|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
1-643 |
0e+00 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 1388.06 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 1 MFQDNPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVE 80
Cdd:PRK05054 1 MFQDNPLLAQLKQQLHSQTPRVEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHTEKDREIAEPEELIE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 81 PFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVP 160
Cdd:PRK05054 81 PFLTRFVGRVQKKDDRLSIVPDHPLLKDAIPCRAAKGLNHEFKEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHFAP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 161 WWVTLARHNLEKEAPDG-VATEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGS 239
Cdd:PRK05054 161 WWVTLARHNLEREAPAGgVAWEMLDEGLEREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIAEGS 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 240 KLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDW 319
Cdd:PRK05054 241 KLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDDIRFFAAWIESKAKLAYDNVSDW 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 320 LENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANIC 399
Cdd:PRK05054 321 LENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMIAANIC 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 400 AARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEIST 479
Cdd:PRK05054 401 AARVLRDKLGFGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEGFCKLRRELDAQPTGYLDSRIRRFQSFAEIST 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 480 EPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAG 559
Cdd:PRK05054 481 EPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAERPQDEITVQLAERRRLNRMAERDVGDWLYARYLKDKAG 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 560 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSII 639
Cdd:PRK05054 561 TDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSII 640
|
....
gi 16129247 640 ARPV 643
Cdd:PRK05054 641 ARPV 644
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
1-643 |
0e+00 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 1298.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 1 MFQDNPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVE 80
Cdd:COG4776 1 MFQNNPLLAQLKQQLHEQTPRVEGVVKATDKGFGFLEVDDQKSYFIPPPQMKKVMHGDRIKAVIRTEKDKESAEPETLIE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 81 PFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVP 160
Cdd:COG4776 81 PFLTRFVGRVQKKDGRLFVVPDHPLIKDAIKARPKKGLEEGLKEGDWVVAELKRHPLKGDRGFFAEITEFIADADDPFAP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 161 WWVTLARHNLEKEAPDGVA-TEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGS 239
Cdd:COG4776 161 WWVTLARHNLEREAPEGDDeWELLDEGLEREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGS 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 240 KLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDW 319
Cdd:COG4776 241 ELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDDIEFFAAWIRSKAKLAYDNVSDW 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 320 LENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANIC 399
Cdd:COG4776 321 LEGKGEWQPENEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANIC 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 400 AARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEIST 479
Cdd:COG4776 401 AARVLREHLGFGIFNVHSGFDPEKLEQAVELLAEHGIEFDPEQLLTLEGFCALRRELDAQPTSYLDSRLRRFQTFAEIST 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 480 EPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAG 559
Cdd:COG4776 481 EPGPHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVILGQPAEKPDEELTERLAERRRLNRMAERDVADWLYARYLKPKVG 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 560 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSII 639
Cdd:COG4776 561 SGQVFTAEIIDINRGGLRVRLLENGAVAFIPASFIHSVRDELVCSQEEGTVYIKGEVRYKLGDTIQVTLAEVREETRSII 640
|
....
gi 16129247 640 ARPV 643
Cdd:COG4776 641 AKPA 644
|
|
| RNase_B |
TIGR02062 |
exoribonuclease II; This family consists of exoribonuclease II, the product of the rnb gene, ... |
4-642 |
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: 1223.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 4 DNPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVEPFL 83
Cdd:TIGR02062 1 DNPLLAQLKQQLHSQTPRVEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDKIIAVIHSEKERESAEPEELIEPFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 84 TRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWV 163
Cdd:TIGR02062 81 TRFVGKVQGKDDKLAIVPDHPLLKDAIPCRAAKGLNHEFQEGDWAVAELRRHPLKGDRSFYAELTQYITFADDHLAPWWV 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 164 TLARHNLEKEAPDGVATEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDK 243
Cdd:TIGR02062 161 TLARHNLEREEPDGVADEMLLDGLVREDLTALDFVTIDSESTKDMDDALFAEALPNGKLQLIVAIADPTAYIAEGSKLDK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 244 AAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENT 323
Cdd:TIGR02062 241 AAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRITISKDGNIEDKIEFFAATIKSKAKLVYDQVSDWLENT 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 324 GDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARV 403
Cdd:TIGR02062 321 SDWQPESEEIAQQVRLLHQFCQARIEWRHTHALVFKDRPDYRFILSEKGEVLDIVAEPRRIANRIVEEAMIIANICAARF 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 404 LRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGP 483
Cdd:TIGR02062 401 LRDKLGFGIYNTHAGFDPANAENVVALLKTNGLHVDAEELATLDGFCKLRRELDAQETGYLDSRIRRYQSFAEISTEPGP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 484 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAGTDTR 563
Cdd:TIGR02062 481 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQEDITVQLAERRRLNRIAERDVADWLYARFLADKAAKNTR 560
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16129247 564 FAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARP 642
Cdd:TIGR02062 561 FAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIARP 639
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
189-517 |
2.11e-102 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 313.05 E-value: 2.11e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 189 REDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSD 268
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 269 DLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLEntgdwqpeseaiaeqvrllaqicqrrg 348
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGGEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 349 ewrhnhalvfkdrpdyRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFDPANADAL- 427
Cdd:smart00955 134 ----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAELl 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 428 AALLKTHGLHVDAEEvlTLDGFCKLRRELDAQPT-GFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMI 506
Cdd:smart00955 198 KEFLALLGLLLLGGD--GPKALAKLLEKIRDSPEeRLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDLI 275
|
330
....*....|.
gi 16129247 507 NHRLLKAVIKG 517
Cdd:smart00955 276 VHRQLKAALRG 286
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
189-515 |
1.83e-99 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 306.52 E-value: 1.83e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 189 REDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSD 268
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 269 DLCSLRANEVRPVLACRMTLSADGTIEdNIEFFAATIESKAKLVYDQVSDWLEnTGDWQPESEAIAEQVRLLAQICQRRG 348
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVT-SYEIYPSVIRSKARLTYEEVDDLLE-GKDAEKDKPDLAEDLRLLYELAKILR 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 349 EWRHNHALVFKDRPDYRFILGEKGeVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFDPanadala 428
Cdd:pfam00773 159 AKRLQRGALDLDTPENKLILDEEG-VIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDL------- 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 429 alLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGfLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINH 508
Cdd:pfam00773 231 --EKLNSLIKLLQLLPDDKGLSKSLEKIKDDERL-LSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLIVH 307
|
....*..
gi 16129247 509 RLLKAVI 515
Cdd:pfam00773 308 RQLKALL 314
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
1-643 |
0e+00 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 1388.06 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 1 MFQDNPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVE 80
Cdd:PRK05054 1 MFQDNPLLAQLKQQLHSQTPRVEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHTEKDREIAEPEELIE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 81 PFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVP 160
Cdd:PRK05054 81 PFLTRFVGRVQKKDDRLSIVPDHPLLKDAIPCRAAKGLNHEFKEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHFAP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 161 WWVTLARHNLEKEAPDG-VATEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGS 239
Cdd:PRK05054 161 WWVTLARHNLEREAPAGgVAWEMLDEGLEREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIAEGS 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 240 KLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDW 319
Cdd:PRK05054 241 KLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDDIRFFAAWIESKAKLAYDNVSDW 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 320 LENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANIC 399
Cdd:PRK05054 321 LENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMIAANIC 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 400 AARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEIST 479
Cdd:PRK05054 401 AARVLRDKLGFGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEGFCKLRRELDAQPTGYLDSRIRRFQSFAEIST 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 480 EPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAG 559
Cdd:PRK05054 481 EPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAERPQDEITVQLAERRRLNRMAERDVGDWLYARYLKDKAG 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 560 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSII 639
Cdd:PRK05054 561 TDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSII 640
|
....
gi 16129247 640 ARPV 643
Cdd:PRK05054 641 ARPV 644
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
1-643 |
0e+00 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 1298.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 1 MFQDNPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVE 80
Cdd:COG4776 1 MFQNNPLLAQLKQQLHEQTPRVEGVVKATDKGFGFLEVDDQKSYFIPPPQMKKVMHGDRIKAVIRTEKDKESAEPETLIE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 81 PFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVP 160
Cdd:COG4776 81 PFLTRFVGRVQKKDGRLFVVPDHPLIKDAIKARPKKGLEEGLKEGDWVVAELKRHPLKGDRGFFAEITEFIADADDPFAP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 161 WWVTLARHNLEKEAPDGVA-TEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGS 239
Cdd:COG4776 161 WWVTLARHNLEREAPEGDDeWELLDEGLEREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGS 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 240 KLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDW 319
Cdd:COG4776 241 ELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDDIEFFAAWIRSKAKLAYDNVSDW 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 320 LENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANIC 399
Cdd:COG4776 321 LEGKGEWQPENEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANIC 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 400 AARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEIST 479
Cdd:COG4776 401 AARVLREHLGFGIFNVHSGFDPEKLEQAVELLAEHGIEFDPEQLLTLEGFCALRRELDAQPTSYLDSRLRRFQTFAEIST 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 480 EPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAG 559
Cdd:COG4776 481 EPGPHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVILGQPAEKPDEELTERLAERRRLNRMAERDVADWLYARYLKPKVG 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 560 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSII 639
Cdd:COG4776 561 SGQVFTAEIIDINRGGLRVRLLENGAVAFIPASFIHSVRDELVCSQEEGTVYIKGEVRYKLGDTIQVTLAEVREETRSII 640
|
....
gi 16129247 640 ARPV 643
Cdd:COG4776 641 AKPA 644
|
|
| RNase_B |
TIGR02062 |
exoribonuclease II; This family consists of exoribonuclease II, the product of the rnb gene, ... |
4-642 |
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: 1223.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 4 DNPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVEPFL 83
Cdd:TIGR02062 1 DNPLLAQLKQQLHSQTPRVEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDKIIAVIHSEKERESAEPEELIEPFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 84 TRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWV 163
Cdd:TIGR02062 81 TRFVGKVQGKDDKLAIVPDHPLLKDAIPCRAAKGLNHEFQEGDWAVAELRRHPLKGDRSFYAELTQYITFADDHLAPWWV 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 164 TLARHNLEKEAPDGVATEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDK 243
Cdd:TIGR02062 161 TLARHNLEREEPDGVADEMLLDGLVREDLTALDFVTIDSESTKDMDDALFAEALPNGKLQLIVAIADPTAYIAEGSKLDK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 244 AAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENT 323
Cdd:TIGR02062 241 AAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRITISKDGNIEDKIEFFAATIKSKAKLVYDQVSDWLENT 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 324 GDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARV 403
Cdd:TIGR02062 321 SDWQPESEEIAQQVRLLHQFCQARIEWRHTHALVFKDRPDYRFILSEKGEVLDIVAEPRRIANRIVEEAMIIANICAARF 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 404 LRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGP 483
Cdd:TIGR02062 401 LRDKLGFGIYNTHAGFDPANAENVVALLKTNGLHVDAEELATLDGFCKLRRELDAQETGYLDSRIRRYQSFAEISTEPGP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 484 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAGTDTR 563
Cdd:TIGR02062 481 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQEDITVQLAERRRLNRIAERDVADWLYARFLADKAAKNTR 560
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16129247 564 FAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARP 642
Cdd:TIGR02062 561 FAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIARP 639
|
|
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
6-643 |
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: 897.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 6 PLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDA--QKSYFIPPPQMKKVMHGDRIIAVIHSEKERE--SAEPEELVEP 81
Cdd:TIGR00358 1 QLLATLKYALPEKDDLVKGVVKAHNKGFGFLRPDDddKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGrfEAEVERILEP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 82 FLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGlNHEFKEGDWAVAEMRRHPLKGDrSFYAELTQYITFGDDHFVPW 161
Cdd:TIGR00358 81 ALTRFVGKFLGENDFGFVVPDDPRIYLDIIVPKASV-KNELAEGDKVVVELTEYPLRRN-LFYGEITQILGNNDDPLIPW 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 162 WVTLARHNLEKEAPDGVATEMLDEGL--------VREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTA 233
Cdd:TIGR00358 159 WVTLARHEIPFEFPDGVEQQAAKLQFdvdeqakkYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 234 WIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNiEFFAATIESKAKLVY 313
Cdd:TIGR00358 239 YVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDN-EFYPATIESKARLTY 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 314 DQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAM 393
Cdd:TIGR00358 318 DKVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAM 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 394 IAANICAARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGL---HVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRR 470
Cdd:TIGR00358 398 IVANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLtlpGGNAENVTTLDGACWLREVKDRPEYEILVTRLLR 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 471 FQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVI-KGETATR---PQDEITVQMAER---RRLNRMAER 543
Cdd:TIGR00358 478 SLSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLaKEQTDTEryqPQDELLQIAEHCsdtERRARDAER 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 544 DVGDWLYARFLKDKAGtdTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAvrDELVCSQENGTVQIKGE-TVYKVTD 622
Cdd:TIGR00358 558 DVADWLKCRYLLDKVG--TEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHN--DYYVFDQEKMALIGKGTgKVYRIGD 633
|
650 660
....*....|....*....|.
gi 16129247 623 VIDVTIAEVRMETRSIIARPV 643
Cdd:TIGR00358 634 RVTVKLTEVNMETRSIIFELV 654
|
|
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
23-638 |
1.34e-124 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 384.84 E-value: 1.34e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 23 EGVVKATEKGFGFLEVD-AQKSYFIPPPQMKKVMHGDRIIAVIHSEKE--RESAEPEELVEPFLTRFVGKVQGKNDRLAI 99
Cdd:COG0557 71 EGRVRGHRDGFGFVIPDdGEEDIFIPPRELNGALHGDRVLVRVTKEDRrgRPEGRVVEILERANTRVVGRFEKEKGFGFV 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 100 VPDHP-LLKD-AIPCRAARGLnhefKEGDWAVAEMRRHPLKGdRSFYAELTQYITFGDDHFVPWWVTLARHNL------- 170
Cdd:COG0557 151 VPDDKrLLQDiFIPPDDLNGA----KDGDLVVVEITRYPERR-GPPEGRVVEVLGSPGDPGAEILIAIRKHGLphefpee 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 171 -EKEApDGVATEMLDEGLV-REDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIR 248
Cdd:COG0557 226 vLAEA-EALPDEVPEADLKgRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKR 304
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 249 AFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNiEFFAATIESKAKLVYDQVSDWLENT-GDWQ 327
Cdd:COG0557 305 GTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSY-EFYRSVIRSDARLTYEEVQAILDGKdEELR 383
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 328 PESEAIAEQVRLLAQICQRRGEWRHNH-ALVFkDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRD 406
Cdd:COG0557 384 EEYADLVPMLEELYELAKILRKAREKRgAIDF-DLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEK 462
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 407 -KLGFgIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSR-IRRFQSFAEISTEPGPH 484
Cdd:COG0557 463 lKLPF-LYRVHEEPDPEKLEALREFLANLGLKLKGGDEPTPKDLQKLLEQVKGRPEEELLNTlLLRSMKQAVYSPENIGH 541
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 485 FGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAE-------RRRLNRMAERDVGDWLYARFLKDK 557
Cdd:COG0557 542 FGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGKRSPGLQEYLEEELEEiaehcseTERRADEAERDVVDLKKAEYMKDR 621
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 558 AGTDtrFAAEIVDISRGGMRVRLVDNGAIAFIPAPFL-------HAVRDELVcsqengtvqikGE---TVYKVTDVIDVT 627
Cdd:COG0557 622 VGEE--FEGVISGVTSFGLFVELDELGVEGLVHVSSLgddyyeyDERRQALV-----------GErtgKRYRLGDRVEVR 688
|
650
....*....|.
gi 16129247 628 IAEVRMETRSI 638
Cdd:COG0557 689 VVRVDLDRRQI 699
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
24-639 |
3.71e-104 |
|
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: 331.54 E-value: 3.71e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 24 GVVKATEKGFGFLEVDAQK--SYFIPPPQMKKVMHGDRIIAVIH-SEKERESAEPE--ELVEPFLTRFVGKVQGKNDRLA 98
Cdd:TIGR02063 71 GTVIAHRDGFGFLRPEDDDedDIFIPPRQMNGAMHGDRVLVRITgKPDGGDRFEARviKILERANDQIVGTFYIENGIGF 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 99 IVPDHPLLKDAIpcRAARGLNHEFKEGDWAVAEMRRHPLKgDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGV 178
Cdd:TIGR02063 151 VIPDDKRIYLDI--FIPPEQILGAEEGDKVLVEITKYPDR-NRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEV 227
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 179 ATEM------LDEGLV--REDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAF 250
Cdd:TIGR02063 228 LDEAakipeeVPEEEIkgRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGT 307
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 251 TNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEdNIEFFAATIESKAKLVYDQVSDWLENTGDWQPES 330
Cdd:TIGR02063 308 SVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVK-KYEFYEAVINSHARLTYNQVNDIIEGKDALDKKE 386
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 331 EAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAAR-VLRDKLG 409
Cdd:TIGR02063 387 PPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEhLEKAKLP 466
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 410 FgIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLD--GFCKLRRELDAQPTGFLDSRIR-RFQSFAEISTEPGPHFG 486
Cdd:TIGR02063 467 F-IYRVHERPSEEKLQNLREFLKTLGITLKGGTSDKPQpkDFQKLLEKVKGRPEEELINTVLlRSMQQAKYSPENIGHFG 545
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 487 LGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQ----------DEITVQMAERRRLNRMAERDVGDWLYARFLKD 556
Cdd:TIGR02063 546 LALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEkereyleaklEEIAEHSSKTERRADEAERDVNDWKKAEYMSE 625
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 557 KAGtdTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHavRDELVCSQENGTvqIKGE---TVYKVTDVIDVTIAEVRM 633
Cdd:TIGR02063 626 KIG--EEFEGVISGVTSFGLFVELENNTIEGLVHISTLK--DDYYVFDEKGLA--LVGErtgKVFRLGDRVKVRVVKADL 699
|
....*.
gi 16129247 634 ETRSII 639
Cdd:TIGR02063 700 DTGKID 705
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
189-517 |
2.11e-102 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 313.05 E-value: 2.11e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 189 REDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSD 268
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 269 DLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLEntgdwqpeseaiaeqvrllaqicqrrg 348
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGGEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 349 ewrhnhalvfkdrpdyRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFDPANADAL- 427
Cdd:smart00955 134 ----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAELl 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 428 AALLKTHGLHVDAEEvlTLDGFCKLRRELDAQPT-GFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMI 506
Cdd:smart00955 198 KEFLALLGLLLLGGD--GPKALAKLLEKIRDSPEeRLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDLI 275
|
330
....*....|.
gi 16129247 507 NHRLLKAVIKG 517
Cdd:smart00955 276 VHRQLKAALRG 286
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
189-515 |
1.83e-99 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 306.52 E-value: 1.83e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 189 REDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSD 268
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 269 DLCSLRANEVRPVLACRMTLSADGTIEdNIEFFAATIESKAKLVYDQVSDWLEnTGDWQPESEAIAEQVRLLAQICQRRG 348
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVT-SYEIYPSVIRSKARLTYEEVDDLLE-GKDAEKDKPDLAEDLRLLYELAKILR 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 349 EWRHNHALVFKDRPDYRFILGEKGeVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFDPanadala 428
Cdd:pfam00773 159 AKRLQRGALDLDTPENKLILDEEG-VIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDL------- 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 429 alLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGfLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINH 508
Cdd:pfam00773 231 --EKLNSLIKLLQLLPDDKGLSKSLEKIKDDERL-LSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLIVH 307
|
....*..
gi 16129247 509 RLLKAVI 515
Cdd:pfam00773 308 RQLKALL 314
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
24-638 |
7.58e-39 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 153.36 E-value: 7.58e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 24 GVVKATEKGFGFLEVDAQKS-YFIPPPQMKKVMHGDRIIAVIHSE--KERESAEPEELVEPFLTRFVGKVQGKNDRLAIV 100
Cdd:PRK11642 87 GTVIGHRDGYGFLRVEGRKDdLYLSSEQMKTCIHGDQVLAQPLGAdrKGRREARIVRVLVPKTSQIVGRYFTDAGVGFVV 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 101 PDHPLLK-DA-IPCRAARGLnhefKEGDWAVAEMRRHPlkgdrsfyAELTQYI-----TFGDDHFVPWWVTLA--RHNLE 171
Cdd:PRK11642 167 PDDSRLSfDIlIPPEQIMGA----RMGFVVVVELTQRP--------TRRTKAVgkiveVLGDNMGTGMAVDIAlrTHEIP 234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 172 KEAPDGVATEM--LDEGLV------REDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDK 243
Cdd:PRK11642 235 YIWPQAVEQQVagLKEEVPeeakagRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDR 314
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 244 AAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEdNIEFFAATIESKAKLVYDQVsdWLENT 323
Cdd:PRK11642 315 EARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLT-GYKFYEAVMSSHARLTYTKV--WHILQ 391
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 324 GD------WQPESEAIAEQVRLLAQICQRRGEwrhNHALVFKDRpDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAAN 397
Cdd:PRK11642 392 GDqdlreqYAPLVKHLEELHNLYKVLDKAREE---RGGISFESE-EAKFIFNAERRIERIEQTQRNDAHKLIEECMILAN 467
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 398 ICAARVLRDKLGFGIYNVHmgfdpanaDALAALLKTHGLHVDAEEVLTLDG--------FCKLRRELDAQPTG-FLDSRI 468
Cdd:PRK11642 468 ISAARFVEKAKEPALFRIH--------DKPSTEAITSFRSVLAELGLELPGgnkpeprdYAELLESVADRPDAeMLQTML 539
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 469 RRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEIT----------------VQMA 532
Cdd:PRK11642 540 LRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTTETggyhysmeemlqlgqhCSMT 619
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129247 533 ERRRlnRMAERDVGDWLYARFLKDKAGtdTRFAAEIVDISRGGMRVRLVDngaiAFIPAPFLHAVRDELVCSQENGTVQI 612
Cdd:PRK11642 620 ERRA--DEATRDVADWLKCDFMLDQVG--NVFKGVISSVTGFGFFVRLDD----LFIDGLVHVSSLDNDYYRFDQVGQRL 691
|
650 660
....*....|....*....|....*....
gi 16129247 613 KGET---VYKVTDVIDVTIAEVRMETRSI 638
Cdd:PRK11642 692 IGESsgqTYRLGDRVEVRVEAVNMDERKI 720
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
24-81 |
5.43e-17 |
|
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: 75.27 E-value: 5.43e-17
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 16129247 24 GVVKATEKGFGFLEVDA-QKSYFIPPPQMKKVMHGDRIIAVIHsEKERESAEPEELVEP 81
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDeEDDIFIPPNQMKKAMHGDRVLVRIT-KGDRRGRREGRIVRI 58
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
23-81 |
6.93e-12 |
|
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: 61.08 E-value: 6.93e-12
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16129247 23 EGVVKATEKGFGFLEVDA-QKSYFIPPPQ----MKKVMHGDRIIAVIHSEKERESAEPEELVEP 81
Cdd:smart00357 1 TGVVKWFNKGFGFIRPDDgGKDVFVHPSQiqggLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
560-635 |
4.48e-08 |
|
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.
Pssm-ID: 425760 [Multi-domain] Cd Length: 72 Bit Score: 50.36 E-value: 4.48e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16129247 560 TDTRFAAEIVDISRGGMRVRLvDNGAIAFIPAPFLHAVRDElvcsqENGTVQIKGETVYKVTDVIDVTIAEVRMET 635
Cdd:pfam00575 3 KGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHVE-----DPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
99-175 |
3.50e-06 |
|
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: 45.07 E-value: 3.50e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16129247 99 IVPDHPLLKD--AIPCRAARGLnhefKEGDWAVAEMRRHPlkGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAP 175
Cdd:pfam17876 2 VVPDDKRIPQdiFIPKEDLKGA----KDGDKVVVEITEYP--DGKNPEGKIVEVLGDPGDPGVEILSIIRKHGLPHEFP 74
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
566-639 |
1.50e-03 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 37.58 E-value: 1.50e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16129247 566 AEIVDISRGGMRVRLvDNGAIAFIPApflhavrdelvcSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSII 639
Cdd:smart00316 8 GTVTEITPGGAFVDL-GNGVEGLIPI------------SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRII 68
|
|
| |
