Citrus Sinensis ID: 005716
Local Sequence Feature Prediction
| Prediction and (Method) | Result |
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Close Homologs for Annotation Transfer
Close Homologs in SWISS-PROT Database Detected by BLAST 
Original result of BLAST against SWISS-PROT Database
| ID | Alignment graph | Length |
Definition |
RBH(Q2H) |
RBH(H2Q) |
Q cover |
H cover |
Identity |
E-value |
| Query | 681 | 2.2.26 [Sep-21-2011] | |||||||
| Q45388 | 791 | Protein tex OS=Bordetella | yes | no | 0.132 | 0.113 | 0.363 | 4e-05 | |
| P57072 | 757 | Uncharacterized protein N | yes | no | 0.132 | 0.118 | 0.363 | 4e-05 | |
| Q51152 | 757 | Uncharacterized protein N | yes | no | 0.132 | 0.118 | 0.363 | 5e-05 |
| >sp|Q45388|TEX_BORPE Protein tex OS=Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) GN=tex PE=4 SV=2 | Back alignment and function desciption |
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Score = 50.4 bits (119), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 36/99 (36%), Positives = 50/99 (50%), Gaps = 9/99 (9%)
Query: 253 PGRRKR----GKDYEEGMYELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGN 308
PGR R ++EG+ L +PG + EG VT V + GAFVDIG DG V I
Sbjct: 644 PGRDPRPEFKTAQFKEGVETLNDLFPGMVLEGVVTNVANF-GAFVDIGVHQDGLVHISAL 702
Query: 309 DWYWI---RHHIKVGMHVIVEILAKRDPYRFRFPIEMRF 344
++ R ++VG V V++L + D R R + MR
Sbjct: 703 AEKFVKDPRDVVRVGQTVTVKVL-EVDVARKRVALTMRL 740
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Transcription accessory protein. Exact function not known. Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) (taxid: 257313) |
| >sp|P57072|YHGF_NEIMA Uncharacterized protein NMA0194 OS=Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) GN=NMA0194 PE=4 SV=1 | Back alignment and function description |
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| >sp|Q51152|YHGF_NEIMB Uncharacterized protein NMB0075 OS=Neisseria meningitidis serogroup B (strain MC58) GN=NMB0075 PE=4 SV=2 | Back alignment and function description |
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Close Homologs in the Non-Redundant Database Detected by BLAST
Original result of BLAST against Nonredundant Database
| GI | Alignment Graph | Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 681 | ||||||
| 225456246 | 674 | PREDICTED: uncharacterized protein LOC10 | 0.986 | 0.997 | 0.756 | 0.0 | |
| 449440582 | 672 | PREDICTED: uncharacterized protein LOC10 | 0.972 | 0.985 | 0.723 | 0.0 | |
| 356508784 | 674 | PREDICTED: uncharacterized protein LOC10 | 0.977 | 0.988 | 0.722 | 0.0 | |
| 356516583 | 676 | PREDICTED: uncharacterized protein LOC10 | 0.988 | 0.995 | 0.730 | 0.0 | |
| 356516585 | 705 | PREDICTED: uncharacterized protein LOC10 | 0.988 | 0.954 | 0.701 | 0.0 | |
| 295322838 | 680 | plastid RNA-binding protein [Nicotiana b | 0.945 | 0.947 | 0.754 | 0.0 | |
| 297816052 | 675 | PDE312/PTAC10 [Arabidopsis lyrata subsp. | 0.975 | 0.983 | 0.715 | 0.0 | |
| 42565717 | 668 | CONSTANS interacting protein 5-like prot | 0.964 | 0.983 | 0.705 | 0.0 | |
| 45544875 | 600 | CONSTANS interacting protein 5, partial | 0.879 | 0.998 | 0.768 | 0.0 | |
| 145332787 | 697 | CONSTANS interacting protein 5-like prot | 0.964 | 0.942 | 0.676 | 0.0 |
| >gi|225456246|ref|XP_002279352.1| PREDICTED: uncharacterized protein LOC100264639 [Vitis vinifera] | Back alignment and taxonomy information |
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Score = 1023 bits (2646), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 517/683 (75%), Positives = 577/683 (84%), Gaps = 11/683 (1%)
Query: 1 MQILQSSHLFTFPKPLNPNRPLLHNNNNNRRHVTFPAA--ATTKSFPPKCFSSDEFPVDE 58
MQILQS HLFTFP +RP + R V F A + + F K SSDEFPVDE
Sbjct: 1 MQILQSPHLFTFPS----HRPPRTLPKSYRLPVPFRAGNLSVSGKFVVKSVSSDEFPVDE 56
Query: 59 TFLEQFGPKDKETEDEARRRNWIERGWAPWEEILTPEADFARKSLNEGDEVALQSPEAVE 118
TFLE+FGPKDKETEDEARR+NWIERGWAPWEEILTPEADFARKSLNEG+EV L++PEA+E
Sbjct: 57 TFLEKFGPKDKETEDEARRKNWIERGWAPWEEILTPEADFARKSLNEGEEVPLKTPEAIE 116
Query: 119 AFKMLKPSYRMKKIKEMGITEDEWYKKQFEIKGEIPEKLETVWAAPLLVTHVAPRDWPPR 178
AFKML P YR KK++E G+TEDEWY KQFEIKGEIPE + T W PL+V HV PRDWPPR
Sbjct: 117 AFKMLNPKYRKKKMEESGLTEDEWYAKQFEIKGEIPEPVRTFWDGPLVVRHVPPRDWPPR 176
Query: 179 GWEVDRKELEYIREAHKLQNVRVEIGELERKAKFEREGFNFDMYRVFLKQYNQWVAANKD 238
GWEV+RKEL +IREAHKLQ VRV+ LE A+ + N + Y+ FLKQYN+WV NKD
Sbjct: 177 GWEVNRKELAFIREAHKLQAVRVDPKGLE-SARTNTDDLNLERYKTFLKQYNEWVEHNKD 235
Query: 239 RLEEESYKYDQDYYPGRRKRGKDYEEGMYELPFYYPGQICEGKVTTVHLYQGAFVDIGGV 298
RLEEES++ DQDY+PGRRKRGKDYEEGMYELPFYYPGQIC GKVTT+HLYQGAFVDIGGV
Sbjct: 236 RLEEESFQDDQDYHPGRRKRGKDYEEGMYELPFYYPGQICAGKVTTLHLYQGAFVDIGGV 295
Query: 299 YDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQPNIDHLIFNRFD 358
YDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV PNIDHLIFNRFD
Sbjct: 296 YDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFVDPNIDHLIFNRFD 355
Query: 359 FAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAEQLIL 418
F PIFH DED NPDELRRDCGRPP+P+K PG+K EEE LLS HPYVDKLWQIH AEQ+IL
Sbjct: 356 FPPIFHHDEDTNPDELRRDCGRPPIPKKDPGIKVEEEPLLSNHPYVDKLWQIHVAEQMIL 415
Query: 419 DDMEANPDKYKGKKLSELTDDEEFDDENSVEYTKVNYKKALLAKIILKTSVKELDLEAAL 478
DDME NP KY+GKKL+ELTDDE+FD+ENSVEYTKV YKK+LL K ILKTSVKELDLEAAL
Sbjct: 416 DDMEVNPHKYEGKKLTELTDDEDFDEENSVEYTKVYYKKSLLPKKILKTSVKELDLEAAL 475
Query: 479 AEREHHNKLQREAKERGEQYKVYKLRRNFEMDEYNFIHWRRSLEEREALIRDISCRQALG 538
AERE+HNKL++EAKERGE+YK+YKLRRN EMDEY+ IHWRRS EEREALIRDISCRQALG
Sbjct: 476 AEREYHNKLRKEAKERGEEYKIYKLRRNIEMDEYDLIHWRRSFEEREALIRDISCRQALG 535
Query: 539 LPLEEPGRYKEDSFFGKDEYDPSNPLYRYDYWGEPKNSEKSLQERMRDAHNKSIVGKGMV 598
LPLEEPG+ + S+FGK +YDP +PLYRYDYWGEPKNSEKS Q+RM DAHNKSIVGKG V
Sbjct: 536 LPLEEPGKLVDASYFGKGQYDPQHPLYRYDYWGEPKNSEKSKQQRMTDAHNKSIVGKGTV 595
Query: 599 WYEMSYDDVIKQKMQREARSKCVTPEEVEEEDSTSGHGNGDDDDDGDFDYSILSDSSSLS 658
WYEMSY+D IKQ+MQREAR+K + E EE+D T + DDD+ SIL D SS+
Sbjct: 596 WYEMSYEDAIKQRMQREARAKEMRKEAAEEDDDTEEEDDDDDDEFDF---SILGD-SSVD 651
Query: 659 FSNQPVVNGTESSSISDEGMFED 681
+SNQP+VNGTESS +SDEGMFE+
Sbjct: 652 YSNQPLVNGTESSRMSDEGMFEN 674
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Source: Vitis vinifera Species: Vitis vinifera Genus: Vitis Family: Vitaceae Order: Vitales Class: Phylum: Streptophyta Superkingdom: Eukaryota |
| >gi|449440582|ref|XP_004138063.1| PREDICTED: uncharacterized protein LOC101217647 [Cucumis sativus] gi|449501394|ref|XP_004161354.1| PREDICTED: uncharacterized LOC101217647 [Cucumis sativus] | Back alignment and taxonomy information |
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| >gi|356508784|ref|XP_003523134.1| PREDICTED: uncharacterized protein LOC100775818 [Glycine max] | Back alignment and taxonomy information |
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| >gi|356516583|ref|XP_003526973.1| PREDICTED: uncharacterized protein LOC100783002 isoform 1 [Glycine max] | Back alignment and taxonomy information |
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| >gi|356516585|ref|XP_003526974.1| PREDICTED: uncharacterized protein LOC100783002 isoform 2 [Glycine max] | Back alignment and taxonomy information |
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| >gi|295322838|gb|ADG01868.1| plastid RNA-binding protein [Nicotiana benthamiana] | Back alignment and taxonomy information |
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| >gi|297816052|ref|XP_002875909.1| PDE312/PTAC10 [Arabidopsis lyrata subsp. lyrata] gi|297321747|gb|EFH52168.1| PDE312/PTAC10 [Arabidopsis lyrata subsp. lyrata] | Back alignment and taxonomy information |
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| >gi|42565717|ref|NP_190419.3| CONSTANS interacting protein 5-like protein [Arabidopsis thaliana] gi|332644902|gb|AEE78423.1| CONSTANS interacting protein 5-like protein [Arabidopsis thaliana] | Back alignment and taxonomy information |
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| >gi|45544875|gb|AAS67373.1| CONSTANS interacting protein 5, partial [Solanum lycopersicum] | Back alignment and taxonomy information |
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| >gi|145332787|ref|NP_001078259.1| CONSTANS interacting protein 5-like protein [Arabidopsis thaliana] gi|110738909|dbj|BAF01376.1| hypothetical protein [Arabidopsis thaliana] gi|332644903|gb|AEE78424.1| CONSTANS interacting protein 5-like protein [Arabidopsis thaliana] | Back alignment and taxonomy information |
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Prediction of Gene Ontology (GO) Terms
Close Homologs with Gene Ontology terms Detected by BLAST
Original result of BLAST against Gene Ontology (AMIGO)
| ID |
Alignment graph |
Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 681 | ||||||
| TAIR|locus:2101150 | 697 | PDE312 "PIGMENT DEFECTIVE 312" | 0.430 | 0.420 | 0.741 | 1.9e-124 |
| TAIR|locus:2101150 PDE312 "PIGMENT DEFECTIVE 312" [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
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Score = 1223 (435.6 bits), Expect = 1.9e-124, P = 1.9e-124
Identities = 221/298 (74%), Positives = 253/298 (84%)
Query: 45 PPKCFSSDEFPVDETFLEQFGPKDKETEDEARRRNWIERGWAPWEEILTPEADFARKSLN 104
P + FSSDEFPVDETFLE+FGPKDK+TEDEARRRNWIERGWAPWEEILTPEADFARKSLN
Sbjct: 38 PCRGFSSDEFPVDETFLEKFGPKDKDTEDEARRRNWIERGWAPWEEILTPEADFARKSLN 97
Query: 105 EGDEVALQSPEAVEAFKMLKPSYRMKKIKEMGITEDEWYKKQFEIKGEIPEKLETVWAAP 164
EG+EV LQSPEA+EAFKML+PSYR KKIKEMGITEDEWY KQFEI+G+ P LET WA P
Sbjct: 98 EGEEVPLQSPEAIEAFKMLRPSYRKKKIKEMGITEDEWYAKQFEIRGDKPPPLETSWAGP 157
Query: 165 LLVTHVAPRDWPPRGWEVDRKELEYIREAHKLQNVRVEIGELERKAKFEREG----FNFD 220
+++ + PRDWPPRGWEVDRKELE+IREAHKL RV + +L++ + + +
Sbjct: 158 MVLRQIPPRDWPPRGWEVDRKELEFIREAHKLMAERVWLEDLDKDLRVGEDATVDKMCLE 217
Query: 221 MYRVFLKQYNQWVAANKDRLEEESYKYDQDYYPGRRKRGKDYEEGMYELPFYYPGQICEG 280
++VFLKQY +WV NKDRLEEESYK DQD+YPGRRKRGKDYE+GMYELPFYYPG +CEG
Sbjct: 218 RFKVFLKQYKEWVEDNKDRLEEESYKLDQDFYPGRRKRGKDYEDGMYELPFYYPGMVCEG 277
Query: 281 KVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEI-LAKRDPYRFR 337
VTT+HLYQGAFVDIGGV++GWVPIKGNDW+WIRH IKVGMHVIVEI + R + FR
Sbjct: 278 TVTTLHLYQGAFVDIGGVHEGWVPIKGNDWFWIRHFIKVGMHVIVEITVILRHIFFFR 335
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Prediction of Enzyme Commission (EC) Number
EC Number Prediction by Annotation Transfer from SWISS-PROT Entries
Original result of BLAST against SWISS-PROT
No confident hit for EC number transfering in SWISSPROT detected by BLAST
EC Number Prediction by Ezypred Server
Original result from Ezypred Server
Fail to connect to Ezypred Server
EC Number Prediction by EFICAz Software
No EC number assignment, probably not an enzyme!
Prediction of Functionally Associated Proteins
Functionally Associated Proteins Detected by STRING
Original result from the STRING server
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 | GSVIVG00017894001 | SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (674 aa) | |||||||||
(Vitis vinifera) | |||||||||||
 | GSVIVG00030097001 | • | • | 0.589 | |||||||
 | GSVIVG00028352001 | • | • | 0.582 | |||||||
 | GSVIVG00026730001 | • | • | 0.564 | |||||||
 | GSVIVG00015449001 | • | • | 0.482 | |||||||
 | GSVIVG00021441001 | • | • | 0.458 | |||||||
 | GSVIVG00000431001 | • | • | 0.413 |
Conserved Domains and Related Protein Families
Conserved Domains Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
| ID | Alignment Graph | Length |
Definition |
E-value |
| Query | 681 | |||
| smart00316 | 72 | smart00316, S1, Ribosomal protein S1-like RNA-bind | 3e-05 | |
| cd05688 | 68 | cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R | 2e-04 | |
| PRK00087 | 647 | PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d | 0.002 |
| >gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain | Back alignment and domain information |
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Score = 42.2 bits (100), Expect = 3e-05
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 274 PGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRH---HIKVGMHVIVEILAK 330
G + EG VT + GAFVD+G +G +PI ++ +KVG V V++L+
Sbjct: 2 VGDVVEGTVTEI-TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV 60
Query: 331 RD 332
+
Sbjct: 61 DE 62
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Length = 72 |
| >gnl|CDD|240193 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain | Back alignment and domain information |
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| >gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed | Back alignment and domain information |
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Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 681 | |||
| COG0539 | 541 | RpsA Ribosomal protein S1 [Translation, ribosomal | 99.97 | |
| COG0539 | 541 | RpsA Ribosomal protein S1 [Translation, ribosomal | 99.92 | |
| PTZ00248 | 319 | eukaryotic translation initiation factor 2 subunit | 99.9 | |
| PRK07899 | 486 | rpsA 30S ribosomal protein S1; Reviewed | 99.9 | |
| PRK13806 | 491 | rpsA 30S ribosomal protein S1; Provisional | 99.89 | |
| PRK12269 | 863 | bifunctional cytidylate kinase/ribosomal protein S | 99.89 | |
| PRK12269 | 863 | bifunctional cytidylate kinase/ribosomal protein S | 99.87 | |
| PRK13806 | 491 | rpsA 30S ribosomal protein S1; Provisional | 99.87 | |
| PRK06299 | 565 | rpsA 30S ribosomal protein S1; Reviewed | 99.86 | |
| COG1098 | 129 | VacB Predicted RNA binding protein (contains ribos | 99.84 | |
| PRK06676 | 390 | rpsA 30S ribosomal protein S1; Reviewed | 99.83 | |
| COG2183 | 780 | Tex Transcriptional accessory protein [Transcripti | 99.82 | |
| TIGR00717 | 516 | rpsA ribosomal protein S1. This model provides tru | 99.82 | |
| TIGR00717 | 516 | rpsA ribosomal protein S1. This model provides tru | 99.81 | |
| PRK06299 | 565 | rpsA 30S ribosomal protein S1; Reviewed | 99.79 | |
| PRK00087 | 647 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 99.78 | |
| cd05705 | 74 | S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a | 99.74 | |
| PRK07400 | 318 | 30S ribosomal protein S1; Reviewed | 99.74 | |
| PRK07400 | 318 | 30S ribosomal protein S1; Reviewed | 99.73 | |
| PRK08582 | 139 | hypothetical protein; Provisional | 99.72 | |
| cd05694 | 74 | S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp | 99.71 | |
| cd05704 | 72 | S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a | 99.69 | |
| PRK06676 | 390 | rpsA 30S ribosomal protein S1; Reviewed | 99.68 | |
| cd04461 | 83 | S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp | 99.68 | |
| cd05686 | 73 | S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom | 99.67 | |
| PRK07899 | 486 | rpsA 30S ribosomal protein S1; Reviewed | 99.67 | |
| PLN00207 | 891 | polyribonucleotide nucleotidyltransferase; Provisi | 99.65 | |
| PF00575 | 74 | S1: S1 RNA binding domain; InterPro: IPR003029 Rib | 99.64 | |
| cd05698 | 70 | S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp | 99.62 | |
| PRK07252 | 120 | hypothetical protein; Provisional | 99.62 | |
| cd04452 | 76 | S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr | 99.61 | |
| PRK05807 | 136 | hypothetical protein; Provisional | 99.61 | |
| cd05690 | 69 | S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p | 99.6 | |
| cd05703 | 73 | S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R | 99.6 | |
| cd05706 | 73 | S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a | 99.6 | |
| cd05684 | 79 | S1_DHX8_helicase S1_DHX8_helicase: The N-terminal | 99.59 | |
| cd05708 | 77 | S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a | 99.57 | |
| cd05696 | 71 | S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t | 99.57 | |
| cd05697 | 69 | S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t | 99.57 | |
| PRK08059 | 123 | general stress protein 13; Validated | 99.57 | |
| cd05707 | 68 | S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a | 99.56 | |
| cd05692 | 69 | S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p | 99.55 | |
| cd05691 | 73 | S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p | 99.55 | |
| cd05693 | 100 | S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp | 99.54 | |
| cd05687 | 70 | S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib | 99.52 | |
| cd05689 | 72 | S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p | 99.52 | |
| cd05789 | 86 | S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. | 99.52 | |
| cd04453 | 88 | S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik | 99.51 | |
| PRK11824 | 693 | polynucleotide phosphorylase/polyadenylase; Provis | 99.49 | |
| TIGR02696 | 719 | pppGpp_PNP guanosine pentaphosphate synthetase I/p | 99.47 | |
| cd05685 | 68 | S1_Tex S1_Tex: The C-terminal S1 domain of a trans | 99.46 | |
| PRK00087 | 647 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 99.46 | |
| cd04472 | 68 | S1_PNPase S1_PNPase: Polynucleotide phosphorylase | 99.46 | |
| cd05688 | 68 | S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p | 99.45 | |
| cd04471 | 83 | S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai | 99.45 | |
| cd05695 | 66 | S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t | 99.42 | |
| PRK03987 | 262 | translation initiation factor IF-2 subunit alpha; | 99.4 | |
| smart00316 | 72 | S1 Ribosomal protein S1-like RNA-binding domain. | 99.37 | |
| cd04465 | 67 | S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib | 99.37 | |
| cd04473 | 77 | S1_RecJ_like S1_RecJ_like: The S1 domain of the ar | 99.36 | |
| PHA02945 | 88 | interferon resistance protein; Provisional | 99.33 | |
| cd04460 | 99 | S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. | 99.31 | |
| COG1093 | 269 | SUI2 Translation initiation factor 2, alpha subuni | 99.29 | |
| cd05702 | 70 | S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R | 99.25 | |
| COG1185 | 692 | Pnp Polyribonucleotide nucleotidyltransferase (pol | 99.25 | |
| cd04454 | 82 | S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA- | 99.23 | |
| TIGR03591 | 684 | polynuc_phos polyribonucleotide nucleotidyltransfe | 99.22 | |
| cd00164 | 65 | S1_like S1_like: Ribosomal protein S1-like RNA-bin | 99.18 | |
| cd04455 | 67 | S1_NusA S1_NusA: N-utilizing substance A protein ( | 99.16 | |
| PRK09521 | 189 | exosome complex RNA-binding protein Csl4; Provisio | 99.14 | |
| PRK04163 | 235 | exosome complex RNA-binding protein Rrp4; Provisio | 99.05 | |
| TIGR00448 | 179 | rpoE DNA-directed RNA polymerase (rpoE), archaeal | 99.02 | |
| TIGR02063 | 709 | RNase_R ribonuclease R. This family consists of an | 98.92 | |
| PRK11642 | 813 | exoribonuclease R; Provisional | 98.82 | |
| TIGR00358 | 654 | 3_prime_RNase VacB and RNase II family 3'-5' exori | 98.73 | |
| PRK08563 | 187 | DNA-directed RNA polymerase subunit E'; Provisiona | 98.72 | |
| COG1095 | 183 | RPB7 DNA-directed RNA polymerase, subunit E' [Tran | 98.66 | |
| PRK09202 | 470 | nusA transcription elongation factor NusA; Validat | 98.65 | |
| TIGR00757 | 414 | RNaseEG ribonuclease, Rne/Rng family. The C-termin | 98.53 | |
| KOG1067 | 760 | consensus Predicted RNA-binding polyribonucleotide | 98.51 | |
| KOG1070 | 1710 | consensus rRNA processing protein Rrp5 [RNA proces | 98.3 | |
| cd05791 | 92 | S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. | 98.25 | |
| PRK12327 | 362 | nusA transcription elongation factor NusA; Provisi | 98.24 | |
| TIGR01953 | 341 | NusA transcription termination factor NusA. This m | 98.19 | |
| cd04462 | 88 | S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly | 98.11 | |
| KOG1070 | 1710 | consensus rRNA processing protein Rrp5 [RNA proces | 97.91 | |
| PTZ00162 | 176 | DNA-directed RNA polymerase II subunit 7; Provisio | 97.87 | |
| PRK05054 | 644 | exoribonuclease II; Provisional | 97.81 | |
| COG0557 | 706 | VacB Exoribonuclease R [Transcription] | 97.6 | |
| PRK11712 | 489 | ribonuclease G; Provisional | 97.55 | |
| COG1107 | 715 | Archaea-specific RecJ-like exonuclease, contains D | 97.49 | |
| PF13509 | 61 | S1_2: S1 domain; PDB: 3GO5_A. | 97.46 | |
| PRK10811 | 1068 | rne ribonuclease E; Reviewed | 97.45 | |
| TIGR02062 | 639 | RNase_B exoribonuclease II. This family consists o | 97.39 | |
| COG1097 | 239 | RRP4 RNA-binding protein Rrp4 and related proteins | 97.34 | |
| cd05790 | 86 | S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai | 97.13 | |
| COG1530 | 487 | CafA Ribonucleases G and E [Translation, ribosomal | 97.04 | |
| PF10447 | 82 | EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I | 96.79 | |
| PRK12328 | 374 | nusA transcription elongation factor NusA; Provisi | 96.79 | |
| KOG2916 | 304 | consensus Translation initiation factor 2, alpha s | 96.76 | |
| PHA02858 | 86 | EIF2a-like PKR inhibitor; Provisional | 96.43 | |
| KOG1856 | 1299 | consensus Transcription elongation factor SPT6 [RN | 96.19 | |
| COG1096 | 188 | Predicted RNA-binding protein (consists of S1 doma | 96.17 | |
| cd05699 | 72 | S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t | 96.09 | |
| COG2996 | 287 | Predicted RNA-bindining protein (contains S1 and H | 96.08 | |
| COG2996 | 287 | Predicted RNA-bindining protein (contains S1 and H | 95.51 | |
| cd05705 | 74 | S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a | 95.02 | |
| PRK12329 | 449 | nusA transcription elongation factor NusA; Provisi | 94.8 | |
| TIGR02696 | 719 | pppGpp_PNP guanosine pentaphosphate synthetase I/p | 93.77 | |
| COG1098 | 129 | VacB Predicted RNA binding protein (contains ribos | 93.45 | |
| cd04453 | 88 | S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik | 93.43 | |
| cd05689 | 72 | S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p | 92.91 | |
| PRK09521 | 189 | exosome complex RNA-binding protein Csl4; Provisio | 92.88 | |
| PLN00207 | 891 | polyribonucleotide nucleotidyltransferase; Provisi | 92.87 | |
| cd05704 | 72 | S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a | 92.69 | |
| PTZ00248 | 319 | eukaryotic translation initiation factor 2 subunit | 92.09 | |
| PRK08582 | 139 | hypothetical protein; Provisional | 91.64 | |
| cd05686 | 73 | S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom | 90.79 | |
| cd05690 | 69 | S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p | 90.55 | |
| cd05706 | 73 | S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a | 89.92 | |
| PF00313 | 66 | CSD: 'Cold-shock' DNA-binding domain; InterPro: IP | 89.85 | |
| cd05696 | 71 | S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t | 89.8 | |
| cd05707 | 68 | S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a | 89.6 | |
| KOG3298 | 170 | consensus DNA-directed RNA polymerase subunit E' [ | 89.37 | |
| COG1185 | 692 | Pnp Polyribonucleotide nucleotidyltransferase (pol | 88.84 | |
| cd05703 | 73 | S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R | 88.4 | |
| cd05698 | 70 | S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp | 88.17 | |
| cd04461 | 83 | S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp | 88.06 | |
| cd04473 | 77 | S1_RecJ_like S1_RecJ_like: The S1 domain of the ar | 87.26 | |
| cd05697 | 69 | S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t | 86.64 | |
| PRK08059 | 123 | general stress protein 13; Validated | 86.06 | |
| PF08292 | 122 | RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I | 85.73 | |
| PF10246 | 104 | MRP-S35: Mitochondrial ribosomal protein MRP-S35; | 85.61 | |
| TIGR03591 | 684 | polynuc_phos polyribonucleotide nucleotidyltransfe | 85.53 | |
| PRK05807 | 136 | hypothetical protein; Provisional | 84.87 | |
| PRK12442 | 87 | translation initiation factor IF-1; Reviewed | 83.94 | |
| PRK11824 | 693 | polynucleotide phosphorylase/polyadenylase; Provis | 82.66 | |
| cd05695 | 66 | S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t | 81.69 | |
| cd04452 | 76 | S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr | 81.42 | |
| PRK09937 | 74 | stationary phase/starvation inducible regulatory p | 81.31 | |
| COG4044 | 247 | Uncharacterized protein conserved in archaea [Func | 81.28 | |
| PF00575 | 74 | S1: S1 RNA binding domain; InterPro: IPR003029 Rib | 80.72 |
| >COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
Probab=99.97 E-value=1.8e-32 Score=293.10 Aligned_cols=120 Identities=25% Similarity=0.400 Sum_probs=116.5
Q ss_pred CCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccccc---ccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 269 LPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRH---HIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 269 L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~d---VLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
|+.|++||+|+|+|++||+| |||||||| +|||||||||||.++.+ ++++||+|+|+||++ |.+|+|||||||++
T Consensus 187 ~~~l~~G~vV~G~V~~It~~-GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~-D~e~~RVsLSlK~l 263 (541)
T COG0539 187 LNKLEVGEVVEGVVKNITDY-GAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISL-DEERGRVSLSLKQL 263 (541)
T ss_pred HhcCCCCceEEEEEEEeecC-cEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEE-ccCCCeEEEEehhc
Confidence 68999999999999999999 99999999 59999999999999865 999999999999999 89999999999999
Q ss_pred CCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehh
Q 005716 346 QPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHN 412 (681)
Q Consensus 346 ~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~ 412 (681)
.++||..|.++|++|..+. |.|.+ ++.|||||++.|||+||+|||.
T Consensus 264 ~~dPw~~i~~~~~~g~~v~-------G~Vt~--------------i~~~GafVei~~GvEGlvhvSE 309 (541)
T COG0539 264 EEDPWEGIEKKYPVGDKVE-------GKVTN--------------LTDYGAFVEIEEGVEGLVHVSE 309 (541)
T ss_pred ccCcHHHHhhhcCCCCEEE-------EEEEE--------------eecCcEEEEecCCccceeechh
Confidence 9999999999999999999 99999 9999999999999999999994
|
|
| >COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional | Back alignment and domain information |
|---|
| >PRK07899 rpsA 30S ribosomal protein S1; Reviewed | Back alignment and domain information |
|---|
| >PRK13806 rpsA 30S ribosomal protein S1; Provisional | Back alignment and domain information |
|---|
| >PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional | Back alignment and domain information |
|---|
| >PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional | Back alignment and domain information |
|---|
| >PRK13806 rpsA 30S ribosomal protein S1; Provisional | Back alignment and domain information |
|---|
| >PRK06299 rpsA 30S ribosomal protein S1; Reviewed | Back alignment and domain information |
|---|
| >COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >PRK06676 rpsA 30S ribosomal protein S1; Reviewed | Back alignment and domain information |
|---|
| >COG2183 Tex Transcriptional accessory protein [Transcription] | Back alignment and domain information |
|---|
| >TIGR00717 rpsA ribosomal protein S1 | Back alignment and domain information |
|---|
| >TIGR00717 rpsA ribosomal protein S1 | Back alignment and domain information |
|---|
| >PRK06299 rpsA 30S ribosomal protein S1; Reviewed | Back alignment and domain information |
|---|
| >PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed | Back alignment and domain information |
|---|
| >cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >PRK07400 30S ribosomal protein S1; Reviewed | Back alignment and domain information |
|---|
| >PRK07400 30S ribosomal protein S1; Reviewed | Back alignment and domain information |
|---|
| >PRK08582 hypothetical protein; Provisional | Back alignment and domain information |
|---|
| >cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >PRK06676 rpsA 30S ribosomal protein S1; Reviewed | Back alignment and domain information |
|---|
| >cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains | Back alignment and domain information |
|---|
| >cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >PRK07899 rpsA 30S ribosomal protein S1; Reviewed | Back alignment and domain information |
|---|
| >PLN00207 polyribonucleotide nucleotidyltransferase; Provisional | Back alignment and domain information |
|---|
| >PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms | Back alignment and domain information |
|---|
| >cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >PRK07252 hypothetical protein; Provisional | Back alignment and domain information |
|---|
| >cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >PRK05807 hypothetical protein; Provisional | Back alignment and domain information |
|---|
| >cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain | Back alignment and domain information |
|---|
| >cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide | Back alignment and domain information |
|---|
| >cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >PRK08059 general stress protein 13; Validated | Back alignment and domain information |
|---|
| >cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain | Back alignment and domain information |
|---|
| >cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain | Back alignment and domain information |
|---|
| >cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain | Back alignment and domain information |
|---|
| >cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain | Back alignment and domain information |
|---|
| >cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional | Back alignment and domain information |
|---|
| >TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase | Back alignment and domain information |
|---|
| >cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa | Back alignment and domain information |
|---|
| >PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed | Back alignment and domain information |
|---|
| >cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain | Back alignment and domain information |
|---|
| >cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain | Back alignment and domain information |
|---|
| >cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >PRK03987 translation initiation factor IF-2 subunit alpha; Validated | Back alignment and domain information |
|---|
| >smart00316 S1 Ribosomal protein S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain | Back alignment and domain information |
|---|
| >cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease | Back alignment and domain information |
|---|
| >PHA02945 interferon resistance protein; Provisional | Back alignment and domain information |
|---|
| >cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase | Back alignment and domain information |
|---|
| >cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >PRK09521 exosome complex RNA-binding protein Csl4; Provisional | Back alignment and domain information |
|---|
| >PRK04163 exosome complex RNA-binding protein Rrp4; Provisional | Back alignment and domain information |
|---|
| >TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form | Back alignment and domain information |
|---|
| >TIGR02063 RNase_R ribonuclease R | Back alignment and domain information |
|---|
| >PRK11642 exoribonuclease R; Provisional | Back alignment and domain information |
|---|
| >TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases | Back alignment and domain information |
|---|
| >PRK08563 DNA-directed RNA polymerase subunit E'; Provisional | Back alignment and domain information |
|---|
| >COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] | Back alignment and domain information |
|---|
| >PRK09202 nusA transcription elongation factor NusA; Validated | Back alignment and domain information |
|---|
| >TIGR00757 RNaseEG ribonuclease, Rne/Rng family | Back alignment and domain information |
|---|
| >KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only] | Back alignment and domain information |
|---|
| >KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification] | Back alignment and domain information |
|---|
| >cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >PRK12327 nusA transcription elongation factor NusA; Provisional | Back alignment and domain information |
|---|
| >TIGR01953 NusA transcription termination factor NusA | Back alignment and domain information |
|---|
| >cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain | Back alignment and domain information |
|---|
| >KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification] | Back alignment and domain information |
|---|
| >PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional | Back alignment and domain information |
|---|
| >PRK05054 exoribonuclease II; Provisional | Back alignment and domain information |
|---|
| >COG0557 VacB Exoribonuclease R [Transcription] | Back alignment and domain information |
|---|
| >PRK11712 ribonuclease G; Provisional | Back alignment and domain information |
|---|
| >COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >PF13509 S1_2: S1 domain; PDB: 3GO5_A | Back alignment and domain information |
|---|
| >PRK10811 rne ribonuclease E; Reviewed | Back alignment and domain information |
|---|
| >TIGR02062 RNase_B exoribonuclease II | Back alignment and domain information |
|---|
| >COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions [] | Back alignment and domain information |
|---|
| >PRK12328 nusA transcription elongation factor NusA; Provisional | Back alignment and domain information |
|---|
| >KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >PHA02858 EIF2a-like PKR inhibitor; Provisional | Back alignment and domain information |
|---|
| >KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification] | Back alignment and domain information |
|---|
| >COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only] | Back alignment and domain information |
|---|
| >COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only] | Back alignment and domain information |
|---|
| >cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >PRK12329 nusA transcription elongation factor NusA; Provisional | Back alignment and domain information |
|---|
| >TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase | Back alignment and domain information |
|---|
| >COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain | Back alignment and domain information |
|---|
| >PRK09521 exosome complex RNA-binding protein Csl4; Provisional | Back alignment and domain information |
|---|
| >PLN00207 polyribonucleotide nucleotidyltransferase; Provisional | Back alignment and domain information |
|---|
| >cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional | Back alignment and domain information |
|---|
| >PRK08582 hypothetical protein; Provisional | Back alignment and domain information |
|---|
| >cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain | Back alignment and domain information |
|---|
| >cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate [] | Back alignment and domain information |
|---|
| >cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription] | Back alignment and domain information |
|---|
| >COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains | Back alignment and domain information |
|---|
| >cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease | Back alignment and domain information |
|---|
| >cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >PRK08059 general stress protein 13; Validated | Back alignment and domain information |
|---|
| >PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit | Back alignment and domain information |
|---|
| >PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms | Back alignment and domain information |
|---|
| >TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase | Back alignment and domain information |
|---|
| >PRK05807 hypothetical protein; Provisional | Back alignment and domain information |
|---|
| >PRK12442 translation initiation factor IF-1; Reviewed | Back alignment and domain information |
|---|
| >PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional | Back alignment and domain information |
|---|
| >cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits | Back alignment and domain information |
|---|
| >cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain | Back alignment and domain information |
|---|
| >PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional | Back alignment and domain information |
|---|
| >COG4044 Uncharacterized protein conserved in archaea [Function unknown] | Back alignment and domain information |
|---|
| >PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms | Back alignment and domain information |
|---|
Homologous Structure Templates
Structure Templates Detected by BLAST
Original result of BLAST against Protein Data Bank
| ID | Alignment Graph | Length |
Definition |
E-value | |
| Query | 681 | ||||
| 3bzc_A | 785 | Crystal Structure Of The Tex Protein From Pseudomon | 4e-04 | ||
| 2oce_A | 780 | Crystal Structure Of Tex Family Protein Pa5201 From | 4e-04 |
| >pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas Aeruginosa, Crystal Form I Length = 785 | Back alignment and structure |
|
| >pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From Pseudomonas Aeruginosa Length = 780 | Back alignment and structure |
Structure Templates Detected by RPS-BLAST
Original result of RPS-BLAST against PDB70 database
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
Score = 65.6 bits (159), Expect = 4e-11
Identities = 83/557 (14%), Positives = 157/557 (28%), Gaps = 214/557 (38%)
Query: 120 FKMLKPSYRMKKIKEMGITEDEWYKKQFEIKGEIPEKLETVWAAPLLVTHVAPRDWPPRG 179
F+ + Y+ K I + + ED + F+ K ++ + +++
Sbjct: 9 FETGEHQYQYKDI--LSVFEDA-FVDNFDCK-DVQDMPKSI------------------- 45
Query: 180 WEVDRKELEYI-REAHKLQNVRVEIGELERK-----AKFEREGFNFDMYRVFLKQYNQWV 233
+ ++E+++I + L K KF E + Y+ FL +
Sbjct: 46 --LSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRIN-YK-FL--MSPIK 99
Query: 234 AANKDR-LEEESYKYDQD--------YYPGRRKRGKDYE---EGMYEL-PFYY------P 274
+ + Y +D + R + Y + + EL P
Sbjct: 100 TEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVL 159
Query: 275 GQICEGK-VTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGM----HVIVEILA 329
G GK + + + D + +W+ + ++E+L
Sbjct: 160 G--S-GKTWVALDVCL--SYKVQCKMDFKI-------FWL----NLKNCNSPETVLEMLQ 203
Query: 330 KRDPYRFRFPIEMRFVQPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPG 389
K + I+ + DH + I R ELRR
Sbjct: 204 K-----LLYQIDPNWTS-RSDHS-------SNIKLRIHSIQ-AELRR------------- 236
Query: 390 VKPEEEGLLSTHPYVDKLWQIHNAEQLILDDMEANPDKYKG-----KKLSELT--DDEEF 442
LL + PY + L L+L +++ N + K L LT +
Sbjct: 237 -------LLKSKPYENCL--------LVLLNVQ-NAKAWNAFNLSCKIL--LTTRFKQVT 278
Query: 443 DDENSVEYTKV-----------NYKKALLAKIILKTSVKELDLEAA---------LAERE 482
D ++ T + + K+LL K L ++L E +AE
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPDEVKSLLLKY-LDCRPQDLPREVLTTNPRRLSIIAE-- 335
Query: 483 HHNKLQREAKERGEQYKVY---KLRRNFEMDEYNFIHWRRSLEEREALIRDISCRQALGL 539
R+ + +K KL E SL E
Sbjct: 336 ----SIRDGLATWDNWKHVNCDKLTTIIES----------SLNVLE-------------- 367
Query: 540 PLEEPGRYKEDSFFGKDEYDPSNPLYRYDYWGEPKNSEKSLQERMRDAHNKSIVGKGMVW 599
P E + S F + P+ L ++W
Sbjct: 368 PAEYRKMFDRLSVFPPSAHIPTILL-------------------------------SLIW 396
Query: 600 YEMSYDDV--IKQKMQR 614
+++ DV + K+ +
Sbjct: 397 FDVIKSDVMVVVNKLHK 413
|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B* Length = 266 | Back alignment and structure |
|---|
| >1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1 Length = 308 | Back alignment and structure |
|---|
| >1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 Length = 182 | Back alignment and structure |
|---|
| >2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A Length = 175 | Back alignment and structure |
|---|
| >2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80 | Back alignment and structure |
|---|
| >2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130 | Back alignment and structure |
|---|
| >2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 119 | Back alignment and structure |
|---|
Structure Templates Detected by HHsearch
Original result of HHsearch against PDB70 database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 681 | |||
| 1kl9_A | 182 | Eukaryotic translation initiation factor 2 subuni; | 99.93 | |
| 3go5_A | 285 | Multidomain protein with S1 RNA-binding domains; s | 99.86 | |
| 2a19_A | 175 | EIF-2- alpha, eukaryotic translation initiation fa | 99.84 | |
| 2khi_A | 115 | 30S ribosomal protein S1; acetylation, phosphoprot | 99.84 | |
| 1q8k_A | 308 | Eukaryotic translation initiation factor 2 subunit | 99.82 | |
| 2eqs_A | 103 | ATP-dependent RNA helicase DHX8; S1 domain, OB-fol | 99.8 | |
| 2cqo_A | 119 | Nucleolar protein of 40 kDa; S1 domain, OB-fold, s | 99.8 | |
| 2k52_A | 80 | Uncharacterized protein MJ1198; metal-binding, zin | 99.79 | |
| 2k4k_A | 130 | GSP13, general stress protein 13; cytoplasm, stres | 99.79 | |
| 1luz_A | 88 | Protein K3, protein K2; stranded anti-parallel bet | 99.78 | |
| 3aev_A | 275 | Translation initiation factor 2 subunit alpha; pro | 99.76 | |
| 3psi_A | 1219 | Transcription elongation factor SPT6; nucleus; 3.3 | 99.75 | |
| 3cw2_C | 266 | Translation initiation factor 2 subunit alpha; AIF | 99.73 | |
| 3bzc_A | 785 | TEX; helix-turn-helix, helix-hairpin-helix, S1 dom | 99.73 | |
| 2khj_A | 109 | 30S ribosomal protein S1; OB fold, acetylation, ph | 99.72 | |
| 3psf_A | 1030 | Transcription elongation factor SPT6; nucleus; 2.5 | 99.72 | |
| 1e3p_A | 757 | Guanosine pentaphosphate synthetase; polyribonucle | 99.61 | |
| 1wi5_A | 119 | RRP5 protein homolog; S1 domain, OB-fold, structur | 99.6 | |
| 4aid_A | 726 | Polyribonucleotide nucleotidyltransferase; transfe | 99.6 | |
| 3go5_A | 285 | Multidomain protein with S1 RNA-binding domains; s | 99.59 | |
| 3cdi_A | 723 | Polynucleotide phosphorylase; mRNA turnover, RNAse | 99.57 | |
| 1go3_E | 187 | DNA-directed RNA polymerase subunit E; transferase | 99.55 | |
| 4ayb_E | 180 | DNA-directed RNA polymerase; transferase, multi-su | 99.52 | |
| 2b8k_G | 215 | B16, DNA-directed RNA polymerase II 19 kDa polypep | 99.5 | |
| 1y14_B | 171 | B16, RPB7, DNA-directed RNA polymerase II 19 kDa p | 99.46 | |
| 2nn6_I | 209 | 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, | 99.45 | |
| 2c35_B | 172 | Human RPB7, DNA-directed RNA polymerase II 19 kDa | 99.45 | |
| 3m7n_A | 179 | Putative uncharacterized protein AF_0206; exosome, | 99.41 | |
| 3h0g_G | 172 | DNA-directed RNA polymerase II subunit RPB7; trans | 99.34 | |
| 2je6_I | 251 | RRP4, exosome complex RNA-binding protein 1; nucle | 99.28 | |
| 2z0s_A | 235 | Probable exosome complex RNA-binding protein 1; al | 99.26 | |
| 2ba0_A | 229 | Archeal exosome RNA binding protein RRP4; RNAse PH | 99.22 | |
| 2bx2_L | 517 | Ribonuclease E, RNAse E; RNA-binding, RNA turnover | 99.07 | |
| 1hh2_P | 344 | NUSA, N utilization substance protein A; transcrip | 99.03 | |
| 2bh8_A | 101 | 1B11; transcription, molecular evolution, unique a | 98.94 | |
| 2id0_A | 644 | Exoribonuclease 2; RNAse, exonuclease, hydrolyase, | 98.86 | |
| 2bh8_A | 101 | 1B11; transcription, molecular evolution, unique a | 98.81 | |
| 3ayh_B | 203 | DNA-directed RNA polymerase III subunit RPC8; tran | 98.81 | |
| 2nn6_H | 308 | Exosome complex exonuclease RRP4; RNA, exosome, PM | 98.8 | |
| 2vnu_D | 760 | Exosome complex exonuclease RRP44; hydrolase-RNA c | 98.7 | |
| 2wp8_J | 977 | Exosome complex exonuclease DIS3; nucleus, hydrola | 98.69 | |
| 1k0r_A | 366 | NUSA; two component arrangement, S1 domain, two K- | 98.56 | |
| 2ckz_B | 218 | C25, DNA-directed RNA polymerase III 25 KD polypep | 98.54 | |
| 1e3p_A | 757 | Guanosine pentaphosphate synthetase; polyribonucle | 98.39 | |
| 2ja9_A | 175 | Exosome complex exonuclease RRP40; RNA-binding pro | 98.25 | |
| 2asb_A | 251 | Transcription elongation protein NUSA; protein-RNA | 98.05 | |
| 2khj_A | 109 | 30S ribosomal protein S1; OB fold, acetylation, ph | 98.0 | |
| 3cdi_A | 723 | Polynucleotide phosphorylase; mRNA turnover, RNAse | 97.96 | |
| 2khi_A | 115 | 30S ribosomal protein S1; acetylation, phosphoprot | 97.89 | |
| 2nn6_G | 289 | Exosome complex exonuclease RRP40; RNA, exosome, P | 97.15 | |
| 2cqo_A | 119 | Nucleolar protein of 40 kDa; S1 domain, OB-fold, s | 96.53 | |
| 2r7d_A | 469 | Ribonuclease II family protein; structural genomic | 95.78 | |
| 4aid_A | 726 | Polyribonucleotide nucleotidyltransferase; transfe | 95.76 | |
| 2a19_A | 175 | EIF-2- alpha, eukaryotic translation initiation fa | 95.35 | |
| 1kl9_A | 182 | Eukaryotic translation initiation factor 2 subuni; | 95.22 | |
| 2k4k_A | 130 | GSP13, general stress protein 13; cytoplasm, stres | 94.82 | |
| 2eqs_A | 103 | ATP-dependent RNA helicase DHX8; S1 domain, OB-fol | 94.45 | |
| 2k52_A | 80 | Uncharacterized protein MJ1198; metal-binding, zin | 93.93 | |
| 1go3_E | 187 | DNA-directed RNA polymerase subunit E; transferase | 92.49 | |
| 2k5n_A | 74 | Putative cold-shock protein; GFT protein structure | 92.27 | |
| 3d0f_A | 106 | Penicillin-binding 1 transmembrane protein MRCA; B | 91.98 | |
| 1y14_B | 171 | B16, RPB7, DNA-directed RNA polymerase II 19 kDa p | 91.95 | |
| 1q8k_A | 308 | Eukaryotic translation initiation factor 2 subunit | 90.83 | |
| 3aev_A | 275 | Translation initiation factor 2 subunit alpha; pro | 90.04 | |
| 2b8k_G | 215 | B16, DNA-directed RNA polymerase II 19 kDa polypep | 89.56 | |
| 3cw2_C | 266 | Translation initiation factor 2 subunit alpha; AIF | 88.71 | |
| 1luz_A | 88 | Protein K3, protein K2; stranded anti-parallel bet | 88.69 | |
| 2yty_A | 88 | Cold shock domain-containing protein E1; cell-free | 88.41 | |
| 3aqq_A | 147 | Calcium-regulated heat stable protein 1; compact b | 88.02 | |
| 3psf_A | 1030 | Transcription elongation factor SPT6; nucleus; 2.5 | 87.67 | |
| 3psi_A | 1219 | Transcription elongation factor SPT6; nucleus; 3.3 | 87.27 | |
| 1wfq_A | 89 | UNR protein; beta-barrel, translational regulation | 86.87 | |
| 4ayb_E | 180 | DNA-directed RNA polymerase; transferase, multi-su | 86.4 | |
| 3bzc_A | 785 | TEX; helix-turn-helix, helix-hairpin-helix, S1 dom | 85.74 | |
| 1wi5_A | 119 | RRP5 protein homolog; S1 domain, OB-fold, structur | 84.7 | |
| 2c35_B | 172 | Human RPB7, DNA-directed RNA polymerase II 19 kDa | 84.01 | |
| 2rf4_A | 214 | DNA-directed RNA polymerase I subunit RPA4; transf | 83.13 | |
| 3h0g_G | 172 | DNA-directed RNA polymerase II subunit RPB7; trans | 81.84 |
| >1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 | Back alignment and structure |
|---|
Probab=99.93 E-value=1.4e-27 Score=223.41 Aligned_cols=115 Identities=18% Similarity=0.197 Sum_probs=100.8
Q ss_pred CCCCCEEEEEEEEeeecceeEEEc--CCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeeccC
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDI--GGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQ 346 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDI--GGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~ 346 (681)
.++|+++.|+|++|++| ||||+| +++.+||||||||||.++. +++++||+|+|+|+++ |++++||+||||.+.
T Consensus 13 p~~G~iv~G~V~~I~~f-GaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~v-D~~~~rI~LSlk~~~ 90 (182)
T 1kl9_A 13 PEVEDVVMVNVRSIAEM-GAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRV-DKEKGYIDLSKRRVS 90 (182)
T ss_dssp CCTTCEEEEEEEEECSS-EEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEE-ETTTTEEEEESTTCC
T ss_pred CCCCCEEEEEEEEEecc-EEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEE-ECCCCEEEEEEeecC
Confidence 47899999999999999 999999 4557999999999998764 5999999999999999 788899999999999
Q ss_pred CCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCC-CCcccccCccccceeeeh
Q 005716 347 PNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPE-EEGLLSTHPYVDKLWQIH 411 (681)
Q Consensus 347 pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~e-fgafve~hP~VegL~hIs 411 (681)
++||..+.++|+.+.+++ +.|.+ +++ || +++.|+|+||+|+|
T Consensus 91 ~~p~~~~~~~~~~g~~v~-------g~v~~--------------i~~~~g--v~l~~giegl~h~s 133 (182)
T 1kl9_A 91 PEEAIKCEDKFTKSKTVY-------SILRH--------------VAEVLE--YTKDEQLESLFQRT 133 (182)
T ss_dssp HHHHHHHHHHHHHHHHHH-------HHHHH--------------HHHHTT--CCSHHHHHHHHHHT
T ss_pred cChHHHHHHhccCCCEEE-------EEEEE--------------chhhcC--CcccCChhheEEee
Confidence 999999999999999999 99999 888 99 89999999999998
|
| >3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} | Back alignment and structure |
|---|
| >2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A | Back alignment and structure |
|---|
| >2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} | Back alignment and structure |
|---|
| >1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1 | Back alignment and structure |
|---|
| >2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} | Back alignment and structure |
|---|
| >2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} | Back alignment and structure |
|---|
| >2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} | Back alignment and structure |
|---|
| >2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} | Back alignment and structure |
|---|
| >1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5 | Back alignment and structure |
|---|
| >3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A | Back alignment and structure |
|---|
| >3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B* | Back alignment and structure |
|---|
| >3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A | Back alignment and structure |
|---|
| >2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} | Back alignment and structure |
|---|
| >3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A | Back alignment and structure |
|---|
| >1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5 | Back alignment and structure |
|---|
| >4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A | Back alignment and structure |
|---|
| >3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} | Back alignment and structure |
|---|
| >3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A | Back alignment and structure |
|---|
| >1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1 | Back alignment and structure |
|---|
| >4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E | Back alignment and structure |
|---|
| >2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 | Back alignment and structure |
|---|
| >1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ... | Back alignment and structure |
|---|
| >2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 | Back alignment and structure |
|---|
| >2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1 | Back alignment and structure |
|---|
| >3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A | Back alignment and structure |
|---|
| >3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} | Back alignment and structure |
|---|
| >2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C | Back alignment and structure |
|---|
| >2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1 | Back alignment and structure |
|---|
| >2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 | Back alignment and structure |
|---|
| >2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A | Back alignment and structure |
|---|
| >1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A | Back alignment and structure |
|---|
| >2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} | Back alignment and structure |
|---|
| >2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A | Back alignment and structure |
|---|
| >2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} | Back alignment and structure |
|---|
| >3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} | Back alignment and structure |
|---|
| >2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 | Back alignment and structure |
|---|
| >2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 | Back alignment and structure |
|---|
| >2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 | Back alignment and structure |
|---|
| >2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A | Back alignment and structure |
|---|
| >2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1 | Back alignment and structure |
|---|
| >2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A | Back alignment and structure |
|---|
| >2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} | Back alignment and structure |
|---|
| >3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A | Back alignment and structure |
|---|
| >2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} | Back alignment and structure |
|---|
| >2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 | Back alignment and structure |
|---|
| >2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} | Back alignment and structure |
|---|
| >2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A | Back alignment and structure |
|---|
| >4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A | Back alignment and structure |
|---|
| >2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A | Back alignment and structure |
|---|
| >1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 | Back alignment and structure |
|---|
| >2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} | Back alignment and structure |
|---|
| >2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} | Back alignment and structure |
|---|
| >2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} | Back alignment and structure |
|---|
| >1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1 | Back alignment and structure |
|---|
| >2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, cold shock structural genomics; NMR {Pectobacterium atrosepticum} | Back alignment and structure |
|---|
| >3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, STR genomics, PSI-2, protein structure initiative; 1.64A {Nitrosomonas europaea atcc 19718} | Back alignment and structure |
|---|
| >1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ... | Back alignment and structure |
|---|
| >1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1 | Back alignment and structure |
|---|
| >3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A | Back alignment and structure |
|---|
| >2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 | Back alignment and structure |
|---|
| >3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B* | Back alignment and structure |
|---|
| >1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5 | Back alignment and structure |
|---|
| >2yty_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational REGU RNA chaperone, RNA/DNA binding, QB fold; NMR {Homo sapiens} | Back alignment and structure |
|---|
| >3aqq_A Calcium-regulated heat stable protein 1; compact beta-barrel, cold shock domain, ssDNA binding, DNA B protein; 2.80A {Homo sapiens} | Back alignment and structure |
|---|
| >3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >1wfq_A UNR protein; beta-barrel, translational regulation, RNA chaperone, RNA/DN binding, QB fold, greek-KEY topology, structur genomics; NMR {Homo sapiens} SCOP: b.40.4.5 | Back alignment and structure |
|---|
| >4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E | Back alignment and structure |
|---|
| >3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A | Back alignment and structure |
|---|
| >1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5 | Back alignment and structure |
|---|
| >2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1 | Back alignment and structure |
|---|
| >2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} | Back alignment and structure |
|---|
Homologous Structure Domains
Structure Domains Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
E-value |
| 681 | ||||
| d3bzka4 | 94 | b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae | 1e-06 | |
| d2je6i1 | 87 | b.40.4.5 (I:66-152) S1-domain of exosome complex R | 2e-05 | |
| d1e3pa2 | 62 | b.40.4.5 (A:656-717) S1 RNA-binding domain of poly | 7e-04 | |
| d2nn6h1 | 95 | b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro | 0.002 |
| >d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94 | Back information, alignment and structure |
|---|
class: All beta proteins fold: OB-fold superfamily: Nucleic acid-binding proteins family: Cold shock DNA-binding domain-like domain: Tex S1-domain species: Pseudomonas aeruginosa [TaxId: 287]
Score = 44.9 bits (106), Expect = 1e-06
Identities = 30/86 (34%), Positives = 45/86 (52%), Gaps = 5/86 (5%)
Query: 261 DYEEGMYELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRH---HI 317
+++EG+ L PG + EG VT V + GAFVDIG DG V I +++ +
Sbjct: 5 EFQEGVESLKDLKPGMVLEGVVTNVTNF-GAFVDIGVHQDGLVHISALSEKFVKDPYEVV 63
Query: 318 KVGMHVIVEILAKRDPYRFRFPIEMR 343
K G V V+++ + D R R + MR
Sbjct: 64 KAGDIVKVKVM-EVDIPRNRVGLSMR 88
|
| >d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 87 | Back information, alignment and structure |
|---|
| >d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} Length = 62 | Back information, alignment and structure |
|---|
| >d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 95 | Back information, alignment and structure |
|---|
Homologous Domains Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 681 | |||
| d1sroa_ | 76 | S1 RNA-binding domain of polyribonucleotide phosph | 99.83 | |
| d3bzka4 | 94 | Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287] | 99.82 | |
| d1kl9a2 | 86 | Eukaryotic initiation factor 2alpha, eIF2alpha, N- | 99.77 | |
| d2ahob2 | 84 | Eukaryotic initiation factor 2alpha, eIF2alpha, N- | 99.77 | |
| d1go3e1 | 106 | C-terminal domain of RNA polymerase II subunit RBP | 99.76 | |
| d2ba0a1 | 83 | S1-domain of exosome complex RNA-binding protein 1 | 99.73 | |
| d2je6i1 | 87 | S1-domain of exosome complex RNA-binding protein 1 | 99.69 | |
| d1wi5a_ | 119 | S1-domain of RRP5 protein homolog (PDCD11, KIAA018 | 99.69 | |
| d2z0sa1 | 88 | S1-domain of exosome complex RNA-binding protein 1 | 99.67 | |
| d1e3pa2 | 62 | S1 RNA-binding domain of polyribonucleotide phosph | 99.59 | |
| d2nn6h1 | 95 | S1-domain of Ribosomal RNA-processing protein 4, R | 99.56 | |
| d1y14b1 | 91 | C-terminal domain of RNA polymerase II subunit RBP | 99.27 | |
| d2nn6g1 | 88 | S1-domain of exosome component 3 (RRP40) {Human (H | 99.17 | |
| d2ix0a3 | 87 | Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5 | 99.15 | |
| d2c35b1 | 94 | C-terminal domain of RNA polymerase II subunit RBP | 99.14 | |
| d2ja9a1 | 90 | S1-domain of exosome component 3 (RRP40) {Saccharo | 98.8 | |
| d1hh2p1 | 72 | S1 domain of NusA {Thermotoga maritima [TaxId: 233 | 98.37 | |
| d1smxa_ | 87 | S1-domain of Ribonuclease E {Escherichia coli [Tax | 98.18 | |
| d2nn6i1 | 125 | Exosome component 1, EXOSC1 {Human (Homo sapiens) | 98.18 | |
| d2asba1 | 76 | S1 domain of NusA {Mycobacterium tuberculosis [Tax | 97.64 | |
| d1e3pa2 | 62 | S1 RNA-binding domain of polyribonucleotide phosph | 96.19 | |
| d1sroa_ | 76 | S1 RNA-binding domain of polyribonucleotide phosph | 94.7 | |
| d1kl9a2 | 86 | Eukaryotic initiation factor 2alpha, eIF2alpha, N- | 94.65 | |
| d1k3ra1 | 71 | Hypothetical protein MTH1 (MT0001), insert domain | 93.69 | |
| d1go3e1 | 106 | C-terminal domain of RNA polymerase II subunit RBP | 93.29 | |
| d1yvca1 | 69 | Hypothetical protein MMP0076 {Methanococcus maripa | 91.0 | |
| d2ahob2 | 84 | Eukaryotic initiation factor 2alpha, eIF2alpha, N- | 90.18 | |
| d3bzka4 | 94 | Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287] | 90.08 | |
| d2ba0a1 | 83 | S1-domain of exosome complex RNA-binding protein 1 | 90.06 | |
| d1wfqa_ | 89 | Cold shock domain protein E1 (UNR) {Human (Homo sa | 89.98 | |
| d2je6i1 | 87 | S1-domain of exosome complex RNA-binding protein 1 | 89.2 | |
| d2z0sa1 | 88 | S1-domain of exosome complex RNA-binding protein 1 | 87.83 | |
| d1o7ia_ | 115 | Archaeal ssDNA-binding protein {Archaeon Sulfolobu | 85.8 | |
| d1wi5a_ | 119 | S1-domain of RRP5 protein homolog (PDCD11, KIAA018 | 83.45 | |
| d1c9oa_ | 66 | Major cold shock protein {Bacillus caldolyticus [T | 82.45 | |
| d1mjca_ | 69 | Major cold shock protein {Escherichia coli [TaxId: | 81.74 |
| >d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} | Back information, alignment and structure |
|---|
class: All beta proteins fold: OB-fold superfamily: Nucleic acid-binding proteins family: Cold shock DNA-binding domain-like domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase species: Escherichia coli [TaxId: 562]
Probab=99.83 E-value=2.9e-21 Score=155.09 Aligned_cols=71 Identities=30% Similarity=0.404 Sum_probs=65.5
Q ss_pred CCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeec
Q 005716 271 FYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRF 344 (681)
Q Consensus 271 ~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~ 344 (681)
+|++|++++|+|++|++| ||||+|+++.+||||+|+|||.++. +++++||+|+|+|+++ |+ ++||.||||+
T Consensus 2 d~kvG~iv~G~V~~v~~~-G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~i-d~-~~ri~LS~k~ 75 (76)
T d1sroa_ 2 EIEVGRVYTGKVTRIVDF-GAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEV-DR-QGRIRLSIKE 75 (76)
T ss_dssp CCCTTSEEEEEEEEEETT-EEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEEC-CT-TCCCEEEECC
T ss_pred CCCCCCEEEEEEEEEeCc-EEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEE-CC-CCCEEEEEEc
Confidence 689999999999999999 9999998778999999999998765 5999999999999999 55 4799999996
|
| >d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} | Back information, alignment and structure |
|---|
| >d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} | Back information, alignment and structure |
|---|
| >d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} | Back information, alignment and structure |
|---|
| >d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} | Back information, alignment and structure |
|---|
| >d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} | Back information, alignment and structure |
|---|
| >d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} | Back information, alignment and structure |
|---|
| >d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} | Back information, alignment and structure |
|---|
| >d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} | Back information, alignment and structure |
|---|
| >d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} | Back information, alignment and structure |
|---|
| >d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]} | Back information, alignment and structure |
|---|
| >d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]} | Back information, alignment and structure |
|---|
| >d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]} | Back information, alignment and structure |
|---|
| >d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]} | Back information, alignment and structure |
|---|
| >d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} | Back information, alignment and structure |
|---|
| >d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} | Back information, alignment and structure |
|---|
| >d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d1k3ra1 b.40.4.10 (A:93-163) Hypothetical protein MTH1 (MT0001), insert domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} | Back information, alignment and structure |
|---|
| >d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} | Back information, alignment and structure |
|---|
| >d1yvca1 b.40.4.12 (A:1-69) Hypothetical protein MMP0076 {Methanococcus maripaludis [TaxId: 39152]} | Back information, alignment and structure |
|---|
| >d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} | Back information, alignment and structure |
|---|
| >d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} | Back information, alignment and structure |
|---|
| >d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} | Back information, alignment and structure |
|---|
| >d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} | Back information, alignment and structure |
|---|
| >d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} | Back information, alignment and structure |
|---|
| >d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]} | Back information, alignment and structure |
|---|
| >d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d1c9oa_ b.40.4.5 (A:) Major cold shock protein {Bacillus caldolyticus [TaxId: 1394]} | Back information, alignment and structure |
|---|
| >d1mjca_ b.40.4.5 (A:) Major cold shock protein {Escherichia coli [TaxId: 562]} | Back information, alignment and structure |
|---|