NE+QIV VLSV+
Sbjct: 61 NYEEKTYAAGKIPGGFFKREGRPSEKEILTSRLIDRPIRPLFPKGFRNEVQIVNTVLSVD 120
Query: 185 PQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAG 244
P+ DPDI +++G S ALS+S +PFLGP+G +VGYIDG ++LNPT E+L++S LDL+VAG
Sbjct: 121 PENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGIFVLNPTLEELEESKLDLVVAG 180
Query: 245 TEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKT 304
T+ A+ VESE+ +L E+++L A+ FGHE ++ INA EL VG+KK +P D+
Sbjct: 181 TKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDEE 240
Query: 305 LISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDL 364
L +K+ +++E ++++A I+ KQ R I + I L E + +I IL L
Sbjct: 241 LEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEEELSGEEES--SLKEIKAILEKL 298
Query: 365 ESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSR 424
E K +R+ IL+ +RID R +++RPI I G+LPRTHGS+LFTRG+TQALVV TLGT R
Sbjct: 299 EKKPVRRLILEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPR 358
Query: 425 DEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNK 484
D Q ID L GE+ F+LHYN PPF+ G+ GR+G P RREIGHG LA+RAL PVLP+ +
Sbjct: 359 DAQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRREIGHGALAERALAPVLPSEEE 418
Query: 485 FNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSD 544
F Y+IR+VSEI ESNGSSSMASVCGG LAL+DAGVPI VAGIAMGLIK+G+K +LSD
Sbjct: 419 FPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLSD 478
Query: 545 ILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTE 604
ILGDED GDMDFKVAGT +GITALQMDIKI GIT +I++ AL +AK +IL M
Sbjct: 479 ILGDEDHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEA 538
Query: 605 VPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASF 664
+ + + ELS +APR+ TIKIDP KIRDVIG GG TI+ +TEETG +IDI D+G + IA+
Sbjct: 539 ISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAAS 598
Query: 665 NSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVN 724
+ S ++AK RIE +T V++G+VY G V+R+ DFGA + +L GKDGL+HISQ++ +RV
Sbjct: 599 DGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVE 658
Query: 725 IITDFLKENQKVRVKVLGIDDRGRIKLSMI 754
+ D LKE +V+VKV+ ID +GRI+LS+
Sbjct: 659 KVEDVLKEGDEVKVKVIEIDKQGRIRLSIK 688
>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 586 bits (1512), Expect = 0.0
Identities = 286/736 (38%), Positives = 431/736 (58%), Gaps = 57/736 (7%)
Query: 74 YGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAA 133
G I +E G I RQA+ SV V+ +T++ +V P+ +FFPL+V Y E+ AA
Sbjct: 86 VGDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQERFSAA 145
Query: 134 GRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIAS 193
GR G FFKREG+ + E +I RLIDRP+RP P+G+ +E QI+ +VLS + PD +
Sbjct: 146 GRTSGGFFKREGRTKDHEVLICRLIDRPLRPTMPKGFYHETQILSWVLSYDGLHSPDSLA 205
Query: 194 IIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKAIITVE 253
+ A+++SE+P L + +VG I GK+I+NPTT+++++S LDL++AGT+ AI+ +E
Sbjct: 206 VTAAGIAVALSEVPNLKAIAGVRVGLIGGKFIVNPTTKEMEESELDLIMAGTDSAILMIE 265
Query: 254 SESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKIINIS 313
LPE+ +L A+ G + ++ I LV+ G+ K+ + L + I+
Sbjct: 266 GYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGKPKMLDAIKLPPPELYKHVKEIA 325
Query: 314 EHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDIN------------------ 355
++ KA QI+ K R ++ + + S L + ++ D +
Sbjct: 326 GDELVKALQIRGKIPRRKALSSLEEKVLSILTEEGYVSKDESFGTSETRADLLEDEDEDE 385
Query: 356 ------------------------------DINCILYDLESKIIRKQILDKGLRIDNRGV 385
D+ + ++ SK +R++I++ G R D R
Sbjct: 386 EVVVDGEVDEGDVHIKPIPRKSSPLLFSEVDVKLVFKEVTSKFLRRRIVEGGKRSDGRTP 445
Query: 386 NDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMG-EFTDSFMLHY 444
++IRPI+ G+LPR HGS+LFTRG+TQAL V TLG + Q+ID L+ + F L Y
Sbjct: 446 DEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQY 505
Query: 445 NMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSM 504
+ PP G++GRIG P RREIGHG LA+RAL P+LP+ + F Y+IR+ S ITESNGSSSM
Sbjct: 506 SFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSSM 565
Query: 505 ASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKV------VILSDILGDEDRCGDMDFK 558
ASVCGGCLAL DAGVP+ +AGIAMG++ D E+ +ILSDI G ED GDMDFK
Sbjct: 566 ASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFK 625
Query: 559 VAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPR 618
VAG +GITA QMDIK+ GIT I++ AL +AK G +IL +M P LSK+AP
Sbjct: 626 VAGNEDGITAFQMDIKVGGITLPIMERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPL 685
Query: 619 LITIKIDPSKIRDVIGKGGSTIRTLTEETGTQ-IDINDEGIITIASFNSVSGQEAKRRIE 677
+ +K+ P K+ +IG GG ++++ EETG + ID D+G + I + + S +++K I
Sbjct: 686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIIS 745
Query: 678 KLTESVQIGKVYTGIVLR-LFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 736
LT +G +Y ++ + +GA + I G++GL HIS++SS + D K ++
Sbjct: 746 SLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRI 805
Query: 737 RVKVLGIDDRGRIKLS 752
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 = 572 bits (1476), Expect = 0.0
Identities = 294/713 (41%), Positives = 430/713 (60%), Gaps = 32/713 (4%)
Query: 68 IIKSFKYGSYKISIEIGEIARQATSSVLVSI-EDTVILATVVSCKDPTSTYNFFPLTVDY 126
+I + ++G+ I E G +ARQA SV+ + ++T++L+ + K P ++FFPLTVD
Sbjct: 8 VIDNGRFGTRTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKDQFDFFPLTVDV 67
Query: 127 IEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQ 186
E+ YAAGRIPGSFF+REG+PS + RLIDRP+RP F +G NE+Q+VV VLS+NP
Sbjct: 68 EERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPSFVKGLRNEVQVVVTVLSLNPD 127
Query: 187 IDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGT- 245
D+ +I S + ++ LPF GP+G +V IDG+++ PT EQL+ + D++VAG
Sbjct: 128 HLYDVVAINAASASTQLAGLPFSGPIGGVRVALIDGQWVAFPTHEQLEGAVFDMVVAGRV 187
Query: 246 ----EKAIITVESESKQLPEDIILNA--------IIFGHEKMKIAINAINELVQNVGQK- 292
+ AI+ VE+E+ + D++ + G E K I + ++ +K
Sbjct: 188 LENGDVAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAEKA 247
Query: 293 -KVNWD-PIVKDKT--LISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNE 348
K + P+ D + + + ++ A I KQ R+ + + + L E
Sbjct: 248 AKPTGEFPLFPDYQDDVYEAVEGAVKDELSAALTIAGKQEREEALDEVKALVAAKLA--E 305
Query: 349 NLTIDINDINCILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFT 408
+I+ + K++R+++L +G+RID RGV DIRP+ ++PR HGS+LF
Sbjct: 306 QFEGREKEISAAYRAVTKKLVRERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFE 365
Query: 409 RGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHG 468
RG+TQ L V TL + EQ+ID+L E + +M HYN PP++TG+ GR+G PKRREIGHG
Sbjct: 366 RGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYSTGETGRVGSPKRREIGHG 425
Query: 469 RLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGI 528
LA+RAL+PVLP+ +F Y+IR VSE SNGS+SM SVC L+LL+AGVP+ VAGI
Sbjct: 426 ALAERALVPVLPSREEFPYAIRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGI 485
Query: 529 AMGLIK---DGE-KVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQ 584
AMGLI DGE + V L+DILG ED GDMDFKVAGT +TALQ+D K+ GI ++
Sbjct: 486 AMGLISDEVDGETRYVALTDILGAEDAFGDMDFKVAGTSEFVTALQLDTKLDGIPASVLA 545
Query: 585 IALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLT 644
AL +A+ IL+ M E +E+S +APR+IT+KI KI +VIG G I +
Sbjct: 546 SALKQARDARLAILDVM-AEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQ 604
Query: 645 EETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESV--QIGKVYTGIVLRLFDFGAI 702
+ETG +I I D+G + I + + S + A+ I + ++G+ + G V++ FGA
Sbjct: 605 DETGAEISIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAF 664
Query: 703 IRILSGKDGLLHISQI----SSKRVNIITDFLKENQKVRVKVLGIDDRGRIKL 751
+ +L GKDGLLHISQI KRV + D L QK++V++ IDDRG++ L
Sbjct: 665 VSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSL 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 = 397 bits (1022), Expect = e-135
Identities = 143/222 (64%), Positives = 174/222 (78%), Gaps = 1/222 (0%)
Query: 387 DIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNM 446
+IRPIS G+LPRTHGS+LFTRG+TQ L TLGT D QKID+L GE + FMLHYN
Sbjct: 1 EIRPISCEVGLLPRTHGSALFTRGETQVLCTVTLGTLEDAQKIDSLGGEKSKRFMLHYNF 60
Query: 447 PPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMAS 506
PP++ G+ GR+G P RREIGHG LA+RALLPVLP+ F Y+IR+VSE+ ESNGSSSMAS
Sbjct: 61 PPYSVGETGRVGGPGRREIGHGALAERALLPVLPSPEDFPYTIRVVSEVLESNGSSSMAS 120
Query: 507 VCGGCLALLDAGVPISEHVAGIAMGLIKDG-EKVVILSDILGDEDRCGDMDFKVAGTVNG 565
VCGG LAL+DAGVPI VAGIAMGLI +G + +L+DILG ED GDMDFKVAGT +G
Sbjct: 121 VCGGSLALMDAGVPIKAPVAGIAMGLITEGIDDYRVLTDILGLEDHLGDMDFKVAGTRDG 180
Query: 566 ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPK 607
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 = 336 bits (863), Expect = e-111
Identities = 118/229 (51%), Positives = 166/229 (72%)
Query: 68 IIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYI 127
+ G ++ E G++A+QA SV+V DTV+L T VS K P +FFPLTVDY
Sbjct: 1 KVFEVLVGGRTLTFETGKLAKQADGSVVVQYGDTVVLVTAVSSKKPKEGIDFFPLTVDYR 60
Query: 128 EKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQI 187
EK YAAG+IPG FFKREG+PSE+E + SRLIDRPIRPLFP+G+ NE+Q++ VLSV+
Sbjct: 61 EKLYAAGKIPGGFFKREGRPSEKEILTSRLIDRPIRPLFPKGFRNEVQVIATVLSVDGVN 120
Query: 188 DPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEK 247
DPD+ +I G S ALS+S++PF GP+G +VG IDG++++NPT E+L++S LDL+VAGT+
Sbjct: 121 DPDVLAINGASAALSLSDIPFNGPVGAVRVGRIDGEFVVNPTREELEESDLDLVVAGTKD 180
Query: 248 AIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNW 296
A++ VE+ +K++ E+ +L AI FGHE ++ I A EL VG++K +
Sbjct: 181 AVLMVEAGAKEVSEEDMLEAIKFGHEAIQQLIAAQEELAAEVGKEKREY 229
Score = 45.6 bits (109), Expect = 4e-05
Identities = 50/194 (25%), Positives = 80/194 (41%), Gaps = 25/194 (12%)
Query: 389 RPISIRTGILPR-THGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFML--HYN 445
R ++ TG L + GS + GDT LV A E D F L Y
Sbjct: 10 RTLTFETGKLAKQADGSVVVQYGDTVVLVTAVSSKKPKEG---------IDFFPLTVDYR 60
Query: 446 MPPFATGDI-----GRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNG 500
+A G I R G P +EI RL R + P+ P F +++++ + +G
Sbjct: 61 EKLYAAGKIPGGFFKREGRPSEKEILTSRLIDRPIRPLFPKG--FRNEVQVIATVLSVDG 118
Query: 501 --SSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFK 558
+ ++ G AL + +P + V + +G I DGE V+ +E D+D
Sbjct: 119 VNDPDVLAINGASAALSLSDIPFNGPVGAVRVGRI-DGE-FVVNPTR--EELEESDLDLV 174
Query: 559 VAGTVNGITALQMD 572
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 = 122 bits (308), Expect = 1e-32
Identities = 46/134 (34%), Positives = 66/134 (49%), Gaps = 5/134 (3%)
Query: 387 DIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNM 446
++RPI I TG+L + GS+L GDT+ L T +++ D F + Y
Sbjct: 1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPQKERD----FFPGELTVEYEE 56
Query: 447 PPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMAS 506
PFA+G+ G P REI RL RAL P +P + IR+ + +GS A+
Sbjct: 57 SPFASGERPE-GRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDGSLLDAA 115
Query: 507 VCGGCLALLDAGVP 520
+ LAL DAG+P
Sbjct: 116 INAASLALADAGIP 129
Score = 106 bits (267), Expect = 4e-27
Identities = 56/135 (41%), Positives = 73/135 (54%), Gaps = 14/135 (10%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATVV-SCKDPTSTYNFFP--LTVDYIEKAYAAG 134
I IE G + QA S LV + DT +LATV + P +FFP LTV+Y E +A+G
Sbjct: 4 PIEIETG-VLSQADGSALVELGDTKVLATVTGPIEPPQKERDFFPGELTVEYEESPFASG 62
Query: 135 RIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYL--NEIQIVVYVLSVNPQIDPDIA 192
P EG+PSERE +SRLIDR +RP P EI+I V VLS + A
Sbjct: 63 ERP------EGRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDG--SLLDA 114
Query: 193 SIIGVSTALSISELP 207
+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 = 119 bits (300), Expect = 1e-30
Identities = 53/223 (23%), Positives = 91/223 (40%), Gaps = 26/223 (11%)
Query: 388 IRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMP 447
RP+ I TG+L + GS+L G+T+ + T D L + ++ +
Sbjct: 1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEP----DKLERPDKGTLYVNVEIS 56
Query: 448 PFATGDIGRIGVPKRREIGHGRLAKRALLPVLP---NNNKFNYSIRLVSEITESNGSSSM 504
P A G+ R G P E+ RL +R + + + K ++ + + ++ +G
Sbjct: 57 PGAVGER-RQGPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDGGLLD 115
Query: 505 ASVCGGCLALLDAGVP-------------ISEHVAGIAMGLIKDGEKVVILSDILGDEDR 551
A AL DAG+P + + + +++G I DG V+L D G+E+
Sbjct: 116 ACWNAAIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGISDG---VLLLDPTGEEEE 172
Query: 552 CGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKG 593
D VA +G + L T + I+ L AKK
Sbjct: 173 LADSTLTVAVDKSGKLCLLSKVGGGSLDT-EEIKECLELAKKR 214
Score = 76.2 bits (188), Expect = 1e-15
Identities = 46/222 (20%), Positives = 78/222 (35%), Gaps = 35/222 (15%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATVVSC----KDPTSTYNFFPLTVDYIEKAYAA 133
+ IE G + QA S LV + +T ++ V + D + L V+ A
Sbjct: 3 PVEIETGVL-NQADGSALVKLGNTKVICAV-TGPIVEPDKLERPDKGTLYVNVEISPGAV 60
Query: 134 GRIPGSFFKREGKPSERETIISRLIDRPIR-----PLFPEGYLNEIQIVVYVLSVNPQID 188
G R+G P + E ISRL++R I + + + VLS + +
Sbjct: 61 GER------RQGPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDGGLL 114
Query: 189 PDIASIIGVSTAL-------------SISELPFLGPLGVAKVGYI-DGKYILNPTTEQLK 234
A AL S L + VG I DG +L+PT E+ +
Sbjct: 115 D--ACWNAAIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGISDGVLLLDPTGEEEE 172
Query: 235 KSHLDLLVAGTEK-AIITVESESKQLPE-DIILNAIIFGHEK 274
+ L VA + + + + + I + ++
Sbjct: 173 LADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAKKR 214
>gnl|CDD|235187 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional.
Length = 244
Score = 108 bits (271), Expect = 2e-26
Identities = 76/240 (31%), Positives = 118/240 (49%), Gaps = 25/240 (10%)
Query: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGT----SRDE 426
K IL+ GLR+D R +++RPI I G+L GS+ G+ + + A G R
Sbjct: 7 KLILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKI-IAAVYGPREMHPRHL 65
Query: 427 QKID-ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKF 485
Q D A++ + YNM PF+ + R G P RR I ++ + AL P +
Sbjct: 66 QLPDRAVL-------RVRYNMAPFSVDERKRPG-PDRRSIEISKVIREALEPAIMLELFP 117
Query: 486 NYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDI 545
I + E+ +++ + +A + LAL DAG+P+ + VAG A+G + DG V+ D+
Sbjct: 118 RTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKV-DGVIVL---DL 173
Query: 546 LGDEDRCGDMDFKVAGTVNG--ITALQMDIKIFG-ITYDIIQIALYKAKKGLSYILEKMK 602
+ED G+ D VA IT LQ+D G +T + AL AKKG+ I + +
Sbjct: 174 NKEEDNYGEADMPVAIMPRLGEITLLQLD----GNLTREEFLEALELAKKGIKRIYQLQR 229
Score = 33.1 bits (76), Expect = 0.41
Identities = 47/185 (25%), Positives = 71/185 (38%), Gaps = 43/185 (23%)
Query: 79 ISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTS-------------TYNFFPLTVD 125
I IE+G + A S + + I+A V ++ YN P +VD
Sbjct: 27 IKIEVGVLKN-ADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVD 85
Query: 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRP-----LFPEGYLNEIQIVVYV 180
E+ KR G P R IS++I + P LFP I + + V
Sbjct: 86 --ER------------KRPG-PDRRSIEISKVIREALEPAIMLELFPR---TVIDVFIEV 127
Query: 181 LSVNPQIDPD--IASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHL 238
L Q D +A I S AL+ + +P + VG +DG +L+ E+
Sbjct: 128 L----QADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLNKEEDNYGEA 183
Query: 239 DLLVA 243
D+ VA
Sbjct: 184 DMPVA 188
>gnl|CDD|180170 PRK05626, rpsO, 30S ribosomal protein S15; Reviewed.
Length = 89
Score = 100 bits (252), Expect = 1e-25
Identities = 36/59 (61%), Positives = 41/59 (69%)
Query: 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMM 59
M++ KA II + R + DTGSPEVQVALLT RIN L H K H KDHHSRRGL+ M
Sbjct: 1 MSLTKEKKAEIIKEYGRHEGDTGSPEVQVALLTERINHLTEHLKEHKKDHHSRRGLLKM 59
>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 (257), Expect = 1e-24
Identities = 74/236 (31%), Positives = 117/236 (49%), Gaps = 23/236 (9%)
Query: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS----RDE 426
K IL+ G+R+D R +++RPI I G+L GS+ G T+ + A G R
Sbjct: 1 KLILEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYLEFGGTKI-LAAVYGPREAHPRHL 59
Query: 427 QKID-ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKF 485
Q D A++ + Y+M PF+T + R G P RREI ++ + AL P +
Sbjct: 60 QLPDRAVL-------RVRYHMAPFSTDERKRPG-PSRREIEISKVIREALEPAILLEQFP 111
Query: 486 NYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDI 545
I + E+ +++G + A + LAL DAG+P+ + V G+A+G + V++ D+
Sbjct: 112 RTVIDVFIEVLQADGGTRCAGLTAASLALADAGIPMRDLVVGVAVGKVDG----VVVLDL 167
Query: 546 LGDEDRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILE 599
+ED G+ D VA IT LQ+D +T D + AL A +G+ I E
Sbjct: 168 SEEEDMYGEADMPVAIMPKTGEITLLQLD---GDLTPDEFRQALDLAVEGIKRIYE 220
Score = 35.9 bits (83), Expect = 0.043
Identities = 47/185 (25%), Positives = 71/185 (38%), Gaps = 43/185 (23%)
Query: 79 ISIEIGEIARQATSSVLVSIEDTVILATVVSCKDP-------------TSTYNFFPLTVD 125
I IE G + + A S + T ILA V ++ Y+ P + D
Sbjct: 21 IKIEAG-VLKNADGSAYLEFGGTKILAAVYGPREAHPRHLQLPDRAVLRVRYHMAPFSTD 79
Query: 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRP-----LFPEGYLNEIQIVVYV 180
E+ KR G PS RE IS++I + P FP I + + V
Sbjct: 80 --ER------------KRPG-PSRREIEISKVIREALEPAILLEQFPR---TVIDVFIEV 121
Query: 181 LSVNPQIDPD--IASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHL 238
L Q D A + S AL+ + +P + VG +DG +L+ + E+
Sbjct: 122 L----QADGGTRCAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLSEEEDMYGEA 177
Query: 239 DLLVA 243
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 = 94.1 bits (235), Expect = 1e-23
Identities = 37/68 (54%), Positives = 51/68 (75%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 745
GK+Y G V+++ DFGA + IL GKDGL+HIS++S +RV + D LK +V+VKV+ +DD
Sbjct: 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD 60
Query: 746 RGRIKLSM 753
RGRI LS
Sbjct: 61 RGRISLSR 68
>gnl|CDD|223761 COG0689, Rph, RNase PH [Translation, ribosomal structure and
biogenesis].
Length = 230
Score = 96.2 bits (240), Expect = 2e-22
Identities = 68/241 (28%), Positives = 107/241 (44%), Gaps = 24/241 (9%)
Query: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 430
+ G+R D R +++RPI I G+L GSSL G+T+ + + E
Sbjct: 1 MLESEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTV---SGPREPVPR 57
Query: 431 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPV-----LPNNNKF 485
L G Y M P +T + + + R RL RAL V LP +
Sbjct: 58 FLRGTGKGWLTAEYGMLPRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPES--- 114
Query: 486 NYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDI 545
+I + ++ +++G + AS+ G LAL DAG+P+ + VA I++G++ VI+ D+
Sbjct: 115 --TIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIVDG----VIVLDL 168
Query: 546 LGDEDRCGDMDFKVAGTVNG----ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 601
+ED + D V T NG I L D T D + L A KG + + E
Sbjct: 169 DYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGP---FTEDELLELLDLAIKGCNELRELQ 225
Query: 602 K 602
+
Sbjct: 226 R 226
Score = 45.4 bits (108), Expect = 4e-05
Identities = 60/227 (26%), Positives = 95/227 (41%), Gaps = 38/227 (16%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTY----NFFPLTVDYIEKAYAA 133
I I G + + A S L+ +T ++ TV ++P + LT +Y
Sbjct: 20 PIKITRG-VLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEY------- 71
Query: 134 GRIPGSFFKREG-KPSERETI-ISRLIDRPIRP-----LFPEGYLNEIQIVVYVLSVNPQ 186
G +P S +R+ + T ISRLI R +R L PE + I I VL Q
Sbjct: 72 GMLPRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPE---STIDIDCDVL----Q 124
Query: 187 IDPDI--ASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAG 244
D ASI G S AL+ + +P + VG +DG +L+ E+ + D+ V
Sbjct: 125 ADGGTRTASITGASLALADAGIPLRDLVAAISVGIVDGVIVLDLDYEEDSAAEADMNVVM 184
Query: 245 TEKA-IITVE--SESKQLPEDIILNAIIFGHEKMKIAINAINELVQN 288
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 = 95.1 bits (237), Expect = 4e-22
Identities = 70/224 (31%), Positives = 108/224 (48%), Gaps = 25/224 (11%)
Query: 387 DIRPISIRTGILPRTHGSSLFTRGDTQALVVATLG----TSRDEQKID-ALMGEFTDSFM 441
++RPI I G+L GS+ G+ + + A G R Q D A++
Sbjct: 1 ELRPIKIEVGVLKNADGSAYVEWGNNKIIA-AVYGPREVHPRHLQLPDRAVI-------R 52
Query: 442 LHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGS 501
+ YNM PF+ + R G P RREI ++ K AL P + +I + E+ +++
Sbjct: 53 VRYNMAPFSVDERKRPG-PDRREIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAG 111
Query: 502 SSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAG 561
+ +A + LAL DAG+P+ + VA A G + K+V+ D+ +ED G+ D +A
Sbjct: 112 TRVAGLNAASLALADAGIPMRDLVAACAAGKV--DGKIVL--DLNKEEDNYGEADMPIAM 167
Query: 562 TVNG--ITALQMDIKIFG-ITYDIIQIALYKAKKGLSYILEKMK 602
N IT LQ+D G +T D + A+ AKKG I E K
Sbjct: 168 MPNLGEITLLQLD----GDLTPDEFKQAIELAKKGCKRIYELQK 207
Score = 33.1 bits (76), Expect = 0.34
Identities = 47/186 (25%), Positives = 71/186 (38%), Gaps = 43/186 (23%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTST-------------YNFFPLTV 124
I IE+G + A S V + I+A V ++ YN P +V
Sbjct: 4 PIKIEVGVLKN-ADGSAYVEWGNNKIIAAVYGPREVHPRHLQLPDRAVIRVRYNMAPFSV 62
Query: 125 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRP-----LFPEGYLNEIQIVVY 179
D E+ KR G P RE IS++I + P FP I + V
Sbjct: 63 D--ER------------KRPG-PDRREIEISKVIKEALEPAIILEEFPR---TAIDVFVE 104
Query: 180 VLSVNPQIDPD--IASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSH 237
VL Q D +A + S AL+ + +P + G +DGK +L+ E+
Sbjct: 105 VL----QADAGTRVAGLNAASLALADAGIPMRDLVAACAAGKVDGKIVLDLNKEEDNYGE 160
Query: 238 LDLLVA 243
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: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 745
G V G V RL FGA + + G GL+HISQI+ KRV + D LKE KV+VKVL ID
Sbjct: 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA 60
Query: 746 RGRIKLSM 753
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: 617 PRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRI 676
PR+ T+KI P KIRDVIG GG TI+ + EETG +IDI D+G + IA+ + + ++AK+ I
Sbjct: 1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMI 60
Query: 677 E 677
E
Sbjct: 61 E 61
>gnl|CDD|223262 COG0184, RpsO, Ribosomal protein S15P/S13E [Translation,
ribosomal structure and biogenesis].
Length = 89
Score = 82.2 bits (204), Expect = 4e-19
Identities = 30/59 (50%), Positives = 41/59 (69%)
Query: 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMM 59
M++ + IK + + + DTGS EVQ+ALLT RIN+L H K H KDHHSRRGL+++
Sbjct: 1 MSLTSEIKQELRDEYGIPEVDTGSGEVQLALLTERINNLTEHLKEHKKDHHSRRGLLLL 59
>gnl|CDD|130027 TIGR00952, S15_bact, ribosomal protein S15, bacterial/organelle.
This model is built to recognize specifically
bacterial, chloroplast, and mitochondrial ribosomal
protein S15. The homologous proteins of Archaea and
Eukarya are designated S13 [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 86
Score = 78.5 bits (194), Expect = 7e-18
Identities = 31/54 (57%), Positives = 37/54 (68%)
Query: 8 KASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKG 61
K II + + DTGSPEVQ+ALLT RIN L H K + KDHHSRRGL+ + G
Sbjct: 5 KQEIIKEFQLHEKDTGSPEVQIALLTERINQLTEHLKANKKDHHSRRGLLKLVG 58
>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 390
Score = 86.1 bits (214), Expect = 8e-18
Identities = 40/94 (42%), Positives = 57/94 (60%), Gaps = 2/94 (2%)
Query: 661 IASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISS 720
I S +V +E + E+L S++ G V G V RL DFGA + I G DGL+HIS++S
Sbjct: 168 ILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSH 226
Query: 721 KRVNIITDFLKENQKVRVKVLGID-DRGRIKLSM 753
+RV ++ + Q+V VKVL ID + RI LS+
Sbjct: 227 ERVEKPSEVVSVGQEVEVKVLSIDWETERISLSL 260
Score = 82.6 bits (205), Expect = 9e-17
Identities = 35/78 (44%), Positives = 51/78 (65%), Gaps = 1/78 (1%)
Query: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 736
E + E + G V G V RL DFGA + +L G +GL+HISQIS K + ++ L+E Q+V
Sbjct: 269 EGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEV 328
Query: 737 RVKVLGID-DRGRIKLSM 753
+VKVL ++ + RI LS+
Sbjct: 329 KVKVLEVNEEEKRISLSI 346
Score = 37.2 bits (87), Expect = 0.033
Identities = 21/66 (31%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 681 ESVQIGKVYTGIVLRLFDFGAIIRILSGK-DGLLHISQISSKRVNIITDFLKENQKVRVK 739
+ V++G V TG VL++ D + I K +G++ IS++S+ + I D +K ++ V
Sbjct: 13 KEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVY 72
Query: 740 VLGIDD 745
VL ++D
Sbjct: 73 VLKVED 78
Score = 29.5 bits (67), Expect = 6.5
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 4/83 (4%)
Query: 671 EAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFL 730
EA++ +KL E + G+V V + G ++ + G G + S IS++ V +DF
Sbjct: 91 EAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSDFK 149
Query: 731 KENQKVRVKVLGIDDRG-RIKLS 752
+ + 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 = 9e-16
Identities = 28/71 (39%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 684 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 743
++G V G V + GA + + +G +GL+ IS++S KRV + LK +V+VKVL +
Sbjct: 1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV 60
Query: 744 D-DRGRIKLSM 753
D ++GRI LS+
Sbjct: 61 DEEKGRIILSL 71
>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: 686 GKVYTGIVLRLFDFGAIIRILS---GKDGLLHISQISSK-RVNIITDFLKENQKVRVKVL 741
GK+Y G V + DFG +++ K+GL+HISQ+S + RV +D +K QKV+VKV+
Sbjct: 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVI 60
Query: 742 GIDDRGRIKLSM 753
I G+I LSM
Sbjct: 61 SI-QNGKISLSM 71
>gnl|CDD|235614 PRK05807, PRK05807, hypothetical protein; Provisional.
Length = 136
Score = 73.2 bits (180), Expect = 2e-15
Identities = 30/70 (42%), Positives = 46/70 (65%), Gaps = 1/70 (1%)
Query: 684 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 743
+ G + G V+ + +FGA + + GK GL+HIS+++ V I + LKE KV+VKV+ I
Sbjct: 4 KAGSILEGTVVNITNFGAFVE-VEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISI 62
Query: 744 DDRGRIKLSM 753
DD G+I LS+
Sbjct: 63 DDNGKISLSI 72
>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 = 4e-15
Identities = 30/72 (41%), Positives = 46/72 (63%)
Query: 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 741
S+++G G + + +GA + + GK GL+HIS+I+ V I D LK Q+V+VKVL
Sbjct: 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVL 61
Query: 742 GIDDRGRIKLSM 753
ID+ G+I LS+
Sbjct: 62 DIDENGKISLSI 73
>gnl|CDD|238213 cd00353, Ribosomal_S15p_S13e, Ribosomal protein S15
(prokaryotic)_S13 (eukaryotic) binds the central domain
of 16S rRNA and is required for assembly of the small
ribosomal subunit and for intersubunit association,
thus representing a key element in the assembly of the
whole ribosome. S15 also plays an important
autoregulatory role by binding and preventing its own
mRNA from being translated. S15 has a predominantly
alpha-helical fold that is highly structured except for
the N-terminal alpha helix.
Length = 80
Score = 70.2 bits (173), Expect = 5e-15
Identities = 25/52 (48%), Positives = 36/52 (69%)
Query: 8 KASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMM 59
K I+ + + DTGSPEVQ+ALLT RI +L H + + KD HS+RGL+++
Sbjct: 2 KQEILKEFGLAEGDTGSPEVQLALLTERIVNLTEHLEKNKKDKHSKRGLLLL 53
>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase/S1 RNA-binding domain protein; Reviewed.
Length = 647
Score = 78.4 bits (194), Expect = 5e-15
Identities = 35/93 (37%), Positives = 56/93 (60%), Gaps = 2/93 (2%)
Query: 661 IASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISS 720
+ S ++ +E +++ E+ S++ G V G V RL DFGA + I G DGLLH+S+IS
Sbjct: 453 VLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISW 511
Query: 721 KRVNIITDFLKENQKVRVKVLGID-DRGRIKLS 752
RV +D LK +++V +L ID + ++ LS
Sbjct: 512 GRVEKPSDVLKVGDEIKVYILDIDKENKKLSLS 544
Score = 75.4 bits (186), Expect = 5e-14
Identities = 32/78 (41%), Positives = 50/78 (64%), Gaps = 1/78 (1%)
Query: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 736
E + E +G + G V+R+ FGA + + G DGL+HISQIS KR++ D L E ++V
Sbjct: 554 ENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEV 613
Query: 737 RVKVLGID-DRGRIKLSM 753
+ K+L +D + RI+LS+
Sbjct: 614 KAKILEVDPEEKRIRLSI 631
Score = 32.6 bits (75), Expect = 0.93
Identities = 15/83 (18%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 671 EAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFL 730
E + +L + ++ G + G V+ + + + + +G++ + +++ ++ + + +
Sbjct: 288 EQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESV 347
Query: 731 KENQKVRVKVLGI-DDRGRIKLS 752
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: 624 IDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESV 683
+D +RD+ G + E +D ++ S +V +E + E+L +
Sbjct: 137 VDVRPVRDLDPLIGKELEFKILE----LDKKRNNVV--LSRRAVLEEERSEQREELLNKL 190
Query: 684 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 743
++G+V G+V + D+GA + I G DGLLHIS+IS KRV+ ++ +K +V+VKV+ +
Sbjct: 191 EVGEVVEGVVKNITDYGAFVDI-GGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISL 249
Query: 744 D-DRGRIKLSM 753
D +RGR+ LS+
Sbjct: 250 DEERGRVSLSL 260
Score = 71.6 bits (176), Expect = 7e-13
Identities = 30/78 (38%), Positives = 47/78 (60%), Gaps = 1/78 (1%)
Query: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 736
E + + +G G V L D+GA + I G +GL+H+S+IS + N+ ++ +K Q+V
Sbjct: 269 EGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEV 328
Query: 737 RVKVLGID-DRGRIKLSM 753
VKVL ID +R RI L +
Sbjct: 329 EVKVLDIDPERRRISLGL 346
Score = 48.8 bits (117), Expect = 9e-06
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 736
E+ + +G V G V + DFGA + + G DGL+H+S +S R + K+ +V
Sbjct: 355 EEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEV 414
Query: 737 RVKVLGID-DRGRIKLS 752
KVL +D ++ RI L
Sbjct: 415 EAKVLAVDKEKERISLG 431
Score = 36.1 bits (84), Expect = 0.070
Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 665 NSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVN 724
S E +R EKL E+ + G++ G + G + I G L S + + V
Sbjct: 85 LSRRKAERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDI-EGVRAFLPGSLVDVRPVR 143
Query: 725 IITDFLKENQKVRVKVLGID-DRGRIKLS 752
+ +++ K+L +D R + LS
Sbjct: 144 DLDPL--IGKELEFKILELDKKRNNVVLS 170
Score = 33.8 bits (78), Expect = 0.37
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 745
G V G V + D GA + + G +GL+ +S++S LK +V V+ ID
Sbjct: 450 GSVVKGKVKSVKDKGAFVELGGGVEGLIRLSELSRDV-------LKVGDEVEAVVVSIDK 502
Query: 746 R-GRIKLS 752
+ +I LS
Sbjct: 503 KNRKILLS 510
Score = 32.3 bits (74), Expect = 1.2
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 680 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVK 739
E + G V G V+ + G ++ I +G++ IS+ S++ V D ++ +V V
Sbjct: 16 DEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVE---DVVQVGDEVEVL 72
Query: 740 VLGI-DDRGRIKLS 752
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 = 5e-14
Identities = 31/69 (44%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 685 IGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID 744
G V G V + DFGA + L G DGLLHIS +S RV ++ + +V VKVL ID
Sbjct: 1 EGDVVEGTVKSITDFGAFVD-LGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKID 59
Query: 745 -DRGRIKLS 752
+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: 670 QEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDF 729
+ +R E+L E+++ G+V G+V + D+GA + L G DGLLHI+ IS KRVN ++
Sbjct: 188 RAEER--EELLENLEEGQVVEGVVKNITDYGAFVD-LGGVDGLLHITDISWKRVNHPSEV 244
Query: 730 LKENQKVRVKVLGID-DRGRIKLSM 753
+ +V+VKVL D ++ R+ L +
Sbjct: 245 VNVGDEVKVKVLKFDKEKKRVSLGL 269
Score = 58.6 bits (143), Expect = 8e-09
Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 14/97 (14%)
Query: 671 EAKRRI------------EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQI 718
E KRRI E+ E +G V G V + DFGA + + G DGL+H+S I
Sbjct: 347 EEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDI 406
Query: 719 S-SKRVNIITDFLKENQKVRVKVLGID-DRGRIKLSM 753
S K+ + K+ +V VL +D ++ RI L +
Sbjct: 407 SWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGI 443
Score = 58.3 bits (142), Expect = 1e-08
Identities = 24/79 (30%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 735
E + + +G G V + D+GA + + G +GL+H+S++S +K+ + + Q+
Sbjct: 278 EAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQE 337
Query: 736 VRVKVLGID-DRGRIKLSM 753
V V VL ID ++ RI L +
Sbjct: 338 VEVMVLEIDEEKRRISLGL 356
Score = 55.2 bits (134), Expect = 9e-08
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 736
E+ + + G + TG V + D GA + + G +GL+ S++S RV T+ LK +V
Sbjct: 452 EEFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEV 511
Query: 737 RVKVLGIDDRGR-IKLSM 753
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: 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 741
+ G V G V R+ GA + + +G +G + IS+IS RV + LK +V VKVL
Sbjct: 1 KPEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVL 60
Query: 742 GID-DRGRIKLSM 753
+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: 377 GLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLG----TSRDEQKIDAL 432
GLR+D R N++R I R G+ GS+ +G+T+ L G +R + D
Sbjct: 1 GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVY-GPHEPRNRSQALHDRA 59
Query: 433 MGEFTDSFMLHYNMPPFATGDIGRIGVPKRR--EIGHGRLAKRALLPVLPNNNKFNYSIR 490
Y+M F+TG+ R G RR E+ ++ V+ + I
Sbjct: 60 ------VVNCEYSMATFSTGERKRRGKGDRRSTELSL--AIRQTFEAVILTHLYPRSQID 111
Query: 491 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 550
+ ++ +++G A + LAL+DAG+P+ ++V + G + L D+ E+
Sbjct: 112 IYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYLDS----TPLLDLNYLEE 167
Query: 551 RCGDMDFKVA--GTVNGITALQMDIKI 575
D VA + + LQM+ ++
Sbjct: 168 SGDLPDLTVAVLPKSDKVVLLQMESRL 194
>gnl|CDD|109373 pfam00312, Ribosomal_S15, Ribosomal protein S15.
Length = 83
Score = 63.9 bits (156), Expect = 1e-12
Identities = 27/55 (49%), Positives = 34/55 (61%)
Query: 7 IKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKG 61
II + + + DTGS EVQ+ALLT RI L H + H KD+HS+RGLI M
Sbjct: 2 ATGLIISEFLKAEKDTGSVEVQIALLTERIVRLRKHLEEHKKDYHSKRGLIKMVS 56
>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 = 62.4 bits (152), Expect = 2e-12
Identities = 26/65 (40%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 689 YTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDR-G 747
TG V+ + FG + + G +GL+HIS++S K V ++ K +V VKVL +D G
Sbjct: 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKG 60
Query: 748 RIKLS 752
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 = 7e-12
Identities = 36/84 (42%), Positives = 56/84 (66%), Gaps = 2/84 (2%)
Query: 671 EAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFL 730
E + E+L E+++ G V G+V + DFGA + L G DGLLHI+ +S KRV ++++
Sbjct: 173 ERSQAREELLENLKEGDVVKGVVKNITDFGAFV-DLGGVDGLLHITDMSWKRVKHPSEYV 231
Query: 731 KENQKVRVKVLGID-DRGRIKLSM 753
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: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 735
E + + +G TG V L D+G + I G +GL+H+S++S K+ + + +K+ +
Sbjct: 264 EAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDE 323
Query: 736 VRVKVLGID-DRGRIKLSM 753
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: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKV 736
EK ++G V G V + DFGA + + G +GL+ S++S R TD +K +V
Sbjct: 438 EKFAAKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEV 497
Query: 737 RVKVLGID-DRGRIKLS 752
KV+ ID ++ LS
Sbjct: 498 EAKVVDIDKKNRKVSLS 514
Score = 42.8 bits (101), Expect = 6e-04
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 735
E+ E +G TG + ++ DFGA + + G DGL+H+S IS K K+ +
Sbjct: 351 EQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDE 410
Query: 736 VRVKVLGIDDRG-RIKLS 752
+ 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 = 59.6 bits (145), Expect = 3e-11
Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 363
L K+ ++E ++ +AY I KQ R I D+ ++ E+ +D +I I
Sbjct: 1 ELEEKVAALAEERLSEAYTITGKQERYAALDEIKADVVAAFAA-EDDELDEKEIKAIFKA 59
Query: 364 LESKIIRKQILDKGLRIDNRG 384
LE K++R +ILD G RID RG
Sbjct: 60 LEKKVVRSRILDGGPRIDGRG 80
>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional.
Length = 491
Score = 66.3 bits (162), Expect = 3e-11
Identities = 34/88 (38%), Positives = 48/88 (54%), Gaps = 5/88 (5%)
Query: 670 QEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDF 729
+E K +E E+V+ G V G V RL FGA + + G +G++HIS++S RV +
Sbjct: 187 REQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEA 246
Query: 730 LKENQKVRVKVLGIDDRG-----RIKLS 752
+ 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: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 735
+ + + ++ G TG V+RL FGA + IL G +GL+H+S++S ++RVN D +
Sbjct: 284 DTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDA 343
Query: 736 VRVKVLGID-DRGRIKLSM 753
V VK+ ID + RI LS+
Sbjct: 344 VAVKIKDIDPAKRRISLSL 362
Score = 30.8 bits (70), Expect = 2.7
Identities = 26/89 (29%), Positives = 32/89 (35%), Gaps = 12/89 (13%)
Query: 672 AKRRI------------EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS 719
AKRRI + E G TG V + FG + + G GLL S IS
Sbjct: 354 AKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVIS 413
Query: 720 SKRVNIITDFLKENQKVRVKVLGIDDRGR 748
+ 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 = 8e-11
Identities = 29/68 (42%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID- 744
G V G+V + DFGA + I +DGL+HIS+++ + V+ +D + V VKV+ ID
Sbjct: 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDE 60
Query: 745 DRGRIKLS 752
+RGRI LS
Sbjct: 61 ERGRISLS 68
>gnl|CDD|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit
alpha; Validated.
Length = 262
Score = 60.6 bits (148), Expect = 4e-10
Identities = 28/66 (42%), Positives = 41/66 (62%), Gaps = 3/66 (4%)
Query: 691 GIVLRLFDFGAIIRIL--SGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID-DRG 747
G V + DFGA + + GK+G +HIS+++S V I D +KE QKV KV+ +D +G
Sbjct: 14 GTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKG 73
Query: 748 RIKLSM 753
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: 685 IGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLG 742
G++ V + D GA + +L +G++ +S++S +R+ I +K +K VKV+
Sbjct: 3 EGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIR 62
Query: 743 ID-DRGRIKLSM 753
+D ++G I LS
Sbjct: 63 VDKEKGYIDLSK 74
>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit
(eIF-2alpha) [Translation, ribosomal structure and
biogenesis].
Length = 269
Score = 60.0 bits (146), Expect = 9e-10
Identities = 31/83 (37%), Positives = 49/83 (59%), Gaps = 6/83 (7%)
Query: 674 RRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLK 731
+ + E G++ G V ++ D+GA + + GK+G +HIS+++S V I D++K
Sbjct: 3 MKRREYPE---EGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVK 59
Query: 732 ENQKVRVKVLGID-DRGRIKLSM 753
E QKV KVL +D RG I LS+
Sbjct: 60 EGQKVVAKVLRVDPKRGHIDLSL 82
>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated.
Length = 123
Score = 56.6 bits (137), Expect = 1e-09
Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 679 LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRV 738
+ ++G V TG V + +GA + + GL+HIS+I+ V I DFL +V+V
Sbjct: 1 MMSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKV 60
Query: 739 KVLGID-DRGRIKLSM 753
KVL +D ++G+I LS+
Sbjct: 61 KVLSVDEEKGKISLSI 76
>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 = 58.3 bits (142), Expect = 1e-09
Identities = 44/167 (26%), Positives = 72/167 (43%), Gaps = 41/167 (24%)
Query: 388 IRPISIRTGILPRTHGSSLFTRGDTQALVVATLG----TSRDEQKIDALMGEFTDSFMLH 443
+RP+S G+L R GS+ F++GDT L G R E
Sbjct: 1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVY-GPIEVKLRKE----------------- 42
Query: 444 YNMPPFATGDI---GRIGVPKRREIGHGRLAKRALLPVL-----PNNNKFNYSIRLVSEI 495
+P AT ++ + G+P +E L + L P++ P I +V ++
Sbjct: 43 --LPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIILLHLHPRT-----LISVVLQV 95
Query: 496 TESNGSSSMASVC--GGCLALLDAGVPISEHVAGIAMGLIKDGEKVV 540
+ +GS + + CLALLDAGVP+ A + + +DGE ++
Sbjct: 96 LQDDGS--LLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIIL 140
Score = 28.7 bits (65), Expect = 9.7
Identities = 31/121 (25%), Positives = 48/121 (39%), Gaps = 18/121 (14%)
Query: 145 GKPSER--ETIISRLIDRPI-RPLFPEGYLNEIQIVVYVLSVNPQIDP---DIASIIGVS 198
E+ E ++ ++ I L P I +V+ VL D +I
Sbjct: 60 PGVKEKLLELLLRSTLEPIILLHLHPR---TLISVVLQVLQ-----DDGSLLACAINAAC 111
Query: 199 TALSISELPFLG-PLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA---GTEKAIITVES 254
AL + +P G V DG+ IL+PT E+ K++ A G EK ++ ES
Sbjct: 112 LALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDSGEEKNLVLSES 171
Query: 255 E 255
E
Sbjct: 172 E 172
>gnl|CDD|236305 PRK08582, PRK08582, hypothetical protein; Provisional.
Length = 139
Score = 55.8 bits (135), Expect = 3e-09
Identities = 29/71 (40%), Positives = 44/71 (61%)
Query: 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 741
S+++G G V + +FGA + + GK GL+HIS+++ V I D LK +V VKVL
Sbjct: 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVL 61
Query: 742 GIDDRGRIKLS 752
++D G+I LS
Sbjct: 62 NVEDDGKIGLS 72
>gnl|CDD|235268 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42;
Provisional.
Length = 271
Score = 58.0 bits (141), Expect = 4e-09
Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 366 SKIIRKQILD---KGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 416
+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: 684 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 743
IG++ G V +L FGA +R+ G +GL+HIS+++ + V + ++ +V VKV+ I
Sbjct: 292 AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDI 351
Query: 744 D-DRGRIKLSM 753
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: 684 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 743
Q G+V G+V + +FGA + L G DGL+H+S++S K ++ ++ ++ Q+V V+VL +
Sbjct: 207 QKGQVRKGVVSSIVNFGAFVD-LGGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDV 265
Query: 744 D-DRGRIKLSM 753
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 = 51.8 bits (125), Expect = 8e-09
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG--IITIASFNSVSGQEAKRRI 676
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 = 56.2 bits (136), Expect = 1e-08
Identities = 59/209 (28%), Positives = 91/209 (43%), Gaps = 37/209 (17%)
Query: 379 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALM-GEFT 437
R D R + +RP+SI L GS L G+T+ L A++ E+K+ + G
Sbjct: 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASV-----EEKVPPFLRGSGE 55
Query: 438 DSFMLHYNMPPFATGDIGRIGVPKRREIGHG----------RLAKRALLPVLPNNNKFNY 487
Y M P AT RRE G RL RAL V+
Sbjct: 56 GWITAEYGMLPRATQT------RNRRESAKGKQSGRTQEIQRLIGRALRAVVDLEALGER 109
Query: 488 SIRLVSEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDG 536
+I + ++ +++G + AS+ G +AL DA PI + VA +++G++ DG
Sbjct: 110 TIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIV-DG 168
Query: 537 EKVVILSDILGDEDRCGDMDFKVAGTVNG 565
E V+ D+ +ED D+D V T +G
Sbjct: 169 EPVL---DLDYEEDSAADVDMNVVMTGSG 194
Score = 33.9 bits (78), Expect = 0.24
Identities = 64/255 (25%), Positives = 96/255 (37%), Gaps = 70/255 (27%)
Query: 78 KISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVD 125
+SI + A SVL+ +T +L T V K P T+ Y P
Sbjct: 12 PVSITRD-FLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLP---- 66
Query: 126 YIEKAYAAGRIPGSFFKRE---GKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLS 182
R + +RE GK S R I RLI R +R + L E I
Sbjct: 67 ---------RATQTRNRRESAKGKQSGRTQEIQRLIGRALRAVVDLEALGERTIW----- 112
Query: 183 VNPQIDPDI---------ASIIG--VSTALSISEL---------PFLGPLGVAKVGYIDG 222
ID D+ ASI G V+ A +IS+L P + VG +DG
Sbjct: 113 ----IDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIVDG 168
Query: 223 KYILNPTTEQLKKSHLDLLVAGTEK-AIITVE--SESKQLPEDIILNAIIFGHEKMKIAI 279
+ +L+ E+ + +D+ V T + V+ +E D LN + + +A
Sbjct: 169 EPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRD-ELNKL------LDLAK 221
Query: 280 NAINELVQNVGQKKV 294
I EL++ QK+
Sbjct: 222 KGIRELIE--LQKQA 234
>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: 210 GPLGVAKVGYIDGKYILNPTTEQ--LKKSHLDLLVAGTEKAIIT-VESESKQLPEDIILN 266
GP+ VG IDG+ +L+PT E+ L S L ++VAGT + + E +L E+ +L
Sbjct: 1 GPVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGEIVALMKEGGGAELTEEELLE 60
Query: 267 AIIFGHEK 274
A+ HE
Sbjct: 61 ALELAHEG 68
Score = 37.6 bits (88), Expect = 0.001
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 7/71 (9%)
Query: 525 VAGIAMGLIKDGEKVVILSDILGDEDRC--GDMDFKVAGTVNGITALQMDIKIFGITYDI 582
VA + +G I ++ D +E+ D+ VAGT + ++ +T +
Sbjct: 3 VAAVTVGKIDGE----LVLDPTLEEESLADSDLTIVVAGTGEIVALMKEGGGAE-LTEEE 57
Query: 583 IQIALYKAKKG 593
+ AL A +G
Sbjct: 58 LLEALELAHEG 68
>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: 676 IEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQK 735
+E +T+ ++ G + G V + DFGA + I +DGL+HISQ+S K V + +K
Sbjct: 650 VESITD-LKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDI 708
Query: 736 VRVKVLGID-DRGRIKLSMIY 755
V+VKV+ +D R RI LSM
Sbjct: 709 VKVKVIEVDTARKRIALSMRL 729
>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 = 5e-08
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 9/65 (13%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI------NDEGIITI-ASFNSVSGQEA 672
+ + S + +IGKGGSTI+ + EETG +I I ++E I+TI + +V ++A
Sbjct: 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAV--EKA 59
Query: 673 KRRIE 677
K I
Sbjct: 60 KELIL 64
>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 = 53.4 bits (129), Expect = 7e-08
Identities = 56/205 (27%), Positives = 91/205 (44%), Gaps = 45/205 (21%)
Query: 387 DIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALM-----GEFTDSFM 441
+RPISI G GS L GDT+ L A++ E+K+ + G T
Sbjct: 1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASV-----EEKVPPFLRGKGKGWVT---- 51
Query: 442 LHYNMPPFATGDIGRIGVPKRREIGHG----------RLAKRALLPVLPNNNKFNYSIRL 491
Y+M P +T + R +RE G RL R+L + +I +
Sbjct: 52 AEYSMLPRSTHE--R----TQREASKGKQSGRTQEIQRLIGRSLRAAVDLEALGERTITI 105
Query: 492 VSEITESNGSSSMASVCGGCLALLDA-------GV----PISEHVAGIAMGLIKDGEKVV 540
++ +++G + AS+ G +AL DA GV P+ VA +++G++ DGE ++
Sbjct: 106 DCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIV-DGEPLL 164
Query: 541 ILSDILGDEDRCGDMDFKVAGTVNG 565
D+ +ED D+D V T +G
Sbjct: 165 ---DLDYEEDSAADVDMNVVMTGSG 186
Score = 31.8 bits (73), Expect = 1.0
Identities = 54/204 (26%), Positives = 73/204 (35%), Gaps = 58/204 (28%)
Query: 79 ISIEIGEIARQATSSVLVSIEDTVILATV-VSCKDP-----------TSTYNFFPLTVDY 126
ISI G + A SVL+ DT +L T V K P T+ Y+ P
Sbjct: 5 ISITRG-FNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGKGKGWVTAEYSMLP----- 58
Query: 127 IEKAYAAGRIPGSFFKRE---GKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 183
R +RE GK S R I RLI R +R L E I
Sbjct: 59 --------RSTHERTQREASKGKQSGRTQEIQRLIGRSLRAAVDLEALGERTI------- 103
Query: 184 NPQIDPDI---------ASIIGVSTALS-----------ISELPFLGPLGVAKVGYIDGK 223
ID D+ ASI G AL+ + E P + VG +DG+
Sbjct: 104 --TIDCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIVDGE 161
Query: 224 YILNPTTEQLKKSHLDLLVAGTEK 247
+L+ E+ + +D+ V T
Sbjct: 162 PLLDLDYEEDSAADVDMNVVMTGS 185
>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 = 7e-08
Identities = 27/70 (38%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 686 GKVYTGIVLRLFDFGAIIRI-LSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID 744
G+ G V R+ D+G I I + GL H S+IS RV + + KVR KVL ID
Sbjct: 3 GQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKID 62
Query: 745 -DRGRIKLSM 753
++ RI L +
Sbjct: 63 AEKKRISLGL 72
>gnl|CDD|214339 CHL00027, rps15, ribosomal protein S15.
Length = 90
Score = 49.6 bits (119), Expect = 1e-07
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 4 KNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGL 56
N S+I + +N GS E QV T++I L H +LH KD+ S+RGL
Sbjct: 2 VKNSFISVISQEEKEEN-RGSVEFQVFSFTNKIRRLTSHLELHKKDYSSQRGL 53
>gnl|CDD|238361 cd00677, S15_NS1_EPRS_RNA-bind, S15/NS1/EPRS_RNA-binding domain.
This short domain consists of a helix-turn-helix
structure, which can bind to several types of RNA. It
is found in the ribosomal protein S15, the influenza A
viral nonstructural protein (NSA) and in several
eukaryotic aminoacyl tRNA synthetases (aaRSs), where it
occurs as a single or a repeated unit. It is involved
in both protein-RNA interactions by binding tRNA and
protein-protein interactions in the formation of
tRNA-synthetases into multienzyme complexes. While this
domain lacks significant sequence similarity between
the subgroups in which it is found, they share similar
electrostatic surface potentials and thus are likely to
bind to RNA via the same mechanism.
Length = 46
Score = 47.9 bits (115), Expect = 2e-07
Identities = 18/34 (52%), Positives = 24/34 (70%)
Query: 26 EVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMM 59
EVQ+ALLT RI +L H + KD HS+RGL ++
Sbjct: 1 EVQIALLTERIRNLKEHLAKNKKDKHSKRGLDLL 34
>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: 366 SKIIRKQILD---KGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 416
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 = 48.6 bits (116), Expect = 2e-07
Identities = 23/71 (32%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 684 QIGKVYTGIVLRLFDFGAIIRILS-GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLG 742
+ +++ G V + ++GA ++I K GL+H S +SS RV+ ++ + +KV VKV+G
Sbjct: 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIG 61
Query: 743 IDDRGRIKLSM 753
+ + ++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: 363 DLESKIIRKQI----LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVA 418
I+++ L KG+RID R ++ RP+ I TG++P+ +GS+L G+TQ +V
Sbjct: 4 SEIISEIKREYILNLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGV 63
Query: 419 TLGTSR 424
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 = 4e-07
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 681 ESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKV 740
++ G V G V + +G + L G GL S IS + V + K+ Q V KV
Sbjct: 10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKV 69
Query: 741 LGID-DRGRIKLSM 753
+D ++ R LS+
Sbjct: 70 TSVDEEKQRFLLSL 83
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 44.6 bits (106), Expect = 4e-06
Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 5/64 (7%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI----NDEGIITIASFNSVSGQEAKRR 675
I + I K+ +IGKGGSTI+ + EETG +IDI ++E ++ I + ++A
Sbjct: 5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPE-NVEKAAEL 63
Query: 676 IEKL 679
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 = 43.6 bits (103), Expect = 1e-05
Identities = 28/68 (41%), Positives = 41/68 (60%), Gaps = 2/68 (2%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQKVRVKVLGID 744
G V +G + + DFG + + G DGL+HIS IS ++RV ++ K+ Q+V VL ID
Sbjct: 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID 60
Query: 745 -DRGRIKL 751
+R RI L
Sbjct: 61 VERERISL 68
>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed.
Length = 318
Score = 47.9 bits (114), Expect = 1e-05
Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 4/82 (4%)
Query: 674 RR--IEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLK 731
RR +E+ +++G+V G V + +GA I I G GLLHIS+IS + +
Sbjct: 183 RRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFN 241
Query: 732 ENQKVRVKVLGID-DRGRIKLS 752
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: 670 QEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDF 729
+ A++ E+ SV I +G+V FGA I L G DGLLH++ +S V +F
Sbjct: 478 ERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFID-LGGFDGLLHVNDMSWGHVARPREF 536
Query: 730 LKENQKVRVKVLGIDD-RGRIKLSM 753
+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: 685 IGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQKVRVKVLGI 743
+ V G V ++ DFGA I + G +GL HIS+ S K+ + +D +K +V +LG
Sbjct: 578 VNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGY 637
Query: 744 D-DRGRIKLSM 753
D GR+ L +
Sbjct: 638 DIQAGRVSLGL 648
Score = 30.1 bits (67), Expect = 6.1
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 677 EKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-SKRVNIITDFLKENQK 735
E++ +G +T ++++ + GA I + G DG LH+ +S KR L+ ++
Sbjct: 657 EEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKE 716
Query: 736 VRVKVLGIDDRGR 748
+ V+ D + R
Sbjct: 717 IECMVIECDPQAR 729
>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 = 42.9 bits (102), Expect = 2e-04
Identities = 48/192 (25%), Positives = 81/192 (42%), Gaps = 27/192 (14%)
Query: 388 IRPISIRTGILPRTHGSSLFTRGDTQALVVATLG---TSRDEQKIDALMGEFTDS--FML 442
IRPI ++TG++ + GS+ G+T+ ++ + G EF+D
Sbjct: 1 IRPIFLKTGVVSQAKGSAYVELGNTK-VICSVYGPRPIPGRT--------EFSDRGRLNC 51
Query: 443 HYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLP-VLPNNNKF-NYSIRLVSEITESNG 500
PFAT R E L +AL P V K+ I + + ES+G
Sbjct: 52 EVKFAPFATPGRRR-HGQDSEERELSSLLHQALEPAVRL--EKYPKSQIDVFVTVLESDG 108
Query: 501 SS-SMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKV 559
S + A LAL DAG+ + + V + LI G+++++ D +E+ +
Sbjct: 109 SVLAAAITAAS-LALADAGIEMYDLVTACSAALI--GDELLL--DPTREEEEASSGGVML 163
Query: 560 AG--TVNGITAL 569
A ++N +T L
Sbjct: 164 AYMPSLNQVTQL 175
>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 = 3e-04
Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEG----IITI 661
++I R +IGK GS IR + EETG +I D G ITI
Sbjct: 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITI 47
>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: 622 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITI 661
++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: 681 ESVQIGKVYTGIVLRLFDF--GAIIRILSGKDGLLHISQISS---KRVNIITDFLKENQK 735
+G +Y G V ++ A + I GK+G LH+S I K+ I LKE Q+
Sbjct: 3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQE 62
Query: 736 VRVKV 740
+ V+V
Sbjct: 63 ILVQV 67
>gnl|CDD|180908 PRK07252, PRK07252, hypothetical protein; Provisional.
Length = 120
Score = 39.7 bits (93), Expect = 6e-04
Identities = 22/71 (30%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 684 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 743
+IG G + + +GA + + +G GL+HIS+I + ++ I LK ++V V+V+
Sbjct: 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDF 61
Query: 744 DD-RGRIKLSM 753
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 = 7e-04
Identities = 17/40 (42%), Positives = 23/40 (57%)
Query: 377 GLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 416
+R D R D RPI + TG+L T+GS+ G+T LV
Sbjct: 17 NIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLV 56
>gnl|CDD|178914 PRK00173, rph, ribonuclease PH; Reviewed.
Length = 238
Score = 41.2 bits (98), Expect = 0.001
Identities = 55/220 (25%), Positives = 89/220 (40%), Gaps = 59/220 (26%)
Query: 379 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS-----RDEQK--IDA 431
R D R + +RP++I GS L GDT+ L A++ + + + + A
Sbjct: 2 RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTA 61
Query: 432 LMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHG----------RLAKRAL-----L 476
Y M P AT R RE G RL R+L L
Sbjct: 62 -----------EYGMLPRATHT--R----NDREAAKGKQGGRTQEIQRLIGRSLRAVVDL 104
Query: 477 PVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDA-------GV----PISEHV 525
L +I + ++ +++G + AS+ G +AL DA G P+ + V
Sbjct: 105 KALGER-----TITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQV 159
Query: 526 AGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG 565
A +++G++ DGE V+ D+ +ED + D V T +G
Sbjct: 160 AAVSVGIV-DGEPVL---DLDYEEDSAAETDMNVVMTGSG 195
>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 = 0.001
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 745
G + TG V + GA +++ G +G L +++S RV T+ K +V K+ +D
Sbjct: 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60
Query: 746 RGR-IKLS 752
+ 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: 691 GIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID-DRGRI 749
G ++++ G I+ + G L S++S + + + Q V+VKVL D ++ R+
Sbjct: 6 GTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRL 65
Query: 750 KLS 752
LS
Sbjct: 66 LLS 68
>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 = 38.0 bits (89), Expect = 0.001
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 680 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVK 739
E +++GK+Y G V + +G + + GL+H S N++ D+ + +V V+
Sbjct: 11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRS-------NLLRDY-EVGDEVIVQ 62
Query: 740 VLGIDDRGRIKLS 752
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: 622 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITI 661
+KI +I +IGK G T + + E TG +++I+ + G + I
Sbjct: 7 VKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVII 47
Score = 32.9 bits (76), Expect = 0.37
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 632 VIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 689
+IG+GG T R + E TG I + + + I V + A+ IE L E G VY
Sbjct: 109 IIGEGGKTRRIIEELTGVDISVYGKTVAIIGDPEQV--EIAREAIEMLIEGAPHGTVY 164
>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: 690 TGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNII-TDFLKENQKVRVKVLGID-DRG 747
G V L D+G + + G +GL+H+S++ NI + + +V V VL ID +R
Sbjct: 8 FGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERR 67
Query: 748 RIKL 751
RI L
Sbjct: 68 RISL 71
>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: 628 KIRDVIGKGGSTIRTLTEETGTQIDI------NDEGIITI 661
+ +IGKGG TI+ + EETG +I I + E I+TI
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTI 40
>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 = 0.004
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 18/80 (22%)
Query: 691 GIVLRLFDFGAIIRILSGKDGLLHISQIS-------SKRVNIITD----FLKENQKVRVK 739
G V+ + DFGA +RI DGLLHISQI K +I + LK VR +
Sbjct: 5 GEVVEVVDFGAFVRI-GPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRAR 63
Query: 740 VLGI------DDRGRIKLSM 753
++ + +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 = 0.009
Identities = 16/41 (39%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 622 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITI 661
+KI +I +IGKGG T + + E TG ++DI+ + G + I
Sbjct: 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKI 42
Score = 31.4 bits (72), Expect = 0.93
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 632 VIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 689
+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 = 38.9 bits (91), Expect = 0.011
Identities = 23/127 (18%), Positives = 52/127 (40%), Gaps = 11/127 (8%)
Query: 617 PRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRI 676
+K+ I VIGKGG I+ + ++ G +ID+ G++ I
Sbjct: 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDV-------KPLEEEEEGEKVPVEI 537
Query: 677 EKLTES--VQIGKVYTGIVLRLF-DFGAIIRILSGKDGLLHISQISSKRVNIITDFLKEN 733
E+ + + +G + G +R++ + + G++ I + S+ I + +
Sbjct: 538 EEKGKHIVLYVGPDFAGKPVRIYAGDEYLFTATVSRKGVVKIRK-DSEVGKEIEEAIDNG 596
Query: 734 QKVRVKV 740
+ +R +
Sbjct: 597 RDIRASL 603
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 38.7 bits (91), Expect = 0.012
Identities = 23/147 (15%), Positives = 54/147 (36%), Gaps = 22/147 (14%)
Query: 609 KNELSKFAP----------RLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGI 658
+ E+ ++ P + + I VIGKGG I+ + ++ G ID+
Sbjct: 462 EREIKRYLPGPVEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521
Query: 659 ITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD-----FGAIIRILSGKDGLL 713
+ + + + +G Y G + ++ F A + + G +
Sbjct: 522 EPGEEAEEGEEVTVEETKKHVI--LIVGPDYAGKTVDVYAGGEYLFTATV----SRKGEI 575
Query: 714 HISQISSKRVNIITDFLKENQKVRVKV 740
+++ +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: 682 SVQIGKVYTGIVLRLFDFGAIIRILS----------GKDGLLHISQISSKRVNIITDFLK 731
++ G + G V+ + + A++RI+S K +HISQ+S V +TD K
Sbjct: 61 LLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFK 120
Query: 732 ENQKVRVKVLGIDD 745
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 = 0.017
Identities = 14/45 (31%), Positives = 25/45 (55%)
Query: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL 415
++ L + +R D R +++ RP S+ G + GS+L G+T L
Sbjct: 10 RRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVL 54
>gnl|CDD|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E';
Provisional.
Length = 187
Score = 36.7 bits (86), Expect = 0.018
Identities = 27/88 (30%), Positives = 42/88 (47%), Gaps = 20/88 (22%)
Query: 684 QIGKVYTGIVLRLFDFGAIIRILSGK-DGLLHISQISSKRVNIITD-----------FLK 731
++ +V G V+ + +FGA +RI G DGLLHISQI ++ LK
Sbjct: 80 ELQEVVEGEVVEVVEFGAFVRI--GPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLK 137
Query: 732 ENQKVRVKVLGI-----DDRG-RIKLSM 753
VR +++ + RG +I L+M
Sbjct: 138 VGDVVRARIVAVSLKERRPRGSKIGLTM 165
>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 = 37.3 bits (87), Expect = 0.020
Identities = 18/38 (47%), Positives = 24/38 (63%)
Query: 622 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGII 659
+KI PSK+ VIGK GS + L E+TG +I + G I
Sbjct: 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNGRI 187
>gnl|CDD|223631 COG0557, VacB, Exoribonuclease R [Transcription].
Length = 706
Score = 37.8 bits (88), Expect = 0.023
Identities = 23/103 (22%), Positives = 46/103 (44%), Gaps = 19/103 (18%)
Query: 670 QEAKRRIEKLTESV----QIGKVYTGIVLRLFDFGAIIRILS-GKDGLLHISQISSKRV- 723
QEA+R + L ++ ++G+ + G+V + FG + + G +GL+HIS +
Sbjct: 603 QEAERDVIDLLKAEYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYH 662
Query: 724 -----------NIITDFLKENQKVRVKVLGID-DRGRIKLSMI 754
+ + +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 = 34.0 bits (79), Expect = 0.024
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 745
G + G V+ + D ++ I +G++ IS+ S + D +K +V V VL ++D
Sbjct: 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVED 60
Query: 746 R-GRIKLS 752
G + LS
Sbjct: 61 EEGNVVLS 68
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E'
[Transcription].
Length = 183
Score = 35.7 bits (83), Expect = 0.042
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 12/70 (17%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS-------SKRVNIITD----FLKENQ 734
G+V G V+ + +FGA +RI DGL+H+SQI K +I + LK
Sbjct: 82 GEVVEGEVVEVVEFGAFVRIGP-LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGD 140
Query: 735 KVRVKVLGID 744
KVR +++G+
Sbjct: 141 KVRARIVGVS 150
>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 = 0.053
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 10/53 (18%)
Query: 632 VIGKGGSTIRTLTEETGTQIDI-------NDEGIITI-ASFNSVSGQEAKRRI 676
+IGKGGSTI+ + EETG +I + + E ++TI ++V Q+A I
Sbjct: 14 IIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAV--QKALLLI 64
>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: 680 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVK 739
E V+ GK Y GIV R+ +G + + S GL+H + + D ++ V+
Sbjct: 117 MEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGDPDYAVGD------EIIVQ 170
Query: 740 VLGIDDRGRIKLSMIY 755
V + ++
Sbjct: 171 VSDVRPEKG-EIDFEP 185
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 35.1 bits (81), Expect = 0.15
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 632 VIGKGGSTIRTLTEETGTQIDIND-EGIITIASFNSVSGQEAKRRIEKLTESVQI 685
+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 = 0.15
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 374 LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVAT 419
L +GLR+D RG+++ RPI I +G + G T+ L +
Sbjct: 13 LKEGLRLDGRGLDEFRPIKIT---FGLEYGCVEVSLGKTRVLAQVS 55
>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 = 0.24
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI 653
+ + ++ 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 = 33.4 bits (77), Expect = 0.28
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 627 SKIRD-VIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQI 685
+I+ +IG+ G T R + E TG I + + + I F V + A+ +E L
Sbjct: 110 RRIKGRIIGREGKTRRAIEELTGVYISVYGKTVAIIGGFEQV--EIAREAVEMLINGAPH 167
Query: 686 GKVY 689
GKVY
Sbjct: 168 GKVY 171
Score = 31.9 bits (73), Expect = 0.87
Identities = 20/101 (19%), Positives = 44/101 (43%), Gaps = 10/101 (9%)
Query: 615 FAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITI----ASFNSVSG 669
+KI +I +IGK G + + E+TG ++ I+ G +TI + + ++
Sbjct: 5 AEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLAL 64
Query: 670 QEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKD 710
+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 = 0.41
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 632 VIGKGGSTIRTLTEETGTQIDINDE-GIITIASFNSVSGQEAKRRIEKL 679
+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 = 0.88
Identities = 10/39 (25%), Positives = 17/39 (43%)
Query: 442 LHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLP 480
+ +N+ P+ G+ P E+ G LL +LP
Sbjct: 63 VLWNVVPWHPHTPGKNRTPTPAEVEAGLRYLAELLALLP 101
>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 = 31.9 bits (72), Expect = 0.96
Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 14/85 (16%)
Query: 185 PQIDPDIASIIGVSTALSISEL--------PFLGPLGVAKVGYIDGKYILNPTTEQLKKS 236
P + P I + + + ALS+ EL P L +A G D I + +
Sbjct: 194 PLLMPAIMAALALGFALSLGELGATLMIYPPGFATLPIAIFGATDRGNIADAAALSI--- 250
Query: 237 HLDLLVAGTEKAIITVESESKQLPE 261
LL+A + A+I + + +K+L +
Sbjct: 251 ---LLLAASLLALIAIAAIAKRLGQ 272
>gnl|CDD|240278 PTZ00119, PTZ00119, 40S ribosomal protein S15; Provisional.
Length = 302
Score = 31.8 bits (72), Expect = 1.1
Identities = 16/36 (44%), Positives = 21/36 (58%)
Query: 21 DTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGL 56
DTGS VQ+ LT +I +L H L KDH +R +
Sbjct: 123 DTGSAPVQIGCLTEKILNLRAHLILRCKDHPKKRTM 158
>gnl|CDD|180524 PRK06309, PRK06309, DNA polymerase III subunit epsilon; Validated.
Length = 232
Score = 31.3 bits (71), Expect = 1.3
Identities = 14/27 (51%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 644 TEETGTQIDINDEGIITIASFNSVSGQ 670
TE TGTQID + II IA++N V+ +
Sbjct: 9 TETTGTQID--KDRIIEIAAYNGVTSE 33
>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 = 1.3
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID- 744
G V G V + + G + + G D + +S++S + K Q V+ K++ ID
Sbjct: 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDP 60
Query: 745 DRGRIKLS 752
D GRI+++
Sbjct: 61 DNGRIEMT 68
>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 = 31.2 bits (71), Expect = 1.3
Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 10/71 (14%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKD----------GLLHISQISSKRVNIITDFLKENQK 735
G + G V + + A++RI+ + +H+SQ+ V ++D +
Sbjct: 65 GDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDI 124
Query: 736 VRVKVLGIDDR 746
VR +V+ D
Sbjct: 125 VRARVISTGDP 135
>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription].
Length = 190
Score = 31.0 bits (71), Expect = 1.4
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 618 RLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDE 656
+ + + P ++ IGKGG +R ++ TG +IDI
Sbjct: 142 HVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180
>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 = 1.6
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDE-GIITIASFNSVSGQEAKRRIEK 678
+ + D K R +IG+ G IR L TG + I+D + ++ F+ V + A+ +EK
Sbjct: 208 VNLPNDEMKGR-IIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEK 266
Query: 679 L 679
L
Sbjct: 267 L 267
>gnl|CDD|184788 PRK14674, PRK14674, hypothetical protein; Provisional.
Length = 133
Score = 30.3 bits (68), Expect = 1.6
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 3/50 (6%)
Query: 43 FKLHIKDHHSRRG---LIMMKGNFLFNKIIKSFKYGSYKISIEIGEIARQ 89
++ ++HSRRG LI+ +GN L +K+ G+Y + E+ +++Q
Sbjct: 24 YEWVASNYHSRRGEVDLIVKRGNELIFVEVKARGQGNYGQACEMVTLSKQ 73
>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 = 28.7 bits (65), Expect = 1.8
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 693 VLRLFD--FGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGR 748
V++ F+ FG I GKD +H SQI + L+E +V KV+ + +
Sbjct: 3 VVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKS-----LREGDEVEFKVVSPEGGEK 55
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 29.0 bits (66), Expect = 1.9
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 616 APRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND 655
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 = 1.9
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 14/79 (17%)
Query: 676 IEKLTESVQIGKVYTGIVLRLFDF--GAIIRILSGKDGLLHISQI------------SSK 721
IE+ G +Y G V R+ A + I K+G LH S I +
Sbjct: 16 IERPKSRQLKGNIYKGRVTRVLPSLQAAFVDIGLTKNGFLHASDIGPNSECLAPAEAKRE 75
Query: 722 RVNIITDFLKENQKVRVKV 740
I++ L+ Q V V+V
Sbjct: 76 AGASISELLRPGQSVLVQV 94
>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 = 29.1 bits (66), Expect = 2.1
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 7/31 (22%)
Query: 632 VIGKGGSTIRTLTEETGT-------QIDIND 655
VIG+GG IR LTE T QID+ +
Sbjct: 52 VIGRGGKNIRELTEILETKFGLENPQIDVQE 82
>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 = 2.2
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 700 GAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID-DRGRIKLS 752
G +I + G L SQ+ + V + +++ ++++ K++ ID +R I LS
Sbjct: 14 GGLIVDIEGVRAFLPASQVDLRPVEDLDEYV--GKELKFKIIEIDRERNNIVLS 65
>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 = 2.5
Identities = 18/87 (20%), Positives = 40/87 (45%), Gaps = 19/87 (21%)
Query: 684 QIGKVYTGIVLRLFDFGAIIRILSGK-DGLLHISQ--------------ISSKRVNIITD 728
+IG+ + G++ + FG + + + +GL+HIS + +R +
Sbjct: 626 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKV-- 683
Query: 729 FLKENQKVRVKVLGID-DRGRIKLSMI 754
+ +V+V+V+ D D G+I ++
Sbjct: 684 -FRLGDRVKVRVVKADLDTGKIDFELV 709
>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 = 2.6
Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNII--TDFLKENQKVRVKVLGI 743
G + V + +++ G +H+S++ + + K QK++ +V+G
Sbjct: 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGG 60
Query: 744 DD 745
D
Sbjct: 61 HD 62
>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 = 2.8
Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID- 744
G+V G + +L G +++ GL+ ++ R+ K KV+ +VL ++
Sbjct: 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP 60
Query: 745 DRGRIKL 751
+R R+ L
Sbjct: 61 ERKRLVL 67
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 30.7 bits (69), Expect = 3.3
Identities = 10/38 (26%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 139 SFFKREGK--PSERETIISRLIDRPIRPLFPEGYLNEI 174
SF + E E+++ + RL +R +R + Y+ E+
Sbjct: 140 SFLESETTIVRKEKDSPLQRLGERLVREGMSQSYVEEM 177
>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 = 3.5
Identities = 36/127 (28%), Positives = 55/127 (43%), Gaps = 16/127 (12%)
Query: 271 GHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKIINISEHKIRKAYQIKNKQIRD 330
G K ++ N I L+QN G K N + T +K E K R A + + R
Sbjct: 24 GSGKTRVITNKIAYLIQNCGYKARNIAAV----TFTNK--AAREMKERVAKTLGKGEARG 77
Query: 331 L---TFKNISKDI----YSSLIDNENLTI-DINDINCILYDLESKIIR--KQILDKGLRI 380
L TF + DI Y++L N ++ D D +L +L +I+ K +LDK +
Sbjct: 78 LTISTFHTLGLDIIKREYNALGYKSNFSLFDETDQLALLKELTEGLIKDDKDLLDKLIST 137
Query: 381 DNRGVND 387
+ ND
Sbjct: 138 ISNWKND 144
>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 = 4.0
Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 9/57 (15%)
Query: 402 HGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIG 458
HG L+ TLG SR+E L G+ S + +N P DIG IG
Sbjct: 69 HGLYLYA-------AAETLGVSREELLDALLTGKAKYSSI--FNYPTLTWADIGVIG 116
>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 = 28.3 bits (64), Expect = 4.5
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 13/73 (17%)
Query: 414 ALVVATL-----GTSRDEQKIDALM--------GEFTDSFMLHYNMPPFATGDIGRIGVP 460
A V+A L G SR ++AL+ + F L ++ PFA G +G +GV
Sbjct: 28 AFVMALLRGRYGGGSRRRTLLEALLCGLLTLVARSALELFGLPPSLSPFAGGAVGFLGVD 87
Query: 461 KRREIGHGRLAKR 473
K RE+ + K+
Sbjct: 88 KIRELAKRLINKK 100
>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 = 4.7
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 7/62 (11%)
Query: 681 ESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKV 740
+SV++ KV D GA+ + G G +HIS +S +V T K + ++
Sbjct: 5 DSVKVTKVEP-------DLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARI 57
Query: 741 LG 742
+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 = 4.9
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 599 EKMKTEVPKCKNELSKFAPRLIT 621
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 = 5.4
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 3/35 (8%)
Query: 618 RLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQID 652
++ + P VIGK G IR L + +
Sbjct: 28 IIVVARGQPGL---VIGKKGQNIRALQKLLQKLLR 59
>gnl|CDD|184320 PRK13778, paaA, phenylacetate-CoA oxygenase subunit PaaA;
Provisional.
Length = 314
Score = 29.5 bits (67), Expect = 5.9
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 419 TLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIG 458
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 = 6.4
Identities = 20/51 (39%), Positives = 24/51 (47%), Gaps = 10/51 (19%)
Query: 388 IRPISIRTGILPRTHGSSLF-----TRGDTQAL-----VVATLGTSRDEQK 428
P I GI+P HGS+L T+G QAL A G RDE+K
Sbjct: 101 HNPDGIARGIVPFRHGSALHTDVAKTQGLKQALDHHGFDAAIGGARRDEEK 151
>gnl|CDD|235247 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
Length = 207
Score = 29.1 bits (66), Expect = 7.0
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 632 VIGKGGSTIRTLTEETGTQIDIND 655
VIG+GG IR LTE + + +
Sbjct: 54 VIGRGGKNIRELTEILEKKFGLEN 77
>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 = 7.1
Identities = 11/87 (12%), Positives = 33/87 (37%)
Query: 261 EDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKIINISEHKIRKA 320
+DI+ + + + E ++ + ++ D + ++ ++A
Sbjct: 69 DDIVEEYAPEKSYPEEWDLEGLEEELRELLGLDLDIDEEELEGLTEEELKERLIEAAKEA 128
Query: 321 YQIKNKQIRDLTFKNISKDIYSSLIDN 347
Y+ K ++ + + I + I +ID
Sbjct: 129 YEEKEAELGEELMREIERSIMLQVIDE 155
>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 = 7.3
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 285 LVQNVGQKKVNWDPIVKDKTLISKIINISEHKIRK 319
+VQNVG ++ +V K LI +++ ++ IR+
Sbjct: 261 VVQNVGTAFAIYEAVVNGKPLIERVVTVTGDAIRR 295
>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 = 28.9 bits (65), Expect = 8.3
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 7/77 (9%)
Query: 631 DVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYT 690
VIG+GG IR LTE+ + + E A+ + E++ S++
Sbjct: 51 LVIGRGGRRIRELTEKLQKKFGL--ENPQIDVEEVENPELNAQVQAERIARSLE-----R 103
Query: 691 GIVLRLFDFGAIIRILS 707
G+ R + A+ RI+
Sbjct: 104 GLHFRRAAYTAVRRIME 120
>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 = 8.6
Identities = 10/61 (16%), Positives = 20/61 (32%), Gaps = 6/61 (9%)
Query: 393 IRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATG 452
+ ++ +++AT G R+ + + G + PP TG
Sbjct: 173 VTGVVVENRRNGREVRIRAIAGVLLATGGFGRNAELLLPAAGYADTTG------PPANTG 226
Query: 453 D 453
D
Sbjct: 227 D 227
>gnl|CDD|225285 COG2429, COG2429, Archaeal GTP cyclohydrolase III [Nucleotide
transport and metabolism].
Length = 250
Score = 29.0 bits (65), Expect = 9.1
Identities = 18/87 (20%), Positives = 36/87 (41%), Gaps = 1/87 (1%)
Query: 655 DEGIITIASFNSVSGQEAKRRIEK-LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLL 713
+G + IA F+ I +I +VY ++ L GA++ L G + +
Sbjct: 128 TDGYVQIAHFDVNDATGTYTDIVSPYDTYTEIQRVYATLMRFLEKIGALLFFLGGDNIMA 187
Query: 714 HISQISSKRVNIITDFLKENQKVRVKV 740
+S+ V + ++ +V +KV
Sbjct: 188 VCPGLSAGDVLDAIAEVLDDAEVDLKV 214
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 0.385
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: 38,974,017
Number of extensions: 4041812
Number of successful extensions: 4349
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4245
Number of HSP's successfully gapped: 218
Length of query: 755
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 651
Effective length of database: 6,324,786
Effective search space: 4117435686
Effective search space used: 4117435686
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: 63 (27.9 bits)