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Conserved domains on  [gi|393912173|gb|EJD76626|]
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CBR-MOG-5 protein [Loa loa]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 519-675 2.66e-103

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd17971:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 179  Bit Score: 318.66  E-value: 2.66e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 519 EQRESLPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLG 598
Cdd:cd17971    1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173 599 SEVGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVT 675
Cdd:cd17971   81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVT 157
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 221-298 7.88e-35

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


:

Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 127.36  E-value: 7.88e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 393912173 221 GHIYNGRVISIQSFGAFIQLEGLRQRFEGLLHISQIRQD-RVNAVSDVLNRNQKVKVKVIKFELGKIGLSMKEVDQETG 298
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEgRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 815-891 1.60e-29

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


:

Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 112.35  E-value: 1.60e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  815 IQKAICSGFFRNAAKRDPQE-GYRTIVDGQNVYIHPSSALFQNQ---PEWVVYHELVMTTKEYMREVTAIEAKWLVEFAP 890
Cdd:pfam07717   1 LRAALAAGLYPNVARRDPKGkGYTTLSDNQRVFIHPSSVLFNEKtfpPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                  .
gi 393912173  891 S 891
Cdd:pfam07717  81 H 81
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 4-73 2.42e-28

GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI.


:

Pssm-ID: 409668  Cd Length: 68  Bit Score: 108.40  E-value: 2.42e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173   4 LERLSLVSRVCVELDNHFGLADKDVAEFIIYLATENPTFDKFKKSITKEGlaDQFDDSLLANLLRIIQHM 73
Cdd:cd21691    1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENG--AEFPDSFVESLLRLIQRM 68
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 692-758 1.15e-22

Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


:

Pssm-ID: 214852 [Multi-domain]  Cd Length: 82  Bit Score: 92.72  E-value: 1.15e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173   692 MAEFPLEPSLAKLLIMSVDLCCSDEVLTIVSMLSVQNvfYRPKDKQEIADQKKAKFHQPEGDHLTLL 758
Cdd:smart00847  18 MAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDADAARRRFADPESDHLTLL 82
 
Name Accession Description Interval E-value
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 519-675 2.66e-103

DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22) acts late in the splicing of pre-mRNA and mediates the release of the spliced mRNA from spliceosomes. DHX8 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350729 [Multi-domain]  Cd Length: 179  Bit Score: 318.66  E-value: 2.66e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 519 EQRESLPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLG 598
Cdd:cd17971    1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173 599 SEVGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVT 675
Cdd:cd17971   81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVT 157
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
515-675 6.75e-56

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 208.01  E-value: 6.75e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 515 MSLKEQRESLPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMG 594
Cdd:COG1643    1 MSLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 595 CRLGSEVGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLK-AAVKKRPELKLI 673
Cdd:COG1643   81 EPVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLdLQPALRPDLKLL 160


                 ..
gi 393912173 674 VT 675
Cdd:COG1643  161 VM 162
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 522-675 6.52e-47

RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homolog from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273900 [Multi-domain]  Cd Length: 1283  Bit Score: 182.66  E-value: 6.52e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173   522 ESLPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEV 601
Cdd:TIGR01967   64 DNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKV 143

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 393912173   602 GYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVT 675
Cdd:TIGR01967  144 GYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIIIT 217
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 522-675 7.52e-46

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 179.49  E-value: 7.52e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  522 ESLPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEV 601
Cdd:PRK11131   71 ENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCV 150

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 393912173  602 GYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVT 675
Cdd:PRK11131  151 GYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDLKVIIT 224
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 221-298 7.88e-35

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 127.36  E-value: 7.88e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 393912173 221 GHIYNGRVISIQSFGAFIQLEGLRQRFEGLLHISQIRQD-RVNAVSDVLNRNQKVKVKVIKFELGKIGLSMKEVDQETG 298
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEgRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 815-891 1.60e-29

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 112.35  E-value: 1.60e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  815 IQKAICSGFFRNAAKRDPQE-GYRTIVDGQNVYIHPSSALFQNQ---PEWVVYHELVMTTKEYMREVTAIEAKWLVEFAP 890
Cdd:pfam07717   1 LRAALAAGLYPNVARRDPKGkGYTTLSDNQRVFIHPSSVLFNEKtfpPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                  .
gi 393912173  891 S 891
Cdd:pfam07717  81 H 81
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 4-73 2.42e-28

GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI.


Pssm-ID: 409668  Cd Length: 68  Bit Score: 108.40  E-value: 2.42e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173   4 LERLSLVSRVCVELDNHFGLADKDVAEFIIYLATENPTFDKFKKSITKEGlaDQFDDSLLANLLRIIQHM 73
Cdd:cd21691    1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENG--AEFPDSFVESLLRLIQRM 68
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 692-758 1.15e-22

Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 214852 [Multi-domain]  Cd Length: 82  Bit Score: 92.72  E-value: 1.15e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173   692 MAEFPLEPSLAKLLIMSVDLCCSDEVLTIVSMLSVQNvfYRPKDKQEIADQKKAKFHQPEGDHLTLL 758
Cdd:smart00847  18 MAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDADAARRRFADPESDHLTLL 82
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 218-292 1.15e-21

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 100.85  E-value: 1.15e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 393912173 218 PIVGHIYNGRVISIQSFGAFIQLEGLRqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF-ELGKIGLSMKE 292
Cdd:COG1185  614 PEVGEIYEGKVVRIMDFGAFVEILPGK---DGLVHISELADERVEKVEDVLKEGDEVKVKVLEIdDQGRIKLSRKA 686
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 220-294 2.10e-21

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 100.12  E-value: 2.10e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGLRqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF-ELGKIGLSMKEVD 294
Cdd:PRK11824 621 VGEIYEGKVVRIVDFGAFVEILPGK---DGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIdKRGRIRLSRKAVL 693
DEXDc smart00487
DEAD-like helicases superfamily;
530-668 2.58e-20

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 89.86  E-value: 2.58e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173   530 KKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYA-ARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEVGYT---- 604
Cdd:smart00487  14 KEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRgKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYggds 93

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 393912173   605 --IRFEDCTSQDTVVKYMTDGMLLRECLLDP-DLTSYSVIMLDEAHERT--IHTDVLFGLLKAAVKKRP 668
Cdd:smart00487  94 krEQLRKLESGKTDILVTTPGRLLDLLENDKlSLSNVDLVILDEAHRLLdgGFGDQLEKLLKLLPKNVQ 162
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 691-757 6.93e-19

Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 461295 [Multi-domain]  Cd Length: 104  Bit Score: 82.67  E-value: 6.93e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  691 TMAEFPLEPSLAKLLIMSVDLCCSDEVLTIVSMLSVQNVFYRP------KDKQEIADQKKAKFHQ---------PEGDHL 755
Cdd:pfam04408  23 KMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPnfldprSAAKAARRRRRAADEKarakfarldLEGDHL 102


                  ..
gi 393912173  756 TL 757
Cdd:pfam04408 103 TL 104
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
220-291 4.25e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 70.71  E-value: 4.25e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 393912173   220 VGHIYNGRVISIQSFGAFIQLEGlrqRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFEL--GKIGLSMK 291
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGN---GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEekGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 226-295 9.16e-10

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 62.06  E-value: 9.16e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 393912173  226 GRVISIQSFGAFIQLEGlrqrFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMKEVDQ 295
Cdd:TIGR00717 193 GVVKNITDFGAFVDLGG----VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFdkEKGRISLSLKQLGE 260
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 218-290 7.36e-09

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: 53.06  E-value: 7.36e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 393912173  218 PIVGHIYNGRVISIQSFGAFIQLEGlrqRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFEL--GKIGLSM 290
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGN---GVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKdrRRIILSI 72
AAA_22 pfam13401
AAA domain;
540-647 5.04e-04

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 40.79  E-value: 5.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  540 QNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEmgcrLGSEVGYTIRFEDCTSQdtvvky 619
Cdd:pfam13401   5 AGILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKDLLRALLRA----LGLPLSGRLSKEELLAA------ 74

                          90       100
                  ....*....|....*....|....*...
gi 393912173  620 MTDgmLLRECLLDPdltsysVIMLDEAH 647
Cdd:pfam13401  75 LQQ--LLLALAVAV------VLIIDEAQ 94
 
Name Accession Description Interval E-value
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 519-675 2.66e-103

DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22) acts late in the splicing of pre-mRNA and mediates the release of the spliced mRNA from spliceosomes. DHX8 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350729 [Multi-domain]  Cd Length: 179  Bit Score: 318.66  E-value: 2.66e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 519 EQRESLPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLG 598
Cdd:cd17971    1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173 599 SEVGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVT 675
Cdd:cd17971   81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVT 157
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 524-682 1.27e-80

DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably involved in pre-mRNA splicing. DHX16 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350732 [Multi-domain]  Cd Length: 174  Bit Score: 258.59  E-value: 1.27e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARG-RIGCTQPRRVAAMSVAKRVAEEMGCRLGSEVG 602
Cdd:cd17974    1 LPVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAGYTKGGgKIGCTQPRRVAAMSVAARVAEEMGVKLGNEVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 603 YTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVTRCV---- 678
Cdd:cd17974   81 YSIRFEDCTSEKTVLKYMTDGMLLREFLTEPDLASYSVMIIDEAHERTLHTDILFGLVKDIARFRPDLKLLISSATmdae 160


                 ....*.
gi 393912173 679 --SDFF 682
Cdd:cd17974  161 kfSAFF 166
DEXHc_DHX38 cd17983
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ...
 524-682 2.21e-80

DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as PRP16) is involved in pre-mRNA splicing. DHX38 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350741 [Multi-domain]  Cd Length: 173  Bit Score: 257.78  E-value: 2.21e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEVGY 603
Cdd:cd17983    1 LPIFAVRQELLNVIRDNNVVIVVGETGSGKTTQLTQYLHEDGYTDYGMIGCTQPRRVAAMSVAKRVSEEMGVELGEEVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 604 TIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVTRCV----- 678
Cdd:cd17983   81 AIRFEDCTSENTVIKYMTDGILLRESLRDPDLDKYSAIIMDEAHERSLNTDVLFGLLREVVARRRDLKLIVTSATmdadk 160


                 ....*
gi 393912173 679 -SDFF 682
Cdd:cd17983  161 fADFF 165
DEXHc_DHX33 cd17978
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ...
 524-682 1.82e-77

DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA polymerase I transcription of the 47S precursor rRNA. DHX33 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438710 [Multi-domain]  Cd Length: 178  Bit Score: 249.96  E-value: 1.82e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEVGY 603
Cdd:cd17978    1 LPIYSARKRLLEELRKHDTVIIIGETGSGKTTQIPQYLYEAGFARGGMIGITQPRRVAAVSVAKRVAEEMGVELGQLVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 604 TIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKR-----PELKLIVT--- 675
Cdd:cd17978   81 SVRFDDVTSEETRIKYMTDGMLLREAIGDPLLSKYSVIILDEAHERTVHTDVLFGLVKSAQRRRkeqklSPLKVIIMsat 160

                        170
                 ....*....|
gi 393912173 676 ---RCVSDFF 682
Cdd:cd17978  161 ldaDLFSEYF 170
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 541-675 9.22e-76

DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438707 [Multi-domain]  Cd Length: 159  Bit Score: 244.68  E-value: 9.22e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 541 NILIVIGETGSGKTTQITQYMVEVGYA--ARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEVGYTIRFEDCTSQDTVVK 618
Cdd:cd17917    2 QVVVIVGETGSGKTTQVPQFLLEDGLAkgGKGRIVCTQPRRIAAISVAERVAEERGEKLGEEVGYQIRFESKTSSKTRIK 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173 619 YMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVT 675
Cdd:cd17917   82 FCTDGILLRELLSDPLLSGYSHVILDEAHERSLDTDFLLGLLKDLLRKRPDLKVILM 138
DEXHc_DHX35 cd17980
DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and ...
 524-682 5.25e-71

DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and seems to be associated with risk to thyroid cancers. It also has been shown to positively regulate poxviruses, such as Myxoma virus. DEAH-box helicase 35 (DHX35) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350738 [Multi-domain]  Cd Length: 185  Bit Score: 232.74  E-value: 5.25e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGR-IGCTQPRRVAAMSVAKRVAEEMGCRLGSEVG 602
Cdd:cd17980    1 LPVFKLRNHILYLVENYQTIVIVGETGCGKSTQIPQYLAEAGWTAGGRvVGCTQPRRVAAVTVAGRVAEEMGAVLGHEVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 603 YTIRFEDCTSQD-TVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVTRCV--- 678
Cdd:cd17980   81 YCIRFDDCTDPQaTRIKFLTDGMLVREMMLDPLLTKYSVIMLDEAHERTLYTDILIGLLKKIQKKRGDLRLIVASATlda 160


                 ....*..
gi 393912173 679 ---SDFF 682
Cdd:cd17980  161 ekfRDFF 167
DEXHc_DHX15 cd17973
DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA ...
 519-674 2.52e-70

DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA. DHX15 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438709 [Multi-domain]  Cd Length: 187  Bit Score: 231.15  E-value: 2.52e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 519 EQRESLPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGR--IGCTQPRRVAAMSVAKRVAEEMGCR 596
Cdd:cd17973    8 EKRRELPVWEQKEDFLKLLKNNQILVLVGETGSGKTTQIPQFVLDDELPHQPKklVACTQPRRVAAMSVAQRVAEEMDVK 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 393912173 597 LGSEVGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIV 674
Cdd:cd17973   88 LGEEVGYSIRFEDCSSAKTILKYMTDGMLLREAMSDPLLSRYSVIILDEAHERTLATDILMGLLKEVVRRRPDLKLIV 165
DEXHc_DHX40 cd17984
DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the ...
 524-674 6.29e-65

DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350742 [Multi-domain]  Cd Length: 178  Bit Score: 215.87  E-value: 6.29e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEVGY 603
Cdd:cd17984    1 LPIQKQRKKLVQAVRDNSFLIVTGNTGSGKTTQLPKYLYEAGFSQHGMIGVTQPRRVAAISVAQRVAEEMKCTLGSKVGY 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 393912173 604 TIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRP-----ELKLIV 674
Cdd:cd17984   81 QVRFDDCSSKETAIKYMTDGCLLRHILADPNLTKYSVIILDEAHERSLTTDILFGLLKKLFQEKSpnrkeHLKVVV 156
DEXHc_DHX37 cd17982
DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the ...
 524-681 4.73e-56

DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the human nervous system and has been linked to schizophrenia. It also negatively regulates poxviruses such as Myxoma virus. DEAH-box helicase 37 (DHX37) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350740 [Multi-domain]  Cd Length: 191  Bit Score: 191.80  E-value: 4.73e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAAR-----GRIGCTQPRRVAAMSVAKRVAEEMGcRLG 598
Cdd:cd17982    1 LPILAEEQEIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFGSPesdnpGMIGITQPRRVAAVSMAKRVAEELN-VFG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 599 SEVGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPE--------- 669
Cdd:cd17982   80 KEVSYQIRYDSTVSENTKIKFMTDGVLLKEIQTDFLLRKYSVIIIDEAHERSVNTDILIGMLSRIVPLRAKlylqdqtvk 159

                        170
                 ....*....|....*.
gi 393912173 670 -LKLIV---TRCVSDF 681
Cdd:cd17982  160 pLKLVImsaTLRVEDF 175
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
515-675 6.75e-56

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 208.01  E-value: 6.75e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 515 MSLKEQRESLPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMG 594
Cdd:COG1643    1 MSLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 595 CRLGSEVGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLK-AAVKKRPELKLI 673
Cdd:COG1643   81 EPVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLdLQPALRPDLKLL 160


                 ..
gi 393912173 674 VT 675
Cdd:COG1643  161 VM 162
DEXHc_HrpA cd17989
DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA ...
 524-680 1.04e-52

DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpA belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350747 [Multi-domain]  Cd Length: 173  Bit Score: 181.88  E-value: 1.04e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEVGY 603
Cdd:cd17989    1 LPVSQKRDEIAKAIAENQVVIIAGETGSGKTTQLPKICLELGRGIRGLIGHTQPRRLAARSVAERIAEELKTELGGAVGY 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173 604 TIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVTRCVSD 680
Cdd:cd17989   81 KVRFTDQTSDETCVKLMTDGILLAETQTDRYLRAYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKVIITSATID 157
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 522-675 6.52e-47

RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homolog from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273900 [Multi-domain]  Cd Length: 1283  Bit Score: 182.66  E-value: 6.52e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173   522 ESLPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEV 601
Cdd:TIGR01967   64 DNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKV 143

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 393912173   602 GYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVT 675
Cdd:TIGR01967  144 GYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIIIT 217
DEXHc_DHX34 cd17979
DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in ...
 524-674 3.06e-46

DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in the nonsense-mediated decay (NMD), a surveillance mechanism that degrades aberrant mRNAs. DHX34 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350737 [Multi-domain]  Cd Length: 170  Bit Score: 163.38  E-value: 3.06e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYaarGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEVGY 603
Cdd:cd17979    1 LPIAQYREKIIELLKTHQVVIVAGDTGCGKSTQVPQYLLAAGF---RHIACTQPRRIACISLAKRVAFESLNQYGSKVAY 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 393912173 604 TIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIV 674
Cdd:cd17979   78 QIRFERTRTLATKLLFLTEGLLLRQIQRDASLPQYNVLILDEVHERHLHGDFLLGVLRCLLRLRPDLKLIL 148
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 522-675 7.52e-46

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 179.49  E-value: 7.52e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  522 ESLPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEV 601
Cdd:PRK11131   71 ENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCV 150

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 393912173  602 GYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVT 675
Cdd:PRK11131  151 GYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDLKVIIT 224
DEXHc_DHX32 cd17977
DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the ...
 524-677 7.59e-45

DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350735 [Multi-domain]  Cd Length: 176  Bit Score: 159.61  E-value: 7.59e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIG---CTQPRRVAAMSVAKRVAEEMGCRLGSE 600
Cdd:cd17977    1 LPVWEAKYEFMESLAHNQIVIVSGDAKTGKSSQIPQWCAEYCLSAHYQHGvvvCTQVHKQTAVWLALRVADEMDVNIGHE 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173 601 VGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVTRC 677
Cdd:cd17977   81 VGYVIPFENCCTNETILRYCTDDMLLREMMSDPLLESYGVIILDDAHERTVSTDVLLGLLKDVLLSRPELKLVIITC 157
DEXQc_DQX1 cd17986
DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 ...
 524-674 5.54e-42

DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 (DQX1) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350744 [Multi-domain]  Cd Length: 177  Bit Score: 151.59  E-value: 5.54e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAV-AAQNILIVIGETGSGKTTQITQYMVEVGYA---ARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGS 599
Cdd:cd17986    1 LPIWAAKFTFLEQLeSPSGIVLVSGEPGSGKSTQVPQWCAEFALSrgfQKGQVTVTQPHPLAARSLALRVADEMDLNLGH 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 393912173 600 EVGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIV 674
Cdd:cd17986   81 EVGYSIPQEDCTGPNTILRFCWDRLLLQEMTSTPLLGAWGVVVLDEAQERSVASDSLLGLLKDVRLQRPELRVVV 155
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 524-674 3.30e-41

DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 149.02  E-value: 3.30e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEVGY 603
Cdd:cd17990    1 LPIAAVLPALRAALDAGGQVVLEAPPGAGKTTRVPLALLAELWIAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGY 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 393912173 604 TIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLL-KAAVKKRPELKLIV 674
Cdd:cd17990   81 RVRGESRVGRRTRVEVVTEGVLLRRLQRDPELSGVGAVILDEFHERSLDADLALALLlEVQQLLRDDLRLLA 152
DEXHc_DHX29 cd17975
DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of ...
 524-680 1.63e-38

DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of the 43S pre-initiation complex involved in translation initiation of mRNAs with structured 5'-UTRs. DHX29 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350733 [Multi-domain]  Cd Length: 183  Bit Score: 141.59  E-value: 1.63e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVE-----VGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLG 598
Cdd:cd17975    1 LPVFKHRESILETLKRHRVVVVAGETGSGKSTQVPQFLLEdlllnGGTAQKCNIVCTQPRRISAMSLATRVCEELGCESG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 599 -----SEVGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLI 673
Cdd:cd17975   81 pggknSLCGYQIRMESRTGEATRLLYCTTGVLLRKLQEDGLLSSISHIIVDEVHERSVQSDFLLIILKEILHKRSDLHLI 160


                 ....*..
gi 393912173 674 VTRCVSD 680
Cdd:cd17975  161 LMSATVD 167
DEXHc_YTHDC2 cd17987
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ...
 524-687 3.68e-38

DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) regulates mRNA translation and stability via binding to N6-methyladenosine, a modified RNA nucleotide enriched in the stop codons and 3' UTRs of eukaryotic messenger RNAs. YTHDC2 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350745 [Multi-domain]  Cd Length: 176  Bit Score: 140.35  E-value: 3.68e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYAARG--RIGCTQPRRVAAMSVAKRVAEEMGCRLGSEV 601
Cdd:cd17987    1 LPVFEKQEQIVRIIKENKVVLIVGETGSGKTTQIPQFLLDDCYANGIpcRIFCTQPRRLAAIAVAERVAAERGEKIGQTV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 602 GYTIRFEDCTSQDTVVKYMTDGMLLReCLLDPD--LTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVTRCVS 679
Cdd:cd17987   81 GYQIRLESRVSPKTLLTFCTNGVLLR-TLMAGDsaLSTVTHVIVDEVHERDRFSDFLLTKLRDILQKHPNLKLILSSAAL 159


                 ....*...
gi 393912173 680 DFFIYLCY 687
Cdd:cd17987  160 DVNLFIRY 167
DEXHc_DHX36 cd17981
DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as ...
 524-674 5.72e-38

DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as G4-resolvase 1 or G4R1, MLE-like protein 1 and RNA helicase associated with AU-rich element or RHAU) unwinds a G4-quadruplex in human telomerase RNA. DHX36 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350739 [Multi-domain]  Cd Length: 180  Bit Score: 139.98  E-value: 5.72e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYM----VEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMG--CRL 597
Cdd:cd17981    1 LPSYGMKQEIINMIDNNQVTVISGETGCGKTTQVTQFIlddaIERGKGSSCRIVCTQPRRISAISVAERVAAERAesCGL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 393912173 598 GSEVGYTIRFEDCTSQDTV-VKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIV 674
Cdd:cd17981   81 GNSTGYQIRLESRKPRKQGsILYCTTGIVLQWLQSDPHLSNVSHLVLDEIHERNLQSDVLMGIVKDLLPFRSDLKVIL 158
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 221-298 7.88e-35

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 127.36  E-value: 7.88e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 393912173 221 GHIYNGRVISIQSFGAFIQLEGLRQRFEGLLHISQIRQD-RVNAVSDVLNRNQKVKVKVIKFELGKIGLSMKEVDQETG 298
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEgRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
DEXHc_DHX57 cd17985
DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the ...
 524-687 1.72e-34

DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350743 [Multi-domain]  Cd Length: 177  Bit Score: 129.96  E-value: 1.72e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEV----GYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGS 599
Cdd:cd17985    1 LPAWQERETILELLEKHQVLVISGMTGCGKTTQIPQFILDNslqgPPLPVANIICTQPRRISAISVAERVAQERAERVGQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 600 EVGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVTRCVS 679
Cdd:cd17985   81 SVGYQIRLESVKSSATRLLYCTTGVLLRRLEGDPTLQGVTHVIVDEVHERTEESDFLLLVLKDLMVQRPDLKVILMSATL 160


                 ....*...
gi 393912173 680 DFFIYLCY 687
Cdd:cd17985  161 NAELFSDY 168
DEXHc_TDRD9 cd17988
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ...
 524-656 3.89e-32

DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also known as HIG-1or NET54 or C14orf75) is a part of the nuclear PIWI-interacting RNA (piRNA) pathway essential for transposon silencing and male fertility TDRD9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350746 [Multi-domain]  Cd Length: 180  Bit Score: 123.38  E-value: 3.89e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEvGYAARGR---IGCTQPRRVAAMSVAKRVAEEMGCRLGSE 600
Cdd:cd17988    1 LPIYAKREEILSLIEANSVVIIKGATGCGKTTQLPQFILD-HYYKRGKycnIVVTQPRRIAAISIARRVSQEREWTLGSL 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 393912173 601 VGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVL 656
Cdd:cd17988   80 VGYQVGLERPASEETRLIYCTTGVLLQKLINNKTLTEYTHIILDEVHERDQELDFL 135
DEXHc_DHX30 cd17976
DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an ...
 524-680 9.31e-32

DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an important role in the assembly of the mitochondrial large ribosomal subunit. DHX30 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350734 [Multi-domain]  Cd Length: 178  Bit Score: 122.21  E-value: 9.31e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVE----VGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGS 599
Cdd:cd17976    1 LPVDSHKESILSAIEQNPVVVISGDTGCGKTTRIPQFILEdyvlRGRGARCNVVITQPRRISAVSVAQRVAHELGPNLRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 600 EVGYTIRFED-CTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLIVTRCV 678
Cdd:cd17976   81 NVGYQVRLESrPPPRGGALLFCTVGVLLKKLQSNPRLEGVSHVIVDEVHERDVNTDFLLILLKGVLQLNPELRVVLMSAT 160


                 ..
gi 393912173 679 SD 680
Cdd:cd17976  161 GD 162
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 519-674 1.42e-31

DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ATP-dependent RNA helicase A or RHA and leukophysin or LKP) plays an important role in many cellular processes, including regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. DHX9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350730 [Multi-domain]  Cd Length: 234  Bit Score: 123.41  E-value: 1.42e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 519 EQRESLPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYM----VEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMG 594
Cdd:cd17972   54 QERELLPVKKFREEILEAISNNPVVIIRGATGCGKTTQVPQYIlddfIQNDRAAECNIVVTQPRRISAVSVAERVAFERG 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 595 CRLGSEVGYTIRFEDCTSQD-TVVKYMTDGMLLREclLDPDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKKRPELKLI 673
Cdd:cd17972  134 EEVGKSCGYSVRFESVLPRPhASILFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVI 211


                 .
gi 393912173 674 V 674
Cdd:cd17972  212 L 212
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 815-891 1.60e-29

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 112.35  E-value: 1.60e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  815 IQKAICSGFFRNAAKRDPQE-GYRTIVDGQNVYIHPSSALFQNQ---PEWVVYHELVMTTKEYMREVTAIEAKWLVEFAP 890
Cdd:pfam07717   1 LRAALAAGLYPNVARRDPKGkGYTTLSDNQRVFIHPSSVLFNEKtfpPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                  .
gi 393912173  891 S 891
Cdd:pfam07717  81 H 81
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 4-73 2.42e-28

GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI.


Pssm-ID: 409668  Cd Length: 68  Bit Score: 108.40  E-value: 2.42e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173   4 LERLSLVSRVCVELDNHFGLADKDVAEFIIYLATENPTFDKFKKSITKEGlaDQFDDSLLANLLRIIQHM 73
Cdd:cd21691    1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENG--AEFPDSFVESLLRLIQRM 68
DEAH_box_HrpB TIGR01970
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ...
 524-674 1.50e-25

ATP-dependent helicase HrpB; This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273901 [Multi-domain]  Cd Length: 819  Bit Score: 113.71  E-value: 1.50e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  524 LPIFALKKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGyAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEVGY 603
Cdd:TIGR01970   1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAP-GIGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGY 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 393912173  604 TIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGL-LKAAVKKRPELKLIV 674
Cdd:TIGR01970  80 RVRGENKVSRRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLALaLDVQSSLREDLKILA 151
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 692-758 1.15e-22

Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 214852 [Multi-domain]  Cd Length: 82  Bit Score: 92.72  E-value: 1.15e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173   692 MAEFPLEPSLAKLLIMSVDLCCSDEVLTIVSMLSVQNvfYRPKDKQEIADQKKAKFHQPEGDHLTLL 758
Cdd:smart00847  18 MAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDADAARRRFADPESDHLTLL 82
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 218-292 1.15e-21

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 100.85  E-value: 1.15e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 393912173 218 PIVGHIYNGRVISIQSFGAFIQLEGLRqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF-ELGKIGLSMKE 292
Cdd:COG1185  614 PEVGEIYEGKVVRIMDFGAFVEILPGK---DGLVHISELADERVEKVEDVLKEGDEVKVKVLEIdDQGRIKLSRKA 686
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 220-294 2.10e-21

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 100.12  E-value: 2.10e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGLRqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF-ELGKIGLSMKEVD 294
Cdd:PRK11824 621 VGEIYEGKVVRIVDFGAFVEILPGK---DGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIdKRGRIRLSRKAVL 693
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 214-320 3.92e-21

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 89.85  E-value: 3.92e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 214 MSLApiVGHIYNGRVISIQSFGAFIQLEGLRQrfeGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF-ELGKIGLSMKE 292
Cdd:COG1098    1 MSIE--VGDIVEGKVTGITPFGAFVELPEGTT---GLVHISEIADGYVKDINDYLKVGDEVKVKVLSIdEDGKISLSIKQ 75

                         90       100
                 ....*....|....*....|....*...
gi 393912173 293 VdqetgQDLNPHEPTPLADGARPPRNPE 320
Cdd:COG1098   76 A-----EEKPKRPPRPRRNSRPKAGFES 98
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 523-674 1.99e-20

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 97.30  E-value: 1.99e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 523 SLPIFALKKALLEAVAAQNILIVIGETGSGKTT----QITQymvevGYAARGRIGCTQPRRVAAMSVAKRVAEEMGCRLG 598
Cdd:PRK11664   3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTwlplQLLQ-----HGGINGKIIMLEPRRLAARNVAQRLAEQLGEKPG 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 393912173 599 SEVGYTIRFEDCTSQDTVVKYMTDGMLLRECLLDPDLTSYSVIMLDEAHERTIHTDVLFGLL---KAAVkkRPELKLIV 674
Cdd:PRK11664  78 ETVGYRMRAESKVGPNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLldvQQGL--RDDLKLLI 154
DEXDc smart00487
DEAD-like helicases superfamily;
530-668 2.58e-20

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 89.86  E-value: 2.58e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173   530 KKALLEAVAAQNILIVIGETGSGKTTQITQYMVEVGYA-ARGRIGCTQPRRVAAMSVAKRVAEEMGCRLGSEVGYT---- 604
Cdd:smart00487  14 KEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRgKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYggds 93

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 393912173   605 --IRFEDCTSQDTVVKYMTDGMLLRECLLDP-DLTSYSVIMLDEAHERT--IHTDVLFGLLKAAVKKRP 668
Cdd:smart00487  94 krEQLRKLESGKTDILVTTPGRLLDLLENDKlSLSNVDLVILDEAHRLLdgGFGDQLEKLLKLLPKNVQ 162
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 692-894 3.37e-20

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 97.05  E-value: 3.37e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  692 MAEFPLEPSLAKLLIMSVDLCCSDEVLTIVSMLSVQNVFYRPKDKQEIADQKKAKFHQPEGDHLTLLavyNSWKHHHFSQ 771
Cdd:PRK11131  489 LAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRERPMDKQQASDEKHRRFADKESDFLAFV---NLWNYLQEQQ 565

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  772 P---------WC---YENFIQIRTLkraQDIRKQLLSIMDRHKLNTISCGRDVQRIQKAICSGFFRNAAKRDPQEGYRTI 839
Cdd:PRK11131  566 KalssnqfrrLCrtdYLNYLRVREW---QDIYTQLRQVVKELGIPVNSEPAEYREIHTALLTGLLSHIGMKDAEKQEYTG 642

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 393912173  840 VDGQNVYIHPSSALFQNQPEWVVYHELVMTTKEYMREVTAIEAKWLVEFAPSFFK 894
Cdd:PRK11131  643 ARNARFSIFPGSGLFKKPPKWVMVAELVETSRLWGRIAARIEPEWIEPLAQHLIK 697
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 221-290 1.38e-19

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 83.36  E-value: 1.38e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 393912173 221 GHIYNGRVISIQSFGAFIQLEGLRqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF-ELGKIGLSM 290
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGK---DGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVdDRGRISLSR 68
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 691-757 6.93e-19

Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 461295 [Multi-domain]  Cd Length: 104  Bit Score: 82.67  E-value: 6.93e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  691 TMAEFPLEPSLAKLLIMSVDLCCSDEVLTIVSMLSVQNVFYRP------KDKQEIADQKKAKFHQ---------PEGDHL 755
Cdd:pfam04408  23 KMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPnfldprSAAKAARRRRRAADEKarakfarldLEGDHL 102


                  ..
gi 393912173  756 TL 757
Cdd:pfam04408 103 TL 104
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 221-291 6.94e-18

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 78.48  E-value: 6.94e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 393912173 221 GHIYNGRVISIQSFGAFIQLEGlrqRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVI-KFELGKIGLSMK 291
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGG---GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLsIDARGRISLSIK 69
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 220-291 1.61e-17

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 85.10  E-value: 1.61e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMK 291
Cdd:COG0539  189 EGDVVEGTVKNITDFGAFVDLGGV----DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIdrEKERISLSLK 258
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
220-299 3.11e-16

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 83.46  E-value: 3.11e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLE-GLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMKEVDQE 296
Cdd:PRK00087 562 VGSIVLGKVVRIAPFGAFVELEpGV----DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVdpEEKRIRLSIKEVEEE 637


                 ...
gi 393912173 297 TGQ 299
Cdd:PRK00087 638 PGD 640
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 220-293 3.47e-15

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 78.16  E-value: 3.47e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLE-GLrqrfEGLLHISQIRQD-RVNAVSDVLNRNQKVKVKV--IKFELGKIGLSMKEV 293
Cdd:COG0539  274 VGDVVKGKVTRLTDFGAFVELEpGV----EGLVHISEMSWTkRVAHPSDVVKVGDEVEVKVldIDPEERRISLSIKQL 347
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
220-291 4.25e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 70.71  E-value: 4.25e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 393912173   220 VGHIYNGRVISIQSFGAFIQLEGlrqRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFEL--GKIGLSMK 291
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGN---GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEekGRIILSLK 72
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 218-291 1.05e-14

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 69.82  E-value: 1.05e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 393912173 218 PIVGHIYNGRVISIQSFGAFIQLEGLRQrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFEL-GKIGLSMK 291
Cdd:cd05686    1 PALYQIFKGEVASVTEYGAFVKIPGCRK--QGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMkDKMKLSLS 73
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 220-289 1.58e-14

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 69.19  E-value: 1.58e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGlrqrFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLS 289
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLGG----VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIdkERKRISLG 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 220-293 1.67e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 76.45  E-value: 1.67e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMKEV 293
Cdd:PRK06676 192 EGDVVEGTVARLTDFGAFVDIGGV----DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIdwETERISLSLKDT 263
PRK08059 PRK08059
general stress protein 13; Validated
 220-327 9.58e-14

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 68.53  E-value: 9.58e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGLRQrfeGLLHISQIRQDRVNAVSDVLNRNQKVKVKV--IKFELGKIGLSMKEVD--- 294
Cdd:PRK08059   7 VGSVVTGKVTGIQPYGAFVALDEETQ---GLVHISEITHGFVKDIHDFLSVGDEVKVKVlsVDEEKGKISLSIRATEeap 83

                         90       100       110
                 ....*....|....*....|....*....|...
gi 393912173 295 QETGQDLNPHEPTPLADGARPPRNPEAPWMDPS 327
Cdd:PRK08059  84 EAKRKKGKILIPNPSEQGFNTLRDKLEEWIEQS 116
PRK05807 PRK05807
RNA-binding protein S1;
220-292 1.67e-13

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 68.23  E-value: 1.67e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFEL-GKIGLSMKE 292
Cdd:PRK05807   5 AGSILEGTVVNITNFGAFVEVEGK----TGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDnGKISLSIKQ 74
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
220-293 5.38e-13

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 73.06  E-value: 5.38e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMKEV 293
Cdd:PRK00087 477 EGDVVEGEVKRLTDFGAFVDIGGV----DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIdkENKKLSLSLKKL 548
GH2_like cd21690
GIPC homology 2 (GH2) domain-like family; The GIPC (GAIP C-terminus-interacting protein) ...
 7-70 1.50e-12

GIPC homology 2 (GH2) domain-like family; The GIPC (GAIP C-terminus-interacting protein) family of proteins mediate endocytosis by tethering cargo proteins to the motor myosin VI. This model represents the C-terminal GIPC homology 2 or GH2 domain (plus the linker to the PDZ domain located N-terminally of GH2), which mediates the interaction with myosin VI and is involved in homodimerization in the autoinhibited state. The family also includes DEAH box protein 8 (DHX8) and similar proteins. DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 contains a GH2-like domain at the N-terminus, which shows high sequence similarity with the GH2 domain found in GIPC proteins.


Pssm-ID: 409667  Cd Length: 62  Bit Score: 63.26  E-value: 1.50e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 393912173   7 LSLVSRVCVELDNHFGLADKDVAEFIIYLATENPTFDKFKKSITKEGLAdqFDDSLLANLLRII 70
Cdd:cd21690    1 LSAIEKVDDLLKNYLGIDDPELAEFVISLAKKKKNPDEFAEALDENDAA--FPDEFVFDLYRAI 62
PRK08582 PRK08582
RNA-binding protein S1;
220-322 2.98e-12

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 65.05  E-value: 2.98e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGLRQrfeGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFEL-GKIGLSMKE-VDQET 297
Cdd:PRK08582   5 VGSKLQGKVTGITNFGAFVELPEGKT---GLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDdGKIGLSIKKaKDRPK 81

                         90       100
                 ....*....|....*....|....*
gi 393912173 298 GQDLNPHEPTPladgaRPPRNPEAP 322
Cdd:PRK08582  82 RQHDRPRHEDN-----RGGGNDVAP 101
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 220-307 3.39e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 69.13  E-value: 3.39e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 220 VGHIYNGRVISIQSFGAFIQL-EGLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKV--IKFELGKIGLSMKEVDQE 296
Cdd:PRK06676 277 EGDVIEGTVKRLTDFGAFVEVlPGV----EGLVHISQISHKHIATPSEVLEEGQEVKVKVleVNEEEKRISLSIKALEEA 352

                         90
                 ....*....|.
gi 393912173 297 TGQDLNPHEPT 307
Cdd:PRK06676 353 PAEEEDRREEY 363
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 221-291 1.14e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 68.27  E-value: 1.14e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 393912173 221 GHIYNGRVISIQSFGAFIQLEGLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMK 291
Cdd:PRK06299 202 GQVVEGVVKNITDYGAFVDLGGV----DGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFdkEKKRVSLGLK 270
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 221-289 2.07e-10

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 57.24  E-value: 2.07e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 393912173 221 GHIYNGRVISIQSFGAFIQLeGLRQrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIK--FELGKIGLS 289
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDI-GVKQ--DGLIHISKMADRFVSHPSDVVSVGDIVEVKVISidEERGRISLS 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 224-290 3.23e-10

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 56.62  E-value: 3.23e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173 224 YNGRVISIQSFGAFIQLEGlrqRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFELGKIGLSM 290
Cdd:cd00164    1 VTGKVVSITKFGVFVELED---GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 220-291 4.19e-10

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 56.95  E-value: 4.19e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGlrQRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMK 291
Cdd:cd05708    2 VGQKIDGTVRRVEDYGVFIDIDG--TNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIdaEKKRISLGLK 73
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 226-295 9.16e-10

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 62.06  E-value: 9.16e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 393912173  226 GRVISIQSFGAFIQLEGlrqrFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMKEVDQ 295
Cdd:TIGR00717 193 GVVKNITDFGAFVDLGG----VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFdkEKGRISLSLKQLGE 260
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 220-298 1.10e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 60.97  E-value: 1.10e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMKEVDQET 297
Cdd:PRK07400 196 VGEVVVGTVRGIKPYGAFIDIGGV----SGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLdaERGRISLSTKQLEPEP 271


                 .
gi 393912173 298 G 298
Cdd:PRK07400 272 G 272
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 218-291 4.39e-09

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 53.74  E-value: 4.39e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 393912173 218 PIVGHIYNGRVISIQSFGAFIQLEGLrQRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMK 291
Cdd:cd04452    1 PEEGELVVVTVKSIADMGAYVSLLEY-GNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVdkEKGYIDLSKK 75
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 220-296 4.57e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 60.18  E-value: 4.57e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGlrqRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFEL--GKIGLSMKEVDQE 296
Cdd:PRK06299 460 KGSIVTGTVTEVKDKGAFVELED---GVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRknRRISLSIKALDEA 535
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 218-290 7.36e-09

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: 53.06  E-value: 7.36e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 393912173  218 PIVGHIYNGRVISIQSFGAFIQLEGlrqRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFEL--GKIGLSM 290
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGN---GVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKdrRRIILSI 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 220-293 2.25e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 57.87  E-value: 2.25e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLE-GLrqrfEGLLHISQIRQDRVN-AVSDVLNRNQKVKVKV--IKFELGKIGLSMKEV 293
Cdd:PRK06299 286 VGSKVKGKVTNITDYGAFVELEeGI----EGLVHVSEMSWTKKNkHPSKVVSVGQEVEVMVleIDEEKRRISLGLKQC 359
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
234-299 3.05e-08

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 57.73  E-value: 3.05e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 393912173 234 FGAFIQLeGLRQrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFEL--GKIGLSMKEVDQETGQ 299
Cdd:COG2183  655 FGAFVDI-GVHQ--DGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLkrKRISLSMKLDDEAGAA 719
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 218-296 5.13e-08

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 55.22  E-value: 5.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 218 PIVGHIYNGRVISIQSFGAFIQLE---GLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMKE 292
Cdd:PRK03987   6 PEEGELVVGTVKEVKDFGAFVTLDeypGK----EGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVdpRKGHIDLSLKR 81


                 ....*
gi 393912173 293 V-DQE 296
Cdd:PRK03987  82 VnEHQ 86
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 218-296 1.32e-07

Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]; Translation initiation factor 2, alpha subunit (eIF-2alpha) is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440710 [Multi-domain]  Cd Length: 259  Bit Score: 53.66  E-value: 1.32e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 218 PIVGHIYNGRVISIQSFGAFIQL---EGLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF--ELGKIGLSMKE 292
Cdd:COG1093    8 PEEGELVVGTVKEVKDFGAYVTLdeyEGK----EGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVdpKRGHIDLSLKR 83


                 ....
gi 393912173 293 VDQE 296
Cdd:COG1093   84 VNEH 87
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
226-296 1.55e-07

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 50.86  E-value: 1.55e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 393912173 226 GRVISIQSFGAFIQLEGLRQrfeGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFE--LGKIGLSMKEVDQE 296
Cdd:PRK07252   9 GTITGIKPYGAFVALENGTT---GLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDeyTGKASLSLRTLEEE 78
rpsA PRK13806
30S ribosomal protein S1; Provisional
 220-303 2.67e-07

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 54.35  E-value: 2.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLE-GLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFELG------KIGLSMKE 292
Cdd:PRK13806 202 EGDVVEGTVTRLAPFGAFVELApGV----EGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAkkgkglRISLSIKQ 277

                         90
                 ....*....|....*
gi 393912173 293 VD----QETGQDLNP 303
Cdd:PRK13806 278 AGgdpwDTVGDRLKA 292
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 220-307 1.10e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 52.35  E-value: 1.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEglrQRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFELG--KIGLSMKEVDQET 297
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVE---EGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLErrRISLSLKQANEGV 369

                         90
                 ....*....|
gi 393912173 298 GQDLNPHEPT 307
Cdd:PRK07899 370 TPESEDFDPA 379
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 211-291 2.86e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 50.93  E-value: 2.86e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 211 RRRMSLA-------P--------IVGHIYNGRVISIQSFGAFIQLEGlrqRFEGLLHISQIRQDR-VNAVSDVLNRNQKV 274
Cdd:PRK06299 349 KRRISLGlkqckenPweefaekyPVGDVVEGKVKNITDFGAFVGLEG---GIDGLVHLSDISWDKkGEEAVELYKKGDEV 425

                         90
                 ....*....|....*....
gi 393912173 275 KVKVIKF--ELGKIGLSMK 291
Cdd:PRK06299 426 EAVVLKVdvEKERISLGIK 444
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 220-280 3.13e-06

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.


Pssm-ID: 239917 [Multi-domain]  Cd Length: 83  Bit Score: 45.85  E-value: 3.13e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGLRqrFEGLLHISQIRQD--RVNAVSDVL----NRN-----QKVKVKVIK 280
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVELDNLT--VEGLVHVSTLGDDyyEFDEENHALvgerTGKvfrlgDKVKVRVVR 70
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 212-343 1.17e-05

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 49.51  E-value: 1.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 212 RRMSLAPIVGHIY-NGRVISIQSFGAFIQLEGLRqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKF-ELGKIGLS 289
Cdd:PLN00207 745 SSLTMVPTVGDIYrNCEIKSIAPYGAFVEIAPGR---EGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVnDKGQLRLS 821

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 393912173 290 MK----EVDQETGQDLNPHEPTPlaDGARPPRNpeapwmdPSTSRNPDDVSVTQSKSV 343
Cdd:PLN00207 822 RRallpEANSEKSSQKQQGGSTK--DKAPQKKY-------VNTSSRPRRAAQAEKNSA 870
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 549-647 1.23e-05

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 46.00  E-value: 1.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 549 TGSGKTTQITQYMVEVGYAARGRIGCTQPRRVaamsvakrVAEEMGCRL-GSEVGY-TIRFEDCTSQDTVVKYMTDGMLL 626
Cdd:cd17931   10 PGAGKTTRVLPQIIREAIKKRLRTLVLAPTRV--------VAAEMYEALrGLPIRYrTGAVKEEHGGNEIVDYMCHGTFT 81

                         90       100
                 ....*....|....*....|..
gi 393912173 627 REcLLDPDLT-SYSVIMLDEAH 647
Cdd:cd17931   82 CR-LLSPKRVpNYNLIIMDEAH 102
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 220-293 1.67e-05

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 48.58  E-value: 1.67e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 393912173  220 VGHIYNGRVISIQSFGAFIQL-EGLrqrfEGLLHISQIRQDRVNA-VSDVLNRNQKVKVKVIKF--ELGKIGLSMKEV 293
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIeEGI----EGLVHVSEMSWVKKNShPSKVVKKGDEVEVMILDIdpERRRLSLGLKQC 345
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 223-292 5.38e-05

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.


Pssm-ID: 239907 [Multi-domain]  Cd Length: 99  Bit Score: 43.04  E-value: 5.38e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 223 IYNGRVISIQSFGAFIQLeglrQRFEGLLHISQIRQDRV-----------NAVSDVLNRNQKVKVKVI-------KFELG 284
Cdd:cd04460    2 VVEGEVVEVVDFGAFVRI----GPVDGLLHISQIMDDYIsydpknkrligEETKRVLKVGDVVRARIVavslkerRPRES 77


                 ....*...
gi 393912173 285 KIGLSMKE 292
Cdd:cd04460   78 KIGLTMRQ 85
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 218-291 5.94e-05

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 44.82  E-value: 5.94e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 218 PIVGHIYNGRVISIQSFGAFIQLeGlrqRFEGLLHISQIRQDRVNAVSD-----------VLNRNQKVKVKVI------- 279
Cdd:PRK08563  79 PELQEVVEGEVVEVVEFGAFVRI-G---PVDGLLHISQIMDDYISYDPKngrligkeskrVLKVGDVVRARIVavslker 154

                         90
                 ....*....|..
gi 393912173 280 KFELGKIGLSMK 291
Cdd:PRK08563 155 RPRGSKIGLTMR 166
VacB COG0557
Exoribonuclease R [Transcription];
220-297 6.34e-05

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 46.64  E-value: 6.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGLRqrFEGLLHISQIRQD--RVNAVSDVL----NRN-----QKVKVKVIK--FELGKI 286
Cdd:COG0557  622 VGEEFEGVISGVTSFGLFVELDELG--VEGLVHVSSLGDDyyEYDERRQALvgerTGKryrlgDRVEVRVVRvdLDRRQI 699

                         90
                 ....*....|.
gi 393912173 287 GLSMKEVDQET 297
Cdd:COG0557  700 DFELVEGGSEA 710
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 220-291 6.78e-05

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 46.65  E-value: 6.78e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 393912173  220 VGHIYNGRVISIQSFGAFIQLEGlrqRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFEL--GKIGLSMK 291
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPG---GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKknRKVSLSVK 516
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 543-673 8.08e-05

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 43.55  E-value: 8.08e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 543 LIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEMgcRLGSEVGYTIRFED------CTSQDTV 616
Cdd:cd00046    4 VLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELF--GPGIRVAVLVGGSSaeerekNKLGDAD 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 617 VKYMTDGMLLRECLLD--PDLTSYSVIMLDEAHERTIHTDVLFGLLKAAVKK-RPELKLI 673
Cdd:cd00046   82 IIIATPDMLLNLLLREdrLFLKDLKLIIVDEAHALLIDSRGALILDLAVRKAgLKNAQVI 141
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 221-291 2.02e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 45.04  E-value: 2.02e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 393912173 221 GHIYNGRVISIQSFGAFIQLEGLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFELG--KIGLSMK 291
Cdd:PRK07899 209 GQVRKGVVSSIVNFGAFVDLGGV----DGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDreRVSLSLK 277
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 221-290 2.52e-04

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 40.17  E-value: 2.52e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 393912173 221 GHIYNGRVISIQSFGAFIQLEGlrqRFEGLLHISQIR-QDRVNAVSDVLNRNQKVKVKVIKFELGKIGLSM 290
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDG---GIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
rpsA PRK13806
30S ribosomal protein S1; Provisional
 220-292 2.79e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 44.72  E-value: 2.79e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLE-GLrqrfEGLLHISQIRQ-DRVNAVSDVLNRNQKVKVKVIKFELGK--IGLSMKE 292
Cdd:PRK13806 292 AGDKVTGKVVRLAPFGAFVEILpGI----EGLVHVSEMSWtRRVNKPEDVVAPGDAVAVKIKDIDPAKrrISLSLRD 364
AAA_22 pfam13401
AAA domain;
540-647 5.04e-04

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 40.79  E-value: 5.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173  540 QNILIVIGETGSGKTTQITQYMVEVGYAARGRIGCTQPRRVAAMSVAKRVAEEmgcrLGSEVGYTIRFEDCTSQdtvvky 619
Cdd:pfam13401   5 AGILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKDLLRALLRA----LGLPLSGRLSKEELLAA------ 74

                          90       100
                  ....*....|....*....|....*...
gi 393912173  620 MTDgmLLRECLLDPdltsysVIMLDEAH 647
Cdd:pfam13401  75 LQQ--LLLALAVAV------VLIIDEAQ 94
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 220-292 6.43e-04

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 43.57  E-value: 6.43e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 393912173  220 VGHIYNGRVISIQSFGAFIQLEGlrqRFEGLLHISQIRQDRVNAVSDVLNRNQ---KVKVKVIKFELGKIGLSMKE 292
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVELEG---GIDGLIHLSDISWDKDGREADHLYKKGdeiEAVVLAVDKEKKRISLGVKQ 431
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 217-280 7.94e-04

S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay.


Pssm-ID: 239900 [Multi-domain]  Cd Length: 88  Bit Score: 39.11  E-value: 7.94e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 393912173 217 APIVGHIYNGRVI----SIQsfGAFIQLeGLRQrfEGLLHISQIRQ---DRVNAVSDVLNRNQKVKVKVIK 280
Cdd:cd04453    4 EPIVGNIYLGRVKkivpGLQ--AAFVDI-GLGK--NGFLHLSDILPayfKKHKKIAKLLKEGQEILVQVVK 69
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 221-294 9.78e-04

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 38.79  E-value: 9.78e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393912173 221 GHIYNGRVISIQSFGAFIQL-EGLrqrfEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFELG--KIGLSMKEVD 294
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLgDGV----EGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKnrKISLSIKAKE 73
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 220-300 1.46e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 42.17  E-value: 1.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 220 VGHIYNGRVISIQSFGAFIQLEGlrQRFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFELGKIG--LSMKEVDQET 297
Cdd:PRK06676  17 VGDVVTGEVLKVEDKQVFVNIEG--YKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNllLSKRRLEAEK 94


                 ...
gi 393912173 298 GQD 300
Cdd:PRK06676  95 AWD 97
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 220-317 1.59e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 42.39  E-value: 1.59e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 220 VGHIYNGRVISIQSFGAFIQL-EGLrqrfEGLLHISQIRQ-DRVNAVSDVLNRNQKVKVKVIKFEL--GKIGLSMKEVDQ 295
Cdd:PRK12269 578 VNDVVKGRVTKIADFGAFIELaEGI----EGLAHISEFSWvKKTSKPSDMVKIGDEVECMILGYDIqaGRVSLGLKQVTA 653

                         90       100
                 ....*....|....*....|..
gi 393912173 296 ETGQDLNPHEPTpladGARPPR 317
Cdd:PRK12269 654 NPWEEIEARYPV----GARFTR 671
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 225-291 2.23e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 42.01  E-value: 2.23e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 393912173 225 NGRVISIQSFGAFIQLEGlrqrFEGLLHISQIRQDRVNAVSDVLNRNQKVKVKVIKFELG--KIGLSMK 291
Cdd:PRK12269 498 SGVVKSFTSFGAFIDLGG----FDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAekRINLSLK 562
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
 531-645 7.44e-03

DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350690 [Multi-domain]  Cd Length: 189  Bit Score: 38.65  E-value: 7.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393912173 531 KALLEAVAA--QNILIVIGeTGSGKTTQITQ---YMVEVgyaargriGCTQPRRVAAMSVAKRVAEEMGCRLGSEVGYTi 605
Cdd:cd17932    2 PEQREAVTHpdGPLLVLAG-AGSGKTRVLTHriaYLILE--------GGVPPERILAVTFTNKAAKEMRERLRKLLGEQ- 71

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 393912173 606 RFEDCT-------SQDTVVKYMTDGMLLRECL----LDPDLTS-----YSVIMLDE 645
Cdd:cd17932   72 LASGVWigtfhsfALRILRRYGDFDDLLLYALelleENPDVREklqsrFRYILVDE 127
 
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

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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