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exoribonuclease II [Saccharomyces cerevisiae S288C]
Protein Classification
ribonuclease catalytic domain-containing protein ( domain architecture ID 10466333 )
ribonuclease catalytic domain-containing protein may function as a 3'-5'exoribonuclease
List of domain hits
Name
Accession
Description
Interval
E-value
RNB
pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
522-852
2.06e-73
RNB domain; This domain is the catalytic domain of ribonuclease II.
:Pssm-ID: 459934 [Multi-domain]
Cd Length: 314
Bit Score: 244.50
E-value: 2.06e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 522 R Y D FG DL RVFC ID SET A HEI DD GV SV KNYG r D G L Y T L YI HIAD PTSMF P ESTNV D I E gistdilnv A L KR SFTT YLPD T V 601
Cdd:pfam00773 1 R K D LR DL PFIT ID PAD A KDL DD AI SV EKLP - N G G Y R L GV HIAD VSHYV P PGSPL D R E --------- A R KR GTSV YLPD R V 70
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 602 V PMLP QS ---- I C H L sdlg KQ G QRTKTI S FSVDVKITSKCS gksieimyd S FK I RKGIVSNFPKA TYE D VD RI L GTPNS E 677
Cdd:pfam00773 71 I PMLP EK lsnd L C S L ---- NP G EDRLAL S VEITIDADGEVT --------- S YE I YPSVIRSKARL TYE E VD DL L EGKDA E 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 678 ASP -- VKK DL ES L SMIS K L LR EQ R IKNSNAV ifgeg FNKGLVM L NA D S EG ELTEVT fsd QE E T LSTI L VS E M M I LAN TLT 755
Cdd:pfam00773 138 KDK pd LAE DL RL L YELA K I LR AK R LQRGALD ----- LDTPENK L IL D E EG VIDILI --- QE R T DAHS L IE E F M L LAN EAV 209
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 756 G R YFA E NK I GGVF R CYK qlplg E VAQQQYD S M I TSTKKGIFP K -- L K DIV K LSS ----------- LLNSSF Y TGR P FR H E 822
Cdd:pfam00773 210 A R HLQ E LG I PALY R VHP ----- E PDLEKLN S L I KLLQLLPDD K gl S K SLE K IKD derllsilllr TMPRAE Y SPE P LG H F 284
330 340 350
....*....|....*....|....*....|
gi 6323943 823 MI G AKQ Y LTV TSP L RR F PDLI N H L Q IHRH L 852
Cdd:pfam00773 285 GL G LDI Y THF TSP I RR Y PDLI V H R Q LKAL L 314
Name
Accession
Description
Interval
E-value
RNB
pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
522-852
2.06e-73
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain]
Cd Length: 314
Bit Score: 244.50
E-value: 2.06e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 522 R Y D FG DL RVFC ID SET A HEI DD GV SV KNYG r D G L Y T L YI HIAD PTSMF P ESTNV D I E gistdilnv A L KR SFTT YLPD T V 601
Cdd:pfam00773 1 R K D LR DL PFIT ID PAD A KDL DD AI SV EKLP - N G G Y R L GV HIAD VSHYV P PGSPL D R E --------- A R KR GTSV YLPD R V 70
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 602 V PMLP QS ---- I C H L sdlg KQ G QRTKTI S FSVDVKITSKCS gksieimyd S FK I RKGIVSNFPKA TYE D VD RI L GTPNS E 677
Cdd:pfam00773 71 I PMLP EK lsnd L C S L ---- NP G EDRLAL S VEITIDADGEVT --------- S YE I YPSVIRSKARL TYE E VD DL L EGKDA E 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 678 ASP -- VKK DL ES L SMIS K L LR EQ R IKNSNAV ifgeg FNKGLVM L NA D S EG ELTEVT fsd QE E T LSTI L VS E M M I LAN TLT 755
Cdd:pfam00773 138 KDK pd LAE DL RL L YELA K I LR AK R LQRGALD ----- LDTPENK L IL D E EG VIDILI --- QE R T DAHS L IE E F M L LAN EAV 209
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 756 G R YFA E NK I GGVF R CYK qlplg E VAQQQYD S M I TSTKKGIFP K -- L K DIV K LSS ----------- LLNSSF Y TGR P FR H E 822
Cdd:pfam00773 210 A R HLQ E LG I PALY R VHP ----- E PDLEKLN S L I KLLQLLPDD K gl S K SLE K IKD derllsilllr TMPRAE Y SPE P LG H F 284
330 340 350
....*....|....*....|....*....|
gi 6323943 823 MI G AKQ Y LTV TSP L RR F PDLI N H L Q IHRH L 852
Cdd:pfam00773 285 GL G LDI Y THF TSP I RR Y PDLI V H R Q LKAL L 314
RNB
smart00955
This domain is the catalytic domain of ribonuclease II;
522-854
2.48e-53
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain]
Cd Length: 286
Bit Score: 187.86
E-value: 2.48e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 522 R Y D FG DL RV F C ID S E T A HE IDD G VSV KNYG r D G L Y T L YI HIAD PTSMFPESTNV D I E gistdilnv A L KR SFTT YLPD T V 601
Cdd:smart00955 1 R V D LR DL PL F T ID P E D A KD IDD A VSV EKLD - N G G Y R L GV HIAD VSHYVKPGSAL D R E --------- A R KR GTSV YLPD R V 70
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 602 V PMLP QSICH ls D L GKQGQRTKTISF SV DVKITSK cs G KS I E imyd SFKIRKGIVSNFPKA TYE D VD R IL gtpnseaspv 681
Cdd:smart00955 71 I PMLP EELSN -- G L CSLNPGEDRLAL SV EMTLDAD -- G GE I L ---- DYEFYRSVIRSKARL TYE E VD A IL ---------- 132
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 682 kkdleslsmiskllreqrikns NAVIF gegfnkglvmlna D S EG ELTEVTF sd Q E ETLSTI LV S E M MILAN TLTG R YF A E 761
Cdd:smart00955 133 ---------------------- EKIVL ------------- D E EG KIEDIVP -- R E RNDAHS LV E E F MILAN EAVA R FL A K 175
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 762 N K I G G VF R CYKQLPLGEV A QQQYDSM it STKKGIFPKLKDIVK L SS LL NSSFYT ---------- G R PFR H EMIG ------ 825
Cdd:smart00955 176 N G I P G LY R VHEGPDPEKL A ELLKEFL -- ALLGLLLLGGDGPKA L AK LL EKIRDS peerllelll L R SMP H AEYS vdnsgh 253
330 340 350
....*....|....*....|....*....|...
gi 6323943 826 ---- AKQ Y LTV TSP L RR F PDLI N H L Q IHRH L QK 854
Cdd:smart00955 254 fgla LDA Y THF TSP I RR Y PDLI V H R Q LKAA L RG 286
3_prime_RNase
TIGR00358
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ...
387-967
3.23e-31
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases. [Transcription, Degradation of RNA]
Pssm-ID: 273033 [Multi-domain]
Cd Length: 654
Bit Score: 130.99
E-value: 3.23e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 387 A Q V IEK LE ------ ANSYREV N K F VKL V -- NE R K Y R DI salypsviqllkd FAAGNFHN N GI iv A LIS K IFRKIER Y kdc 458
Cdd:TIGR00358 72 A E V ERI LE paltrf VGKFLGE N D F GFV V pd DP R I Y L DI ------------- IVPKASVK N EL -- A EGD K VVVELTE Y --- 133
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 459 DIT R DICQDL I NE I TP N S ip NPL L LNMDLA L PASSKLVKW ---- Q Q KLYD L TNIEEL Q W KK sgtdd D R Y D FG DL RVFC ID 534
Cdd:TIGR00358 134 PLR R NLFYGE I TQ I LG N N -- DDP L IPWWVT L ARHEIPFEF pdgv E Q QAAK L QFDVDE Q A KK ----- Y R E D LT DL AFVT ID 206
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 535 SET A HEI DD G V S VK NY g R DG LYT LY IH IAD PTSMFP E STNV D I E gistdilnv A LK R S F TT YLP DT V V PMLP Q ---- SI C 610
Cdd:TIGR00358 207 GAD A KDL DD A V Y VK KL - P DG GWK LY VA IAD VSYYVA E NSPL D K E --------- A KH R G F SV YLP GF V I PMLP E elsn GL C 276
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 611 H L SDLGKQGQRTKTISF S VDVK IT SK csgksieimydsf KIRKGIVSNFPKA TY ED V DRI L --- GTPNS E ASPVKKD L ES 687
Cdd:TIGR00358 277 S L NPNEDRLVLVCEMTI S AQGR IT DN ------------- EFYPATIESKARL TY DK V NDW L end DELQP E YETLVEQ L KA 343
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 688 L SMI S KL L R E Q R i KNSNAVI F GEGFN K GL V mlna D S EG ELTEVTF sd QEETLSTILVS E M MI L AN TLTG R YFAEN K IG G V 767
Cdd:TIGR00358 344 L HQL S QA L G E W R - HKRGLID F EHPET K FI V ---- D E EG RVIDIVA -- EVRRIAEKIIE E A MI V AN ICAA R FLHNH K VP G I 416
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 768 F R CYK ------------------- Q LP --- LGE V AQQQYDSMITST K KGIFPKLKDIVK L S SL l NSSF Y TGR P FR H EMI G 825
Cdd:TIGR00358 417 Y R VHP gpskkklqslleflaelgl T LP ggn AEN V TTLDGACWLREV K DRPEYEILVTRL L R SL - SQAE Y SPE P LG H FGL G 495
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 826 AKQ Y LTV TSP L RR F PDL I NH LQ I HRH L q K K PLCFNQTQI -- D S L IWPIQSRA D ILK R --- A S R NSSTYWTLN YL KK ltkl 900
Cdd:TIGR00358 496 LEH Y AHF TSP I RR Y PDL T NH RL I KAV L - A K EQTDTERYQ pq D E L LQIAEHCS D TER R ard A E R DVADWLKCR YL LD ---- 570
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 901 EPERT F DVMVT SV --------- PQ NG FT G CV -------- FPDLSFARGT L KLHPSSMH Y p M IGD I V K n C K ISKIDCLEGM 963
Cdd:TIGR00358 571 KVGTE F SGEIS SV trfgmfvrl DD NG ID G LI histlhnd YYVFDQEKMA L IGKGTGKV Y - R IGD R V T - V K LTEVNMETRS 648
....
gi 6323943 964 LEL E 967
Cdd:TIGR00358 649 IIF E 652
VacB
COG0557
Exoribonuclease R [Transcription];
521-856
2.15e-29
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain]
Cd Length: 711
Bit Score: 125.60
E-value: 2.15e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 521 D R Y D FG DL RVFC ID S E T A HEI DD G VS VK n YGRD G LYT L YI HIAD PTSMFPESTNV D I E gistdilnv A L KR SFTT YLPD T 600
Cdd:COG0557 244 G R R D LR DL PLVT ID G E D A KDF DD A VS AE - KLDN G GWR L GV HIAD VSHYVRPGSAL D R E --------- A R KR GTSV YLPD R 313
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 601 V V PMLP QS ---- I C H L sdlg KQ G Q - R tkt ISF S VDVK I TS K cs G KSI eimyd S FKIRKGIV - S nfp K A -- TYE D V DR IL G 672
Cdd:COG0557 314 V I PMLP ER lsng L C S L ---- NP G E d R --- LAM S CEME I DA K -- G EVV ----- S YEFYRSVI r S --- D A rl TYE E V QA IL D 376
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 673 TPNS E AS ---- PVKKD LE S L SMIS K L LR EQ R iknsnavifgeg FNK G LVMLNA ------- D S EG ELTEVTFS dq E ETLST 741
Cdd:COG0557 377 GKDE E LR eeya DLVPM LE E L YELA K I LR KA R ------------ EKR G AIDFDL petkiil D E EG KPEDIVPR -- E RNDAH 442
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 742 I L VS E M M I LAN TLTGRYFAEN K IGGVF R C -------------------- Y K q L PL G EVAQ - QQYDSMITST K KGIFPK L k 800
Cdd:COG0557 443 K L IE E F M L LAN EAVAEFLEKL K LPFLY R V heepdpeklealreflanlg L K - L KG G DEPT p KDLQKLLEQV K GRPEEE L - 520
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 801 divk L SS LL NS S ---- F Y TGRPFR H EMIGAKQ Y LTV TSP L RR F PDL IN H LQIHRH L QK K P 856
Cdd:COG0557 521 ---- L NT LL LR S mkqa V Y SPENIG H FGLALEA Y THF TSP I RR Y PDL LV H RALKAY L EG K R 576
PRK05054
PRK05054
exoribonuclease II; Provisional
491-856
1.90e-14
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain]
Cd Length: 644
Bit Score: 77.61
E-value: 1.90e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 491 A SSKLVK W QQK L -- YD L TNIE --- ELQ W KKSGTDDD R Y D FGD L RVFC IDS ETAHEI DD GVS V KNYGRD GL y T L YIH IADP 565
Cdd:PRK05054 154 A DDHFAP W WVT L ar HN L EREA pag GVA W EMLDEGLE R E D LTA L DFVT IDS ASTEDM DD ALY V EKLPDG GL - Q L TVA IADP 232
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 566 T SMFP E STNV D iegistdil NV A LK R S FT T YLP DTVV PMLP Q sic H LSD ------------------- LGKQ G QRTKT I S 626
Cdd:PRK05054 233 T AYIA E GSKL D --------- KA A RQ R A FT N YLP GFNI PMLP R --- E LSD dlcslrpnerrpalacrvt IDAD G TIEDD I R 300
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 627 F s VDVK I T SK cs G K sie IM YD S fkirkgi VS NF pkat Y E DVDR il GT P N SEA sp VKKDLES L SMISKLLR E Q R IK ns N A V 706
Cdd:PRK05054 301 F - FAAW I E SK -- A K --- LA YD N ------- VS DW ---- L E NGGD -- WQ P E SEA -- IAEQIRL L HQFCLARS E W R KQ -- H A L 357
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 707 I F GEGFNKGLV m L NAD se GE LTEV t FSDQEETLST I l V S E M MI L AN TLTG R YFAENKIG G VFRC --- YKQLPLGEVAQ -- 781
Cdd:PRK05054 358 V F KDRPDYRFE - L GEK -- GE VLDI - VAEPRRIANR I - V E E S MI A AN ICAA R VLRDKLGF G IYNV hsg FDPANAEQAVA ll 432
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 782 QQYD sm ITSTKKGI ----- F P KL K - DIVKLS slln SSFYTG R ------------- P FR H EMI G AKQ Y L T V TSP L R RFP D L 842
Cdd:PRK05054 433 KEHG -- LHFDAEEL ltleg F C KL R r ELDAQP ---- TGYLDS R irrfqsfaeiste P GP H FGL G LEA Y A T W TSP I R KYG D M 506
410
....*....|....
gi 6323943 843 INH LQIHRHLQKKP 856
Cdd:PRK05054 507 INH RLLKAVIKGET 520
Name
Accession
Description
Interval
E-value
RNB
pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
522-852
2.06e-73
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain]
Cd Length: 314
Bit Score: 244.50
E-value: 2.06e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 522 R Y D FG DL RVFC ID SET A HEI DD GV SV KNYG r D G L Y T L YI HIAD PTSMF P ESTNV D I E gistdilnv A L KR SFTT YLPD T V 601
Cdd:pfam00773 1 R K D LR DL PFIT ID PAD A KDL DD AI SV EKLP - N G G Y R L GV HIAD VSHYV P PGSPL D R E --------- A R KR GTSV YLPD R V 70
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 602 V PMLP QS ---- I C H L sdlg KQ G QRTKTI S FSVDVKITSKCS gksieimyd S FK I RKGIVSNFPKA TYE D VD RI L GTPNS E 677
Cdd:pfam00773 71 I PMLP EK lsnd L C S L ---- NP G EDRLAL S VEITIDADGEVT --------- S YE I YPSVIRSKARL TYE E VD DL L EGKDA E 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 678 ASP -- VKK DL ES L SMIS K L LR EQ R IKNSNAV ifgeg FNKGLVM L NA D S EG ELTEVT fsd QE E T LSTI L VS E M M I LAN TLT 755
Cdd:pfam00773 138 KDK pd LAE DL RL L YELA K I LR AK R LQRGALD ----- LDTPENK L IL D E EG VIDILI --- QE R T DAHS L IE E F M L LAN EAV 209
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 756 G R YFA E NK I GGVF R CYK qlplg E VAQQQYD S M I TSTKKGIFP K -- L K DIV K LSS ----------- LLNSSF Y TGR P FR H E 822
Cdd:pfam00773 210 A R HLQ E LG I PALY R VHP ----- E PDLEKLN S L I KLLQLLPDD K gl S K SLE K IKD derllsilllr TMPRAE Y SPE P LG H F 284
330 340 350
....*....|....*....|....*....|
gi 6323943 823 MI G AKQ Y LTV TSP L RR F PDLI N H L Q IHRH L 852
Cdd:pfam00773 285 GL G LDI Y THF TSP I RR Y PDLI V H R Q LKAL L 314
RNB
smart00955
This domain is the catalytic domain of ribonuclease II;
522-854
2.48e-53
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain]
Cd Length: 286
Bit Score: 187.86
E-value: 2.48e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 522 R Y D FG DL RV F C ID S E T A HE IDD G VSV KNYG r D G L Y T L YI HIAD PTSMFPESTNV D I E gistdilnv A L KR SFTT YLPD T V 601
Cdd:smart00955 1 R V D LR DL PL F T ID P E D A KD IDD A VSV EKLD - N G G Y R L GV HIAD VSHYVKPGSAL D R E --------- A R KR GTSV YLPD R V 70
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 602 V PMLP QSICH ls D L GKQGQRTKTISF SV DVKITSK cs G KS I E imyd SFKIRKGIVSNFPKA TYE D VD R IL gtpnseaspv 681
Cdd:smart00955 71 I PMLP EELSN -- G L CSLNPGEDRLAL SV EMTLDAD -- G GE I L ---- DYEFYRSVIRSKARL TYE E VD A IL ---------- 132
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 682 kkdleslsmiskllreqrikns NAVIF gegfnkglvmlna D S EG ELTEVTF sd Q E ETLSTI LV S E M MILAN TLTG R YF A E 761
Cdd:smart00955 133 ---------------------- EKIVL ------------- D E EG KIEDIVP -- R E RNDAHS LV E E F MILAN EAVA R FL A K 175
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 762 N K I G G VF R CYKQLPLGEV A QQQYDSM it STKKGIFPKLKDIVK L SS LL NSSFYT ---------- G R PFR H EMIG ------ 825
Cdd:smart00955 176 N G I P G LY R VHEGPDPEKL A ELLKEFL -- ALLGLLLLGGDGPKA L AK LL EKIRDS peerllelll L R SMP H AEYS vdnsgh 253
330 340 350
....*....|....*....|....*....|...
gi 6323943 826 ---- AKQ Y LTV TSP L RR F PDLI N H L Q IHRH L QK 854
Cdd:smart00955 254 fgla LDA Y THF TSP I RR Y PDLI V H R Q LKAA L RG 286
3_prime_RNase
TIGR00358
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ...
387-967
3.23e-31
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases. [Transcription, Degradation of RNA]
Pssm-ID: 273033 [Multi-domain]
Cd Length: 654
Bit Score: 130.99
E-value: 3.23e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 387 A Q V IEK LE ------ ANSYREV N K F VKL V -- NE R K Y R DI salypsviqllkd FAAGNFHN N GI iv A LIS K IFRKIER Y kdc 458
Cdd:TIGR00358 72 A E V ERI LE paltrf VGKFLGE N D F GFV V pd DP R I Y L DI ------------- IVPKASVK N EL -- A EGD K VVVELTE Y --- 133
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 459 DIT R DICQDL I NE I TP N S ip NPL L LNMDLA L PASSKLVKW ---- Q Q KLYD L TNIEEL Q W KK sgtdd D R Y D FG DL RVFC ID 534
Cdd:TIGR00358 134 PLR R NLFYGE I TQ I LG N N -- DDP L IPWWVT L ARHEIPFEF pdgv E Q QAAK L QFDVDE Q A KK ----- Y R E D LT DL AFVT ID 206
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 535 SET A HEI DD G V S VK NY g R DG LYT LY IH IAD PTSMFP E STNV D I E gistdilnv A LK R S F TT YLP DT V V PMLP Q ---- SI C 610
Cdd:TIGR00358 207 GAD A KDL DD A V Y VK KL - P DG GWK LY VA IAD VSYYVA E NSPL D K E --------- A KH R G F SV YLP GF V I PMLP E elsn GL C 276
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 611 H L SDLGKQGQRTKTISF S VDVK IT SK csgksieimydsf KIRKGIVSNFPKA TY ED V DRI L --- GTPNS E ASPVKKD L ES 687
Cdd:TIGR00358 277 S L NPNEDRLVLVCEMTI S AQGR IT DN ------------- EFYPATIESKARL TY DK V NDW L end DELQP E YETLVEQ L KA 343
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 688 L SMI S KL L R E Q R i KNSNAVI F GEGFN K GL V mlna D S EG ELTEVTF sd QEETLSTILVS E M MI L AN TLTG R YFAEN K IG G V 767
Cdd:TIGR00358 344 L HQL S QA L G E W R - HKRGLID F EHPET K FI V ---- D E EG RVIDIVA -- EVRRIAEKIIE E A MI V AN ICAA R FLHNH K VP G I 416
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 768 F R CYK ------------------- Q LP --- LGE V AQQQYDSMITST K KGIFPKLKDIVK L S SL l NSSF Y TGR P FR H EMI G 825
Cdd:TIGR00358 417 Y R VHP gpskkklqslleflaelgl T LP ggn AEN V TTLDGACWLREV K DRPEYEILVTRL L R SL - SQAE Y SPE P LG H FGL G 495
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 826 AKQ Y LTV TSP L RR F PDL I NH LQ I HRH L q K K PLCFNQTQI -- D S L IWPIQSRA D ILK R --- A S R NSSTYWTLN YL KK ltkl 900
Cdd:TIGR00358 496 LEH Y AHF TSP I RR Y PDL T NH RL I KAV L - A K EQTDTERYQ pq D E L LQIAEHCS D TER R ard A E R DVADWLKCR YL LD ---- 570
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 901 EPERT F DVMVT SV --------- PQ NG FT G CV -------- FPDLSFARGT L KLHPSSMH Y p M IGD I V K n C K ISKIDCLEGM 963
Cdd:TIGR00358 571 KVGTE F SGEIS SV trfgmfvrl DD NG ID G LI histlhnd YYVFDQEKMA L IGKGTGKV Y - R IGD R V T - V K LTEVNMETRS 648
....
gi 6323943 964 LEL E 967
Cdd:TIGR00358 649 IIF E 652
VacB
COG0557
Exoribonuclease R [Transcription];
521-856
2.15e-29
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain]
Cd Length: 711
Bit Score: 125.60
E-value: 2.15e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 521 D R Y D FG DL RVFC ID S E T A HEI DD G VS VK n YGRD G LYT L YI HIAD PTSMFPESTNV D I E gistdilnv A L KR SFTT YLPD T 600
Cdd:COG0557 244 G R R D LR DL PLVT ID G E D A KDF DD A VS AE - KLDN G GWR L GV HIAD VSHYVRPGSAL D R E --------- A R KR GTSV YLPD R 313
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 601 V V PMLP QS ---- I C H L sdlg KQ G Q - R tkt ISF S VDVK I TS K cs G KSI eimyd S FKIRKGIV - S nfp K A -- TYE D V DR IL G 672
Cdd:COG0557 314 V I PMLP ER lsng L C S L ---- NP G E d R --- LAM S CEME I DA K -- G EVV ----- S YEFYRSVI r S --- D A rl TYE E V QA IL D 376
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 673 TPNS E AS ---- PVKKD LE S L SMIS K L LR EQ R iknsnavifgeg FNK G LVMLNA ------- D S EG ELTEVTFS dq E ETLST 741
Cdd:COG0557 377 GKDE E LR eeya DLVPM LE E L YELA K I LR KA R ------------ EKR G AIDFDL petkiil D E EG KPEDIVPR -- E RNDAH 442
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 742 I L VS E M M I LAN TLTGRYFAEN K IGGVF R C -------------------- Y K q L PL G EVAQ - QQYDSMITST K KGIFPK L k 800
Cdd:COG0557 443 K L IE E F M L LAN EAVAEFLEKL K LPFLY R V heepdpeklealreflanlg L K - L KG G DEPT p KDLQKLLEQV K GRPEEE L - 520
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 801 divk L SS LL NS S ---- F Y TGRPFR H EMIGAKQ Y LTV TSP L RR F PDL IN H LQIHRH L QK K P 856
Cdd:COG0557 521 ---- L NT LL LR S mkqa V Y SPENIG H FGLALEA Y THF TSP I RR Y PDL LV H RALKAY L EG K R 576
Rnb
COG4776
Exoribonuclease II [Transcription];
521-856
8.15e-17
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain]
Cd Length: 644
Bit Score: 85.29
E-value: 8.15e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 521 D R Y D FGD L RVFC IDSE TAHEI DD GVSVK n YGRD G LYT L YIH IADPT SMF PE STNV D iegistdil NV A LK R S FT T YLP DT 600
Cdd:COG4776 189 E R E D LTA L PFVT IDSE STEDM DD ALYIE - KLEN G GWK L TVA IADPT AYI PE GSEL D --------- KE A RQ R A FT N YLP GF 258
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 601 VV PMLP Q sic H LSD ------------------- LGKQ G QRTKT I S F SVDV k I T SK cs G K sie IM YD S fkirkgi VS NF pk 661
Cdd:COG4776 259 NI PMLP R --- E LSD dlcslkenekrpalvcrvt IDAD G SIGDD I E F FAAW - I R SK -- A K --- LA YD N ------- VS DW -- 320
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 662 at Y E DVDR il GT P NS E A sp VKKDLES L SMISKLLREQ R IK ns N A VI F GEGFNKGLVM lna D SE G ELTEV t FSDQEETLST 741
Cdd:COG4776 321 -- L E GKGE -- WQ P EN E E -- IAEQIRL L HQFALARSQW R QQ -- H A LV F KDRPDYRFEL --- D EK G NVLDI - HAEPRRIANR 388
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 742 I l V S E M MI L AN TLTG R YFA E NKIG G V F RCY --- KQLP L GEVAQ -- QQYD sm I TSTKKGIF p K L KDIVK L SSL L N --- S S F 813
Cdd:COG4776 389 I - V E E A MI A AN ICAA R VLR E HLGF G I F NVH sgf DPEK L EQAVE ll AEHG -- I EFDPEQLL - T L EGFCA L RRE L D aqp T S Y 464
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 6323943 814 YTG R ------------- P FR H EMI G AKQ Y L T V TSP L R RFP D LI NH LQ I HRHLQKK P 856
Cdd:COG4776 465 LDS R lrrfqtfaeiste P GP H FGL G LDA Y A T W TSP I R KYG D MV NH RL I KAVILGQ P 520
PRK05054
PRK05054
exoribonuclease II; Provisional
491-856
1.90e-14
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain]
Cd Length: 644
Bit Score: 77.61
E-value: 1.90e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 491 A SSKLVK W QQK L -- YD L TNIE --- ELQ W KKSGTDDD R Y D FGD L RVFC IDS ETAHEI DD GVS V KNYGRD GL y T L YIH IADP 565
Cdd:PRK05054 154 A DDHFAP W WVT L ar HN L EREA pag GVA W EMLDEGLE R E D LTA L DFVT IDS ASTEDM DD ALY V EKLPDG GL - Q L TVA IADP 232
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 566 T SMFP E STNV D iegistdil NV A LK R S FT T YLP DTVV PMLP Q sic H LSD ------------------- LGKQ G QRTKT I S 626
Cdd:PRK05054 233 T AYIA E GSKL D --------- KA A RQ R A FT N YLP GFNI PMLP R --- E LSD dlcslrpnerrpalacrvt IDAD G TIEDD I R 300
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 627 F s VDVK I T SK cs G K sie IM YD S fkirkgi VS NF pkat Y E DVDR il GT P N SEA sp VKKDLES L SMISKLLR E Q R IK ns N A V 706
Cdd:PRK05054 301 F - FAAW I E SK -- A K --- LA YD N ------- VS DW ---- L E NGGD -- WQ P E SEA -- IAEQIRL L HQFCLARS E W R KQ -- H A L 357
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 707 I F GEGFNKGLV m L NAD se GE LTEV t FSDQEETLST I l V S E M MI L AN TLTG R YFAENKIG G VFRC --- YKQLPLGEVAQ -- 781
Cdd:PRK05054 358 V F KDRPDYRFE - L GEK -- GE VLDI - VAEPRRIANR I - V E E S MI A AN ICAA R VLRDKLGF G IYNV hsg FDPANAEQAVA ll 432
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 782 QQYD sm ITSTKKGI ----- F P KL K - DIVKLS slln SSFYTG R ------------- P FR H EMI G AKQ Y L T V TSP L R RFP D L 842
Cdd:PRK05054 433 KEHG -- LHFDAEEL ltleg F C KL R r ELDAQP ---- TGYLDS R irrfqsfaeiste P GP H FGL G LEA Y A T W TSP I R KYG D M 506
410
....*....|....
gi 6323943 843 INH LQIHRHLQKKP 856
Cdd:PRK05054 507 INH RLLKAVIKGET 520
PRK11642
PRK11642
ribonuclease R;
522-855
2.05e-13
ribonuclease R;
Pssm-ID: 236944 [Multi-domain]
Cd Length: 813
Bit Score: 74.39
E-value: 2.05e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 522 R Y D FG DL RVFC ID S E T A HEI DD G V SVKN y G R D G LYT L YIH IAD PTSMFPES T NV D I E gistdilnv A LK R SFTT Y L P DT V 601
Cdd:PRK11642 260 R V D LR DL PLVT ID G E D A RDF DD A V YCEK - K R G G GWR L WVA IAD VSYYVRPP T PL D R E --------- A RN R GTSV Y F P SQ V 329
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 602 VPMLP QSICH - L SD L GK Q GQ R tkt ISFSVDVK I T SK cs G K sieim YDSF K IRKGIV S NFPKA TY ED V DR IL - G TPN -- SE 677
Cdd:PRK11642 330 VPMLP EVLSN g L CS L NP Q VD R --- LCMVCEMT I S SK -- G R ----- LTGY K FYEAVM S SHARL TY TK V WH IL q G DQD lr EQ 399
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 678 AS P VK K D LE S L SMIS K L L --- RE Q R ikns NAVI F GEGFN K gl VML NA DSEG E LT E V T FSDQEET lsti L VS E M MILAN TL 754
Cdd:PRK11642 400 YA P LV K H LE E L HNLY K V L dka RE E R ---- GGIS F ESEEA K -- FIF NA ERRI E RI E Q T QRNDAHK ---- L IE E C MILAN IS 469
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943 755 TG R YFAEN K IGGV FR CYKQ l P l GEV A QQQYD S MIT ---- STKK G IF P KLK D ivk LSS LL N S sf YTG RP f RH EM I ------ 824
Cdd:PRK11642 470 AA R FVEKA K EPAL FR IHDK - P - STE A ITSFR S VLA elgl ELPG G NK P EPR D --- YAE LL E S -- VAD RP - DA EM L qtmllr 541
330 340 350 360
....*....|....*....|....*....|....*....|....*...
gi 6323943 825 GA KQ ----------------- Y LTV TSP L RR F PDL IN H LQ I HRH L Q K K 855
Cdd:PRK11642 542 SM KQ aiydpenrghfglalqs Y AHF TSP I RR Y PDL SL H RA I KYL L A K E 589
Blast search parameters
Data Source:
Precalculated data, version = cdd.v.3.21
Preset Options: Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01