|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
1-650 |
0e+00 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 1195.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 1 MFQDNPLLAQLKQQIQETLPKKEGTIKATEKGFGFLEVDNKTSFFIPPPYMKKCVHGDKVIAIIRTEKDREVAEPEELIE 80
Cdd:PRK05054 1 MFQDNPLLAQLKQQLHSQTPRVEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHTEKDREIAEPEELIE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 81 QGLTRFIARVKLFKGRLNVVPDHPQLKKLQLKAKAKkGLNpETLKEGDWVVAHIVQHPLKGDNGFLAQISEKITDADDKI 160
Cdd:PRK05054 81 PFLTRFVGRVQKKDDRLSIVPDHPLLKDAIPCRAAK-GLN-HEFKEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHF 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 161 APWWVTLAQNDLPNSEPQGIDDWKInDDADLERVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYIS 240
Cdd:PRK05054 159 APWWVTLARHNLEREAPAGGVAWEM-LDEGLEREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIA 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 241 PDDVMDKVARERGFTIYLPGRNIPMLPRDLADNLCSLIENEVRPALCCTVTVSKDGVIGDDINFFAANIKSHARLAYDNV 320
Cdd:PRK05054 238 EGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDDIRFFAAWIESKAKLAYDNV 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 321 SDWLETGasEKWQP-SEEIAAIVSDLHQFAQARSAWRSANAVVFPDRPDYRFELSEDNDVVAIHADMRRSANKLVEESMI 399
Cdd:PRK05054 318 SDWLENG--GDWQPeSEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMI 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 400 SANICAGRVLKESFNQGVFNCHSGFKAEKLADVLELVNpEAETPFTEEQIVSLEGFATLRRWLGSLDNSYYDNRIPKFQA 479
Cdd:PRK05054 396 AANICAARVLRDKLGFGIYNVHSGFDPANAEQAVALLK-EHGLHFDAEELLTLEGFCKLRRELDAQPTGYLDSRIRRFQS 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 480 YSEISNEPAPHYAMGLDIYATWTSPIRKYGDMINHRMLKAHILGKAPIQtPDETIGDELALHRRHHGMAERNVGDWLYAR 559
Cdd:PRK05054 475 FAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAER-PQDEITVQLAERRRLNRMAERDVGDWLYAR 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 560 TLANAPAEETRFQAEIFDINRAGMRVRLLDNGAAAFIPGSLILNNKERIECNGDMGTVSIDKEMVYKLGDVLEVVLSEVN 639
Cdd:PRK05054 554 YLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVR 633
|
650
....*....|.
gi 1330287570 640 QENRNLVAKPT 650
Cdd:PRK05054 634 METRSIIARPV 644
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
1-650 |
0e+00 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 1118.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 1 MFQDNPLLAQLKQQIQETLPKKEGTIKATEKGFGFLEVDNKTSFFIPPPYMKKCVHGDKVIAIIRTEKDREVAEPEELIE 80
Cdd:COG4776 1 MFQNNPLLAQLKQQLHEQTPRVEGVVKATDKGFGFLEVDDQKSYFIPPPQMKKVMHGDRIKAVIRTEKDKESAEPETLIE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 81 QGLTRFIARVKLFKGRLNVVPDHPQLKKLQLKAKAKkGLNpETLKEGDWVVAHIVQHPLKGDNGFLAQISEKITDADDKI 160
Cdd:COG4776 81 PFLTRFVGRVQKKDGRLFVVPDHPLIKDAIKARPKK-GLE-EGLKEGDWVVAELKRHPLKGDRGFFAEITEFIADADDPF 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 161 APWWVTLAQNDLPNSEPQGIDDWKINDDaDLERVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYIS 240
Cdd:COG4776 159 APWWVTLARHNLEREAPEGDDEWELLDE-GLEREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIP 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 241 PDDVMDKVARERGFTIYLPGRNIPMLPRDLADNLCSLIENEVRPALCCTVTVSKDGVIGDDINFFAANIKSHARLAYDNV 320
Cdd:COG4776 238 EGSELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDDIEFFAAWIRSKAKLAYDNV 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 321 SDWLETGASekWQP-SEEIAAIVSDLHQFAQARSAWRSANAVVFPDRPDYRFELSEDNDVVAIHADMRRSANKLVEESMI 399
Cdd:COG4776 318 SDWLEGKGE--WQPeNEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMI 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 400 SANICAGRVLKESFNQGVFNCHSGFKAEKLADVLELVNpEAETPFTEEQIVSLEGFATLRRWLGSLDNSYYDNRIPKFQA 479
Cdd:COG4776 396 AANICAARVLREHLGFGIFNVHSGFDPEKLEQAVELLA-EHGIEFDPEQLLTLEGFCALRRELDAQPTSYLDSRLRRFQT 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 480 YSEISNEPAPHYAMGLDIYATWTSPIRKYGDMINHRMLKAhILGKAPIQTPDETIGDELALHRRHHGMAERNVGDWLYAR 559
Cdd:COG4776 475 FAEISTEPGPHFGLGLDAYATWTSPIRKYGDMVNHRLIKA-VILGQPAEKPDEELTERLAERRRLNRMAERDVADWLYAR 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 560 TLANAPAEETRFQAEIFDINRAGMRVRLLDNGAAAFIPGSLILNNKERIECNGDMGTVSIDKEMVYKLGDVLEVVLSEVN 639
Cdd:COG4776 554 YLKPKVGSGQVFTAEIIDINRGGLRVRLLENGAVAFIPASFIHSVRDELVCSQEEGTVYIKGEVRYKLGDTIQVTLAEVR 633
|
650
....*....|.
gi 1330287570 640 QENRNLVAKPT 650
Cdd:COG4776 634 EETRSIIAKPA 644
|
|
| RNase_B |
TIGR02062 |
exoribonuclease II; This family consists of exoribonuclease II, the product of the rnb gene, ... |
4-649 |
0e+00 |
|
exoribonuclease II; This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing. [Transcription, Degradation of RNA]
Pssm-ID: 131117 [Multi-domain] Cd Length: 639 Bit Score: 1019.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 4 DNPLLAQLKQQIQETLPKKEGTIKATEKGFGFLEVDNKTSFFIPPPYMKKCVHGDKVIAIIRTEKDREVAEPEELIEQGL 83
Cdd:TIGR02062 1 DNPLLAQLKQQLHSQTPRVEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDKIIAVIHSEKERESAEPEELIEPFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 84 TRFIARVKLFKGRLNVVPDHPqLKKLQLKAKAKKGLNpETLKEGDWVVAHIVQHPLKGDNGFLAQISEKITDADDKIAPW 163
Cdd:TIGR02062 81 TRFVGKVQGKDDKLAIVPDHP-LLKDAIPCRAAKGLN-HEFQEGDWAVAELRRHPLKGDRSFYAELTQYITFADDHLAPW 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 164 WVTLAQNDLPNSEPQGIDDWKINDDADleRVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYISPDD 243
Cdd:TIGR02062 159 WVTLARHNLEREEPDGVADEMLLDGLV--REDLTALDFVTIDSESTKDMDDALFAEALPNGKLQLIVAIADPTAYIAEGS 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 244 VMDKVARERGFTIYLPGRNIPMLPRDLADNLCSLIENEVRPALCCTVTVSKDGVIGDDINFFAANIKSHARLAYDNVSDW 323
Cdd:TIGR02062 237 KLDKAAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRITISKDGNIEDKIEFFAATIKSKAKLVYDQVSDW 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 324 LETGASekWQP-SEEIAAIVSDLHQFAQARSAWRSANAVVFPDRPDYRFELSEDNDVVAIHADMRRSANKLVEESMISAN 402
Cdd:TIGR02062 317 LENTSD--WQPeSEEIAQQVRLLHQFCQARIEWRHTHALVFKDRPDYRFILSEKGEVLDIVAEPRRIANRIVEEAMIIAN 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 403 ICAGRVLKESFNQGVFNCHSGFKAEKLADVLELVNPEAETpFTEEQIVSLEGFATLRRWLGSLDNSYYDNRIPKFQAYSE 482
Cdd:TIGR02062 395 ICAARFLRDKLGFGIYNTHAGFDPANAENVVALLKTNGLH-VDAEELATLDGFCKLRRELDAQETGYLDSRIRRYQSFAE 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 483 ISNEPAPHYAMGLDIYATWTSPIRKYGDMINHRMLKAHILGKAPIQtPDETIGDELALHRRHHGMAERNVGDWLYARTLA 562
Cdd:TIGR02062 474 ISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATR-PQEDITVQLAERRRLNRIAERDVADWLYARFLA 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 563 NAPAEETRFQAEIFDINRAGMRVRLLDNGAAAFIPGSLILNNKERIECNGDMGTVSIDKEMVYKLGDVLEVVLSEVNQEN 642
Cdd:TIGR02062 553 DKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMET 632
|
....*..
gi 1330287570 643 RNLVAKP 649
Cdd:TIGR02062 633 RSIIARP 639
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
193-521 |
1.67e-100 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 309.98 E-value: 1.67e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 193 RVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYISPDDVMDKVARERGFTIYLPGRNIPMLPRDLAD 272
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 273 NLCSLIENEVRPALCCTVTVSKDGVIgDDINFFAANIKSHARLAYDNVSDWLETGASEKwqPSEEIAAIVSDLHQFAQAR 352
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEV-TSYEIYPSVIRSKARLTYEEVDDLLEGKDAEK--DKPDLAEDLRLLYELAKIL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 353 SAWRSANAVVFPDRPDYRFELSEDNdVVAIHADMRRSANKLVEESMISANICAGRVLKESFNQGVFNCHSGFKAEKLADV 432
Cdd:pfam00773 158 RAKRLQRGALDLDTPENKLILDEEG-VIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSL 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 433 LELVNPEAETPFTEEQIVSLEGFATLRRWLgsldnsyydnrIPKFQAYSEISNEPAPHYAMGLDIYATWTSPIRKYGDMI 512
Cdd:pfam00773 237 IKLLQLLPDDKGLSKSLEKIKDDERLLSIL-----------LLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLI 305
|
....*....
gi 1330287570 513 NHRMLKAHI 521
Cdd:pfam00773 306 VHRQLKALL 314
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
193-523 |
7.20e-93 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 289.17 E-value: 7.20e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 193 RVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYISPDDVMDKVARERGFTIYLPGRNIPMLPRDLAD 272
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 273 NLCSLIENEVRPALCCTVTVSKDGVIGDDINFFAANIKSHARLAYDNVSDWLEtgasekwqpseeiaaivsdlhqfaqar 352
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGGEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 353 sawrsanavvfpdrpdyRFELSEDNDVVAIHADMRRSANKLVEESMISANICAGRVLKESFNQGVFNCHSGFKAEKLADV 432
Cdd:smart00955 134 -----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAEL 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 433 leLVNPEAETPFTEEQIVSLEGFATLRRWL-GSLDNSYYDNRIPKFQAYSEISNEPAPHYAMGLDIYATWTSPIRKYGDM 511
Cdd:smart00955 197 --LKEFLALLGLLLLGGDGPKALAKLLEKIrDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDL 274
|
330
....*....|..
gi 1330287570 512 INHRMLKAHILG 523
Cdd:smart00955 275 IVHRQLKAALRG 286
|
|
| S1_RPS1_repeat_ec2_hs2 |
cd04465 |
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
573-646 |
2.55e-04 |
|
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.
Pssm-ID: 239911 [Multi-domain] Cd Length: 67 Bit Score: 39.75 E-value: 2.55e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1330287570 573 AEIFDINRAGMRVRLldNGAAAFIPGSLIlnnkeriecngDMGTVSIDKEMVyklGDVLEVVLSEVNQENRNLV 646
Cdd:cd04465 6 GKVTEKVKGGLIVDI--EGVRAFLPASQV-----------DLRPVEDLDEYV---GKELKFKIIEIDRERNNIV 63
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
1-650 |
0e+00 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 1195.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 1 MFQDNPLLAQLKQQIQETLPKKEGTIKATEKGFGFLEVDNKTSFFIPPPYMKKCVHGDKVIAIIRTEKDREVAEPEELIE 80
Cdd:PRK05054 1 MFQDNPLLAQLKQQLHSQTPRVEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHTEKDREIAEPEELIE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 81 QGLTRFIARVKLFKGRLNVVPDHPQLKKLQLKAKAKkGLNpETLKEGDWVVAHIVQHPLKGDNGFLAQISEKITDADDKI 160
Cdd:PRK05054 81 PFLTRFVGRVQKKDDRLSIVPDHPLLKDAIPCRAAK-GLN-HEFKEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHF 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 161 APWWVTLAQNDLPNSEPQGIDDWKInDDADLERVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYIS 240
Cdd:PRK05054 159 APWWVTLARHNLEREAPAGGVAWEM-LDEGLEREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIA 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 241 PDDVMDKVARERGFTIYLPGRNIPMLPRDLADNLCSLIENEVRPALCCTVTVSKDGVIGDDINFFAANIKSHARLAYDNV 320
Cdd:PRK05054 238 EGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDDIRFFAAWIESKAKLAYDNV 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 321 SDWLETGasEKWQP-SEEIAAIVSDLHQFAQARSAWRSANAVVFPDRPDYRFELSEDNDVVAIHADMRRSANKLVEESMI 399
Cdd:PRK05054 318 SDWLENG--GDWQPeSEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMI 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 400 SANICAGRVLKESFNQGVFNCHSGFKAEKLADVLELVNpEAETPFTEEQIVSLEGFATLRRWLGSLDNSYYDNRIPKFQA 479
Cdd:PRK05054 396 AANICAARVLRDKLGFGIYNVHSGFDPANAEQAVALLK-EHGLHFDAEELLTLEGFCKLRRELDAQPTGYLDSRIRRFQS 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 480 YSEISNEPAPHYAMGLDIYATWTSPIRKYGDMINHRMLKAHILGKAPIQtPDETIGDELALHRRHHGMAERNVGDWLYAR 559
Cdd:PRK05054 475 FAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAER-PQDEITVQLAERRRLNRMAERDVGDWLYAR 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 560 TLANAPAEETRFQAEIFDINRAGMRVRLLDNGAAAFIPGSLILNNKERIECNGDMGTVSIDKEMVYKLGDVLEVVLSEVN 639
Cdd:PRK05054 554 YLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVR 633
|
650
....*....|.
gi 1330287570 640 QENRNLVAKPT 650
Cdd:PRK05054 634 METRSIIARPV 644
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
1-650 |
0e+00 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 1118.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 1 MFQDNPLLAQLKQQIQETLPKKEGTIKATEKGFGFLEVDNKTSFFIPPPYMKKCVHGDKVIAIIRTEKDREVAEPEELIE 80
Cdd:COG4776 1 MFQNNPLLAQLKQQLHEQTPRVEGVVKATDKGFGFLEVDDQKSYFIPPPQMKKVMHGDRIKAVIRTEKDKESAEPETLIE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 81 QGLTRFIARVKLFKGRLNVVPDHPQLKKLQLKAKAKkGLNpETLKEGDWVVAHIVQHPLKGDNGFLAQISEKITDADDKI 160
Cdd:COG4776 81 PFLTRFVGRVQKKDGRLFVVPDHPLIKDAIKARPKK-GLE-EGLKEGDWVVAELKRHPLKGDRGFFAEITEFIADADDPF 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 161 APWWVTLAQNDLPNSEPQGIDDWKINDDaDLERVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYIS 240
Cdd:COG4776 159 APWWVTLARHNLEREAPEGDDEWELLDE-GLEREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIP 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 241 PDDVMDKVARERGFTIYLPGRNIPMLPRDLADNLCSLIENEVRPALCCTVTVSKDGVIGDDINFFAANIKSHARLAYDNV 320
Cdd:COG4776 238 EGSELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDDIEFFAAWIRSKAKLAYDNV 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 321 SDWLETGASekWQP-SEEIAAIVSDLHQFAQARSAWRSANAVVFPDRPDYRFELSEDNDVVAIHADMRRSANKLVEESMI 399
Cdd:COG4776 318 SDWLEGKGE--WQPeNEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMI 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 400 SANICAGRVLKESFNQGVFNCHSGFKAEKLADVLELVNpEAETPFTEEQIVSLEGFATLRRWLGSLDNSYYDNRIPKFQA 479
Cdd:COG4776 396 AANICAARVLREHLGFGIFNVHSGFDPEKLEQAVELLA-EHGIEFDPEQLLTLEGFCALRRELDAQPTSYLDSRLRRFQT 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 480 YSEISNEPAPHYAMGLDIYATWTSPIRKYGDMINHRMLKAhILGKAPIQTPDETIGDELALHRRHHGMAERNVGDWLYAR 559
Cdd:COG4776 475 FAEISTEPGPHFGLGLDAYATWTSPIRKYGDMVNHRLIKA-VILGQPAEKPDEELTERLAERRRLNRMAERDVADWLYAR 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 560 TLANAPAEETRFQAEIFDINRAGMRVRLLDNGAAAFIPGSLILNNKERIECNGDMGTVSIDKEMVYKLGDVLEVVLSEVN 639
Cdd:COG4776 554 YLKPKVGSGQVFTAEIIDINRGGLRVRLLENGAVAFIPASFIHSVRDELVCSQEEGTVYIKGEVRYKLGDTIQVTLAEVR 633
|
650
....*....|.
gi 1330287570 640 QENRNLVAKPT 650
Cdd:COG4776 634 EETRSIIAKPA 644
|
|
| RNase_B |
TIGR02062 |
exoribonuclease II; This family consists of exoribonuclease II, the product of the rnb gene, ... |
4-649 |
0e+00 |
|
exoribonuclease II; This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing. [Transcription, Degradation of RNA]
Pssm-ID: 131117 [Multi-domain] Cd Length: 639 Bit Score: 1019.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 4 DNPLLAQLKQQIQETLPKKEGTIKATEKGFGFLEVDNKTSFFIPPPYMKKCVHGDKVIAIIRTEKDREVAEPEELIEQGL 83
Cdd:TIGR02062 1 DNPLLAQLKQQLHSQTPRVEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDKIIAVIHSEKERESAEPEELIEPFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 84 TRFIARVKLFKGRLNVVPDHPqLKKLQLKAKAKKGLNpETLKEGDWVVAHIVQHPLKGDNGFLAQISEKITDADDKIAPW 163
Cdd:TIGR02062 81 TRFVGKVQGKDDKLAIVPDHP-LLKDAIPCRAAKGLN-HEFQEGDWAVAELRRHPLKGDRSFYAELTQYITFADDHLAPW 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 164 WVTLAQNDLPNSEPQGIDDWKINDDADleRVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYISPDD 243
Cdd:TIGR02062 159 WVTLARHNLEREEPDGVADEMLLDGLV--REDLTALDFVTIDSESTKDMDDALFAEALPNGKLQLIVAIADPTAYIAEGS 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 244 VMDKVARERGFTIYLPGRNIPMLPRDLADNLCSLIENEVRPALCCTVTVSKDGVIGDDINFFAANIKSHARLAYDNVSDW 323
Cdd:TIGR02062 237 KLDKAAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRITISKDGNIEDKIEFFAATIKSKAKLVYDQVSDW 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 324 LETGASekWQP-SEEIAAIVSDLHQFAQARSAWRSANAVVFPDRPDYRFELSEDNDVVAIHADMRRSANKLVEESMISAN 402
Cdd:TIGR02062 317 LENTSD--WQPeSEEIAQQVRLLHQFCQARIEWRHTHALVFKDRPDYRFILSEKGEVLDIVAEPRRIANRIVEEAMIIAN 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 403 ICAGRVLKESFNQGVFNCHSGFKAEKLADVLELVNPEAETpFTEEQIVSLEGFATLRRWLGSLDNSYYDNRIPKFQAYSE 482
Cdd:TIGR02062 395 ICAARFLRDKLGFGIYNTHAGFDPANAENVVALLKTNGLH-VDAEELATLDGFCKLRRELDAQETGYLDSRIRRYQSFAE 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 483 ISNEPAPHYAMGLDIYATWTSPIRKYGDMINHRMLKAHILGKAPIQtPDETIGDELALHRRHHGMAERNVGDWLYARTLA 562
Cdd:TIGR02062 474 ISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATR-PQEDITVQLAERRRLNRIAERDVADWLYARFLA 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 563 NAPAEETRFQAEIFDINRAGMRVRLLDNGAAAFIPGSLILNNKERIECNGDMGTVSIDKEMVYKLGDVLEVVLSEVNQEN 642
Cdd:TIGR02062 553 DKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMET 632
|
....*..
gi 1330287570 643 RNLVAKP 649
Cdd:TIGR02062 633 RSIIARP 639
|
|
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
6-649 |
0e+00 |
|
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: 581.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 6 PLLAQLKQQIQETLPKKEGTIKATEKGFGFLEVDN--KTSFFIPPPYMKKCVHGDKVIAIIRTEKDREV--AEPEELIEQ 81
Cdd:TIGR00358 1 QLLATLKYALPEKDDLVKGVVKAHNKGFGFLRPDDddKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRfeAEVERILEP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 82 GLTRFIARVKLFKGRLNVVPDHPQLKKLQLKAKAKKglnPETLKEGDWVVAHIVQHPLKGDNgFLAQISEKITDADDKIA 161
Cdd:TIGR00358 81 ALTRFVGKFLGENDFGFVVPDDPRIYLDIIVPKASV---KNELAEGDKVVVELTEYPLRRNL-FYGEITQILGNNDDPLI 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 162 PWWVTLAQNDLPNSEPQGIDDW--KINDDADLE----RVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADP 235
Cdd:TIGR00358 157 PWWVTLARHEIPFEFPDGVEQQaaKLQFDVDEQakkyREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADV 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 236 TAYISPDDVMDKVARERGFTIYLPGRNIPMLPRDLADNLCSLIENEVRPALCCTVTVSKDGVIGDDiNFFAANIKSHARL 315
Cdd:TIGR00358 237 SYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDN-EFYPATIESKARL 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 316 AYDNVSDWLETgaSEKWQP-SEEIAAIVSDLHQFAQARSAWRSANAVVFPDRPDYRFELSEDNDVVAIHADMRRSANKLV 394
Cdd:TIGR00358 316 TYDKVNDWLEN--DDELQPeYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKII 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 395 EESMISANICAGRVLKESFNQGVFNCHSGFKAEKLADVLELVNPEAETP--FTEEQIVSLEGFATLRRWLGSLDNSYYDN 472
Cdd:TIGR00358 394 EEAMIVANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLpgGNAENVTTLDGACWLREVKDRPEYEILVT 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 473 RIPKFQAYSEISNEPAPHYAMGLDIYATWTSPIRKYGDMINHRMLKAHILGKAPIQTPD------ETIGDELALHRRHHG 546
Cdd:TIGR00358 474 RLLRSLSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTERYqpqdelLQIAEHCSDTERRAR 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 547 MAERNVGDWLYARTLANAPAEEtrFQAEIFDINRAGMRVRLLDNGAAAFIPGSLILNnkERIECNGDMGTVSIDKE-MVY 625
Cdd:TIGR00358 554 DAERDVADWLKCRYLLDKVGTE--FSGEISSVTRFGMFVRLDDNGIDGLIHISTLHN--DYYVFDQEKMALIGKGTgKVY 629
|
650 660
....*....|....*....|....
gi 1330287570 626 KLGDVLEVVLSEVNQENRNLVAKP 649
Cdd:TIGR00358 630 RIGDRVTVKLTEVNMETRSIIFEL 653
|
|
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
17-645 |
1.07e-111 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 352.10 E-value: 1.07e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 17 ETLPKKEGTIKATEKGFGFLEVDNKTS-FFIPPPYMKKCVHGDKVIAII--RTEKDREVAEPEELIEQGLTRFIARVKLF 93
Cdd:COG0557 65 EKLDLVEGRVRGHRDGFGFVIPDDGEEdIFIPPRELNGALHGDRVLVRVtkEDRRGRPEGRVVEILERANTRVVGRFEKE 144
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 94 KGRLNVVPDHPQLKKLQLKAKAKKGlnpeTLKEGDWVVAHIVQHPLKGDNGFlAQISEKITDADD-----KIApwwvtLA 168
Cdd:COG0557 145 KGFGFVVPDDKRLLQDIFIPPDDLN----GAKDGDLVVVEITRYPERRGPPE-GRVVEVLGSPGDpgaeiLIA-----IR 214
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 169 QNDLPNS-------EPQGIDDwKInDDADLE-RVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYIS 240
Cdd:COG0557 215 KHGLPHEfpeevlaEAEALPD-EV-PEADLKgRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVR 292
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 241 PDDVMDKVARERGFTIYLPGRNIPMLPRDLADNLCSLIENEVRPALCCTVTVSKDG-VIGDDinFFAANIKSHARLAYDN 319
Cdd:COG0557 293 PGSALDREARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGeVVSYE--FYRSVIRSDARLTYEE 370
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 320 VSDWLETGASEKWQPSEEIAAIVSDLHQFAQARSAWRSAN-AVVFpDRPDYRFELSEDNDVVAIHADMRRSANKLVEESM 398
Cdd:COG0557 371 VQAILDGKDEELREEYADLVPMLEELYELAKILRKAREKRgAIDF-DLPETKIILDEEGKPEDIVPRERNDAHKLIEEFM 449
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 399 ISANICAGRVLKESFNQGVFNCHSGFKAEKLADVLELVN--------PEAETPF------------TEEQIVSlegFATL 458
Cdd:COG0557 450 LLANEAVAEFLEKLKLPFLYRVHEEPDPEKLEALREFLAnlglklkgGDEPTPKdlqklleqvkgrPEEELLN---TLLL 526
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 459 RrwlgSLdnsyydnripKfQA-YSEisnEPAPHYAMGLDIYATWTSPIRKYGDMINHRMLKAHILGKAPIQTPDETIGD- 536
Cdd:COG0557 527 R----SM----------K-QAvYSP---ENIGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGKRSPGLQEYLEEEl 588
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 537 -ELALH-----RRhhGM-AERNVGDWLYARTLANAPAEEtrFQAEIFDINRAGMRVRLLDNGAAAFIPGSLILN-----N 604
Cdd:COG0557 589 eEIAEHcseteRR--ADeAERDVVDLKKAEYMKDRVGEE--FEGVISGVTSFGLFVELDELGVEGLVHVSSLGDdyyeyD 664
|
650 660 670 680
....*....|....*....|....*....|....*....|.
gi 1330287570 605 KERIECNGDmgtvsiDKEMVYKLGDVLEVVLSEVNQENRNL 645
Cdd:COG0557 665 ERRQALVGE------RTGKRYRLGDRVEVRVVRVDLDRRQI 699
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
193-521 |
1.67e-100 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 309.98 E-value: 1.67e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 193 RVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYISPDDVMDKVARERGFTIYLPGRNIPMLPRDLAD 272
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 273 NLCSLIENEVRPALCCTVTVSKDGVIgDDINFFAANIKSHARLAYDNVSDWLETGASEKwqPSEEIAAIVSDLHQFAQAR 352
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEV-TSYEIYPSVIRSKARLTYEEVDDLLEGKDAEK--DKPDLAEDLRLLYELAKIL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 353 SAWRSANAVVFPDRPDYRFELSEDNdVVAIHADMRRSANKLVEESMISANICAGRVLKESFNQGVFNCHSGFKAEKLADV 432
Cdd:pfam00773 158 RAKRLQRGALDLDTPENKLILDEEG-VIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSL 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 433 LELVNPEAETPFTEEQIVSLEGFATLRRWLgsldnsyydnrIPKFQAYSEISNEPAPHYAMGLDIYATWTSPIRKYGDMI 512
Cdd:pfam00773 237 IKLLQLLPDDKGLSKSLEKIKDDERLLSIL-----------LLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLI 305
|
....*....
gi 1330287570 513 NHRMLKAHI 521
Cdd:pfam00773 306 VHRQLKALL 314
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
17-643 |
4.10e-97 |
|
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]
Pssm-ID: 273947 [Multi-domain] Cd Length: 709 Bit Score: 313.82 E-value: 4.10e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 17 ETLPKKEGTIKATEKGFGFLEV--DNKTSFFIPPPYMKKCVHGDKVIAII---RTEKDREVAEPEELIEQGLTRFIARVK 91
Cdd:TIGR02063 64 ESLKLVKGTVIAHRDGFGFLRPedDDEDDIFIPPRQMNGAMHGDRVLVRItgkPDGGDRFEARVIKILERANDQIVGTFY 143
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 92 LFKGRLNVVPDHPQLKKLQLkakakkgLNPET---LKEGDWVVAHIVQHPLKgDNGFLAQISEKITDADDKIAPWWVTLA 168
Cdd:TIGR02063 144 IENGIGFVIPDDKRIYLDIF-------IPPEQilgAEEGDKVLVEITKYPDR-NRPAIGKVVEILGHADDPGIDILIIIR 215
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 169 QNDLPNSEPQ-------GIDDwKINDDADLERVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYISP 241
Cdd:TIGR02063 216 KHGIPYEFPEevldeaaKIPE-EVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVRE 294
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 242 DDVMDKVARERGFTIYLPGRNIPMLPRDLADNLCSLIENEVRPALCCTVTVSKDG-VIGDDinFFAANIKSHARLAYDNV 320
Cdd:TIGR02063 295 GSALDKEALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGrVKKYE--FYEAVINSHARLTYNQV 372
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 321 SDWLEtGASEKWQPSEEIAAIVSDLHQFAQARSAWRSANAVVFPDRPDYRFELSEDNDVVAIHADMRRSANKLVEESMIS 400
Cdd:TIGR02063 373 NDIIE-GKDALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIA 451
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 401 ANICAGRVLKESFNQGVFNCHSGFKAEKLADVLE-LVNPEAETP-FTEEQIVSlegfATLRRWLGSLDNSYYDNRIPKF- 477
Cdd:TIGR02063 452 ANETVAEHLEKAKLPFIYRVHERPSEEKLQNLREfLKTLGITLKgGTSDKPQP----KDFQKLLEKVKGRPEEELINTVl 527
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 478 -----QA-YSEisnEPAPHYAMGLDIYATWTSPIRKYGDMINHRMLKaHILGKAPIQTPDETIG------DELALH---- 541
Cdd:TIGR02063 528 lrsmqQAkYSP---ENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIK-KALFGGENTTTEKEREyleaklEEIAEHsskt 603
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 542 -RRHHGmAERNVGDWLYARTLANAPAEEtrFQAEIFDINRAGMRVRLLDNGAAAFIPGSLILNNKERIECNGdMGTVSID 620
Cdd:TIGR02063 604 eRRADE-AERDVNDWKKAEYMSEKIGEE--FEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKG-LALVGER 679
|
650 660
....*....|....*....|...
gi 1330287570 621 KEMVYKLGDVLEVVLSEVNQENR 643
Cdd:TIGR02063 680 TGKVFRLGDRVKVRVVKADLDTG 702
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
193-523 |
7.20e-93 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 289.17 E-value: 7.20e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 193 RVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYISPDDVMDKVARERGFTIYLPGRNIPMLPRDLAD 272
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 273 NLCSLIENEVRPALCCTVTVSKDGVIGDDINFFAANIKSHARLAYDNVSDWLEtgasekwqpseeiaaivsdlhqfaqar 352
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGGEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 353 sawrsanavvfpdrpdyRFELSEDNDVVAIHADMRRSANKLVEESMISANICAGRVLKESFNQGVFNCHSGFKAEKLADV 432
Cdd:smart00955 134 -----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAEL 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 433 leLVNPEAETPFTEEQIVSLEGFATLRRWL-GSLDNSYYDNRIPKFQAYSEISNEPAPHYAMGLDIYATWTSPIRKYGDM 511
Cdd:smart00955 197 --LKEFLALLGLLLLGGDGPKALAKLLEKIrDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDL 274
|
330
....*....|..
gi 1330287570 512 INHRMLKAHILG 523
Cdd:smart00955 275 IVHRQLKAALRG 286
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
19-645 |
1.93e-47 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 179.55 E-value: 1.93e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 19 LPKK----EGTIKATEKGFGFLEVD-NKTSFFIPPPYMKKCVHGDKVIA--IIRTEKDREVAEPEELIEQGLTRFIARVK 91
Cdd:PRK11642 78 LPERldllKGTVIGHRDGYGFLRVEgRKDDLYLSSEQMKTCIHGDQVLAqpLGADRKGRREARIVRVLVPKTSQIVGRYF 157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 92 LFKGRLNVVPDHPQLKKLQLkakakkgLNPETL---KEGDWVVAHIVQHPLKGDNGfLAQISEKITDADDKIAPWWVTLA 168
Cdd:PRK11642 158 TDAGVGFVVPDDSRLSFDIL-------IPPEQImgaRMGFVVVVELTQRPTRRTKA-VGKIVEVLGDNMGTGMAVDIALR 229
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 169 QNDLPNSEPQGID------DWKINDDADLERVDMTHIPFVTIDGESTKDMDDALYAKKKDNGDFELTIAIADPTAYISPD 242
Cdd:PRK11642 230 THEIPYIWPQAVEqqvaglKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPP 309
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 243 DVMDKVARERGFTIYLPGRNIPMLPRDLADNLCSLIENEVRPALCCTVTVSKDGVIgDDINFFAANIKSHARLAYDNVSD 322
Cdd:PRK11642 310 TPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRL-TGYKFYEAVMSSHARLTYTKVWH 388
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 323 WLETGAS--EKWQPseeIAAIVSDLHQFAQARSAWRSANAVVFPDRPDYRFELSEDNDVVAIHADMRRSANKLVEESMIS 400
Cdd:PRK11642 389 ILQGDQDlrEQYAP---LVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMIL 465
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 401 ANICAGRVLKESFNQGVFNCHS-----------------------GFKAEKLaDVLELVNPEAETPFTEEQIVSLegfat 457
Cdd:PRK11642 466 ANISAARFVEKAKEPALFRIHDkpsteaitsfrsvlaelglelpgGNKPEPR-DYAELLESVADRPDAEMLQTML----- 539
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 458 lrrwLGSLDNSYYD--NRipkfqayseisnepaPHYAMGLDIYATWTSPIRKYGDMINHRMLK---AHILGKAPIQTP-- 530
Cdd:PRK11642 540 ----LRSMKQAIYDpeNR---------------GHFGLALQSYAHFTSPIRRYPDLSLHRAIKyllAKEQGHKGNTTEtg 600
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1330287570 531 ------DETI--GDELALHRRHHGMAERNVGDWLYARTLANAPAEEtrFQAEIFDINRAGMRVRLLDngaaAFIPG---- 598
Cdd:PRK11642 601 gyhysmEEMLqlGQHCSMTERRADEATRDVADWLKCDFMLDQVGNV--FKGVISSVTGFGFFVRLDD----LFIDGlvhv 674
|
650 660 670 680
....*....|....*....|....*....|....*....|....*....
gi 1330287570 599 SLILNNKERIECNGD--MGTVSidkEMVYKLGDVLEVVLSEVNQENRNL 645
Cdd:PRK11642 675 SSLDNDYYRFDQVGQrlIGESS---GQTYRLGDRVEVRVEAVNMDERKI 720
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
24-80 |
6.52e-14 |
|
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.
Pssm-ID: 429863 [Multi-domain] Cd Length: 58 Bit Score: 66.41 E-value: 6.52e-14
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1330287570 24 GTIKATEKGFGFLEVD-NKTSFFIPPPYMKKCVHGDKVIAIIrTEKDREVAEPEELIE 80
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDdEEDDIFIPPNQMKKAMHGDRVLVRI-TKGDRRGRREGRIVR 57
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
23-80 |
2.46e-07 |
|
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.
Pssm-ID: 214633 [Multi-domain] Cd Length: 64 Bit Score: 47.98 E-value: 2.46e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1330287570 23 EGTIKATEKGFGFLEVDN-KTSFFIPPP----YMKKCVHGDKVIAIIRTEKDREVAEPEELIE 80
Cdd:smart00357 1 TGVVKWFNKGFGFIRPDDgGKDVFVHPSqiqgGLKSLREGDEVEFKVVSPEGGEKPEAENVVK 63
|
|
| S1_RPS1_repeat_ec2_hs2 |
cd04465 |
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
573-646 |
2.55e-04 |
|
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.
Pssm-ID: 239911 [Multi-domain] Cd Length: 67 Bit Score: 39.75 E-value: 2.55e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1330287570 573 AEIFDINRAGMRVRLldNGAAAFIPGSLIlnnkeriecngDMGTVSIDKEMVyklGDVLEVVLSEVNQENRNLV 646
Cdd:cd04465 6 GKVTEKVKGGLIVDI--EGVRAFLPASQV-----------DLRPVEDLDEYV---GKELKFKIIEIDRERNNIV 63
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
125-173 |
4.58e-04 |
|
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding.
Pssm-ID: 465546 [Multi-domain] Cd Length: 74 Bit Score: 38.91 E-value: 4.58e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 1330287570 125 KEGDWVVAHIVQHPlkGDNGFLAQISEKITDADDKIAPWWVTLAQNDLP 173
Cdd:pfam17876 24 KDGDKVVVEITEYP--DGKNPEGKIVEVLGDPGDPGVEILSIIRKHGLP 70
|
|
| |
